The Kinetics of Enzyme Mixtures
Directory of Open Access Journals (Sweden)
Simon Brown
2014-03-01
Full Text Available Even purified enzyme preparations are often heterogeneous. For example, preparations of aspartate aminotransferase or cytochrome oxidase can consist of several different forms of the enzyme. For this reason we consider how different the kinetics of the reactions catalysed by a mixture of forms of an enzyme must be to provide some indication of the characteristics of the species present. Based on the standard Michaelis-Menten model, we show that if the Michaelis constants (Km of two isoforms differ by a factor of at least 20 the steady-state kinetics can be used to characterise the mixture. However, even if heterogeneity is reflected in the kinetic data, the proportions of the different forms of the enzyme cannot be estimated from the kinetic data alone. Consequently, the heterogeneity of enzyme preparations is rarely reflected in measurements of their steady-state kinetics unless the species present have significantly different kinetic properties. This has two implications: (1 it is difficult, but not impossible, to detect molecular heterogeneity using kinetic data and (2 even when it is possible, a considerable quantity of high quality data is required.
Extracellular enzyme kinetics scale with resource availability
Microbial community metabolism relies on external digestion, mediated by extracellular enzymes that break down complex organic matter into molecules small enough for cells to assimilate. We analyzed the kinetics of 40 extracellular enzymes that mediate the degradation and assimi...
Enzyme Kinetics and the Michaelis-Menten Equation
Biaglow, Andrew; Erickson, Keith; McMurran, Shawnee
2010-01-01
The concepts presented in this article represent the cornerstone of classical mathematical biology. The central problem of the article relates to enzyme kinetics, which is a biochemical system. However, the theoretical underpinnings that lead to the formation of systems of time-dependent ordinary differential equations have been applied widely to…
Practical Enzyme Kinetics: A Biochemical Laboratory Experiment.
Rowe, H. Alan; Brown, Morris
1988-01-01
Describes an experiment that provides a fundamental understanding of the kinetics of the enzyme papain. Discusses background, materials, procedures and results. Mentions analogous experiments that can be conducted with enzymatic contact-lens cleaning solutions. (CW)
A Comprehensive Enzyme Kinetic Exercise for Biochemistry
Barton, Janice S.
2011-01-01
This article describes a comprehensive treatment of experimental enzyme kinetics strongly coupled to electronic data acquisition and use of spreadsheets to organize data and perform linear and nonlinear least-squares analyses, all in a manner that promotes development of important reasoning skills. Kinetic parameters are obtained for the stable…
Modified kinetics of enzymes interacting with nanoparticles
Díaz, Sebastián. A.; Breger, Joyce C.; Malanoski, Anthony; Claussen, Jonathan C.; Walper, Scott A.; Ancona, Mario G.; Brown, Carl W.; Stewart, Michael H.; Oh, Eunkeu; Susumu, Kimihiro; Medintz, Igor L.
2015-08-01
Enzymes are important players in multiple applications, be it bioremediation, biosynthesis, or as reporters. The business of catalysis and inhibition of enzymes is a multibillion dollar industry and understanding the kinetics of commercial enzymes can have a large impact on how these systems are optimized. Recent advances in nanotechnology have opened up the field of nanoparticle (NP) and enzyme conjugates and two principal architectures for NP conjugate systems have been developed. In the first example the enzyme is bound to the NP in a persistent manner, here we find that key factors such as directed enzyme conjugation allow for enhanced kinetics. Through controlled comparative experiments we begin to tease out specific mechanisms that may account for the enhancement. The second system is based on dynamic interactions of the enzymes with the NP. The enzyme substrate is bound to the NP and the enzyme is free in solution. Here again we find that there are many variables , such as substrate positioning and NP selection, that modify the kinetics.
Classical kinetic energy, quantum fluctuation terms and kinetic-energy functionals
Hamilton, I. P.; Mosna, Ricardo A.; Site, L. Delle
2006-01-01
We employ a recently formulated dequantization procedure to obtain an exact expression for the kinetic energy which is applicable to all kinetic-energy functionals. We express the kinetic energy of an N-electron system as the sum of an N-electron classical kinetic energy and an N-electron purely quantum kinetic energy arising from the quantum fluctuations that turn the classical momentum into the quantum momentum. This leads to an interesting analogy with Nelson's stochastic approach to quant...
Nuclear quantum effects and kinetic isotope effects in enzyme reactions.
Vardi-Kilshtain, Alexandra; Nitoker, Neta; Major, Dan Thomas
2015-09-15
Enzymes are extraordinarily effective catalysts evolved to perform well-defined and highly specific chemical transformations. Studying the nature of rate enhancements and the mechanistic strategies in enzymes is very important, both from a basic scientific point of view, as well as in order to improve rational design of biomimetics. Kinetic isotope effect (KIE) is a very important tool in the study of chemical reactions and has been used extensively in the field of enzymology. Theoretically, the prediction of KIEs in condensed phase environments such as enzymes is challenging due to the need to include nuclear quantum effects (NQEs). Herein we describe recent progress in our group in the development of multi-scale simulation methods for the calculation of NQEs and accurate computation of KIEs. We also describe their application to several enzyme systems. In particular we describe the use of combined quantum mechanics/molecular mechanics (QM/MM) methods in classical and quantum simulations. The development of various novel path-integral methods is reviewed. These methods are tailor suited to enzyme systems, where only a few degrees of freedom involved in the chemistry need to be quantized. The application of the hybrid QM/MM quantum-classical simulation approach to three case studies is presented. The first case involves the proton transfer in alanine racemase. The second case presented involves orotidine 5'-monophosphate decarboxylase where multidimensional free energy simulations together with kinetic isotope effects are combined in the study of the reaction mechanism. Finally, we discuss the proton transfer in nitroalkane oxidase, where the enzyme employs tunneling as a catalytic fine-tuning tool. PMID:25769515
A lattice gas model for enzyme kinetics (A correlated walks theory and variational procedures)
International Nuclear Information System (INIS)
We have shown that by using a correlated walks theory or variational procedures, for the lattice gas model we can find for enzyme kinetics some new equations, which in the limit of no interactions between sites reduce to the classical Michaelis-Henri equation. These new equations can be useful for the experimental investigation. (author). 8 refs, 6 figs
Enzyme Molar Fractions: A Powerful Tool for Understanding Enzyme Kinetics.
Serra, Juan L.; And Others
1986-01-01
Deduces the relationship between reduced velocity and molar fractions for productive enzyme complexes; obtains the mathematical expression of molar fractions for an enzyme with two specific binding sites per molecule; and proposes a useful plot to follow the dependence of enzyme molar fractions with the concentration of one of its ligands. (JN)
Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study
International Nuclear Information System (INIS)
Graphical abstract: Stochastic theory of interfacial enzyme kinetics is formulated. Numerical results of macroscopic phenomenon of lag-burst kinetics is obtained by using a kinetic Monte Carlo approach to single enzyme activity. Highlights: ► An enzyme is attached with the fluid state phospholipid molecules on the Langmuir monolayer. ► Through the diffusion, the enzyme molecule reaches the gel–fluid interface. ► After hydrolysing a phospholipid molecule it predominantly leaves the surface in the lag phase. ► The enzyme is strictly attached to the surface with scooting mode of motion and the burst phase appears. - Abstract: In the spirit of Gillespie’s stochastic approach we have formulated a theory to explore the advancement of the interfacial enzyme kinetics at the single enzyme level which is ultimately utilized to obtain the ensemble average macroscopic feature, lag-burst kinetics. We have provided a theory of the transition from the lag phase to the burst phase kinetics by considering the gradual development of electrostatic interaction among the positively charged enzyme and negatively charged product molecules deposited on the phospholipid surface. It is shown that the different diffusion time scales of the enzyme over the fluid and product regions are responsible for the memory effect in the correlation of successive turnover events of the hopping mode in the single trajectory analysis which again is reflected on the non-Gaussian distribution of turnover times on the macroscopic kinetics in the lag phase unlike the burst phase kinetics.
Current IUBMB recommendations on enzyme nomenclature and kinetics
Directory of Open Access Journals (Sweden)
Athel Cornish-Bowden
2014-05-01
Full Text Available The International Union of Biochemistry (IUB, now IUBMB prepared recommendations for describing the kinetic behaviour of enzymes in 1981. Despite the more than 30 years that have passed since these have not subsequently been revised, though in various respects they do not adequately cover current needs. The IUBMB is also responsible for recommendations on the naming and classification of enzymes. In contrast to the case of kinetics, these recommendations are kept continuously up to date.
Reexamining Michaelis-Menten Enzyme Kinetics for Xanthine Oxidase
Bassingthwaighte, James B.; Chinn, Tamara M.
2013-01-01
Abbreviated expressions for enzyme kinetic expressions, such as the Michaelis-Menten (M-M) equations, are based on the premise that enzyme concentrations are low compared with those of the substrate and product. When one does progress experiments, where the solute is consumed during conversion to form a series of products, the idealized conditions…
Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study
Das, Biswajit; Gangopadhyay, Gautam
2012-01-01
In the spirit of Gillespie's stochastic approach we have formulated a theory to explore the advancement of the interfacial enzyme kinetics at the single enzyme level which is ultimately utilized to obtain the ensemble average macroscopic feature, lag-burst kinetics. We have provided a theory of the transition from the lag phase to the burst phase kinetics by considering the gradual development of electrostatic interaction among the positively charged enzyme and negatively charged product molecules deposited on the phospholipid surface. It is shown that the different diffusion time scales of the enzyme over the fluid and product regions are responsible for the memory effect in the correlation of successive turnover events of the hopping mode in the single trajectory analysis which again is reflected on the non-Gaussian distribution of turnover times on the macroscopic kinetics in the lag phase unlike the burst phase kinetics.
Extracting enzyme processivity from kinetic assays
Barel, Itay; Reich, Norbert O.; Brown, Frank L. H.
2015-12-01
A steady-state analysis for the catalytic turnover of molecules containing two substrate sites is presented. A broad class of Markovian dynamic models, motivated by the action of DNA modifying enzymes and the rich variety of translocation mechanisms associated with these systems (e.g., sliding, hopping, intersegmental transfer, etc.), is considered. The modeling suggests an elementary and general method of data analysis, which enables the extraction of the enzyme's processivity directly and unambiguously from experimental data. This analysis is not limited to the initial velocity regime. The predictions are validated both against detailed numerical models and by revisiting published experimental data for EcoRI endonuclease acting on DNA.
Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study
Energy Technology Data Exchange (ETDEWEB)
Das, Biswajit [S.N. Bose National Centre For Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098 (India); Gangopadhyay, Gautam, E-mail: gautam@bose.res.in [S.N. Bose National Centre For Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098 (India)
2012-01-17
Graphical abstract: Stochastic theory of interfacial enzyme kinetics is formulated. Numerical results of macroscopic phenomenon of lag-burst kinetics is obtained by using a kinetic Monte Carlo approach to single enzyme activity. Highlights: Black-Right-Pointing-Pointer An enzyme is attached with the fluid state phospholipid molecules on the Langmuir monolayer. Black-Right-Pointing-Pointer Through the diffusion, the enzyme molecule reaches the gel-fluid interface. Black-Right-Pointing-Pointer After hydrolysing a phospholipid molecule it predominantly leaves the surface in the lag phase. Black-Right-Pointing-Pointer The enzyme is strictly attached to the surface with scooting mode of motion and the burst phase appears. - Abstract: In the spirit of Gillespie's stochastic approach we have formulated a theory to explore the advancement of the interfacial enzyme kinetics at the single enzyme level which is ultimately utilized to obtain the ensemble average macroscopic feature, lag-burst kinetics. We have provided a theory of the transition from the lag phase to the burst phase kinetics by considering the gradual development of electrostatic interaction among the positively charged enzyme and negatively charged product molecules deposited on the phospholipid surface. It is shown that the different diffusion time scales of the enzyme over the fluid and product regions are responsible for the memory effect in the correlation of successive turnover events of the hopping mode in the single trajectory analysis which again is reflected on the non-Gaussian distribution of turnover times on the macroscopic kinetics in the lag phase unlike the burst phase kinetics.
Extracting enzyme processivity from kinetic assays
Energy Technology Data Exchange (ETDEWEB)
Barel, Itay; Brown, Frank L. H. [Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106 (United States); Department of Physics, University of California, Santa Barbara, California 93106 (United States); Reich, Norbert O. [Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106 (United States)
2015-12-14
A steady-state analysis for the catalytic turnover of molecules containing two substrate sites is presented. A broad class of Markovian dynamic models, motivated by the action of DNA modifying enzymes and the rich variety of translocation mechanisms associated with these systems (e.g., sliding, hopping, intersegmental transfer, etc.), is considered. The modeling suggests an elementary and general method of data analysis, which enables the extraction of the enzyme’s processivity directly and unambiguously from experimental data. This analysis is not limited to the initial velocity regime. The predictions are validated both against detailed numerical models and by revisiting published experimental data for EcoRI endonuclease acting on DNA.
Extracting enzyme processivity from kinetic assays
International Nuclear Information System (INIS)
A steady-state analysis for the catalytic turnover of molecules containing two substrate sites is presented. A broad class of Markovian dynamic models, motivated by the action of DNA modifying enzymes and the rich variety of translocation mechanisms associated with these systems (e.g., sliding, hopping, intersegmental transfer, etc.), is considered. The modeling suggests an elementary and general method of data analysis, which enables the extraction of the enzyme’s processivity directly and unambiguously from experimental data. This analysis is not limited to the initial velocity regime. The predictions are validated both against detailed numerical models and by revisiting published experimental data for EcoRI endonuclease acting on DNA
A Comparison of Kinetic Energy and Momentum in Special Relativity and Classical Mechanics
Riggs, Peter J.
2016-01-01
Kinetic energy and momentum are indispensable dynamical quantities in both the special theory of relativity and in classical mechanics. Although momentum and kinetic energy are central to understanding dynamics, the differences between their relativistic and classical notions have not always received adequate treatment in undergraduate teaching.…
Enzyme kinetics and inhibition of histone acetyltransferase KAT8.
Wapenaar, Hannah; van der Wouden, Petra E; Groves, Matthew R; Rotili, Dante; Mai, Antonello; Dekker, Frank J
2015-11-13
Lysine acetyltransferase 8 (KAT8) is a histone acetyltransferase (HAT) responsible for acetylating lysine 16 on histone H4 (H4K16) and plays a role in cell cycle progression as well as acetylation of the tumor suppressor protein p53. Further studies on its biological function and drug discovery initiatives will benefit from the development of small molecule inhibitors for this enzyme. As a first step towards this aim we investigated the enzyme kinetics of this bi-substrate enzyme. The kinetic experiments indicate a ping-pong mechanism in which the enzyme binds Ac-CoA first, followed by binding of the histone substrate. This mechanism is supported by affinity measurements of both substrates using isothermal titration calorimetry (ITC). Using this information, the KAT8 inhibition of a focused compound collection around the non-selective HAT inhibitor anacardic acid has been investigated. Kinetic studies with anacardic acid were performed, based on which a model for the catalytic activity of KAT8 and the inhibitory action of anacardic acid (AA) was proposed. This enabled the calculation of the inhibition constant Ki of anacardic acid derivatives using an adaptation of the Cheng-Prusoff equation. The results described in this study give insight into the catalytic mechanism of KAT8 and present the first well-characterized small-molecule inhibitors for this HAT. PMID:26505788
A Sensitive and Robust Enzyme Kinetic Experiment Using Microplates and Fluorogenic Ester Substrates
Johnson, R. Jeremy; Hoops, Geoffrey C.; Savas, Christopher J.; Kartje, Zachary; Lavis, Luke D.
2015-01-01
Enzyme kinetics measurements are a standard component of undergraduate biochemistry laboratories. The combination of serine hydrolases and fluorogenic enzyme substrates provides a rapid, sensitive, and general method for measuring enzyme kinetics in an undergraduate biochemistry laboratory. In this method, the kinetic activity of multiple protein…
ENZYPLOTW: A USEFUL TOOL TO CALCULATE ENZYME KINETIC PARAMETERS
Directory of Open Access Journals (Sweden)
F.A Leone
2006-07-01
Full Text Available Assays of enzyme activity are among the most frequently employed procedures in biochemistry. They are used to estimate the amount of a given enzyme in a cell or tissue, to quantify kinetic parameters or to investigate a catalytic mechanism. The purpose of enzyme kinetics obtained under steady-state conditions is to estimate KM and VM values by fitting initial rate (v and substrate concentration (S values to the Michaelis-Menten equation, permitting a convenient graphical representation and an accurate estimation of KM and VM. However, there is no ideal assay for any particular enzyme and, since the assay of enzyme activity is essentially a kinetic measurement, various pitfalls await the unwary investigator. Despite difficulties consequent to intrinsic enzyme properties, kinetic parameters can be estimated accurately when steady-state conditions (<10% variation in substrate concentration during activity assay and initial rate measurements (catalytic enzyme concentration are guaranteed.EnzyplotW is an application developed for use on any Intel-based computer running Windows 98 or later, and uses a non-linear regression method to fit steady-state kinetic data for Michaelian enzymes. EnzyplotW can be employed not only for educational purposes but also in routine laboratory work, and includes three important features: teaching students how to obtain and recognize sound data for the best estimation of kinetic parameter values; aid the investigator at the bench in gauging the limitations of the various equivalent plots of the Michaelis-Menten equation used to estimate KM and VM; and allow the student to manipulate the mathematical formula of the corresponding plot to comprehend the qualitative and quantitative issues that govern the relationship between substrate
Veenendaal, van E.; Hoof, van P.J.C.M.; Suchtelen, van J.; Enckevort, van W.J.P.; Bennema, P.
1998-01-01
Kinetic roughening is not a phase transition and, as such, it lacks an exact definition. Many criteria are used to mark the onset of kinetic roughening. Criteria stemming from the classical two-dimensional nucleation theory are widely used. On the other hand, experimentalists observe a transition fr
Catalyst dynamics: consequences for classical kinetic descriptions of reactors
DEFF Research Database (Denmark)
Johannessen, Tue; Larsen, Jane Hvolbæk; Chorkendorff, Ib; Livbjerg, Hans; Topsøe, Henrik
The modelling of catalytic reactions/reactors has undergone great improvements since the introduction of empirical power-law kinetics in chemical reaction engineering and micro-kinetic models based on insight into the nature of elementary steps have appeared for many reactions. However, recent in...... situ studies and surface science investigations has brought added attention to the fact that catalysts may behave in a dynamic manner and reconstruct depending on the reaction conditions. This feature severely limits traditional kinetic descriptions. In the present paper, we present examples of the...... dynamical behaviour of some catalytic systems and discuss the corresponding Limitations in existing models for catalytic reactions and reactors. Catalytic reactors operated in non-steady-state are becoming more frequent in industry. The additional efforts needed to accurately simulate these types of...
International Nuclear Information System (INIS)
Primary tritium isotope effects have been measured for the hydroxylation of [2-3H] dopamine catalyzed by dopamine beta-hydroxylase. Experimental values vary from 8.8 +/- 1.4 at 0.02 mM oxygen to 4.1 +/- 0.6 at 1.0 mM oxygen. It is shown that the observed dependence of the isotope effect on oxygen concentration provides unequivocal evidence for a kinetically significant dissociation of both dopamine and oxygen from enzyme, ternary complex. This approach, which is applicable to any multisubstrate enzyme characterized by detectable kinetic isotope effects, provides an alternate to classical methods for the elucidation of kinetic order in enzyme-catalyzed reactions
On enzyme kinetic parameters modification of gamma irradiation
International Nuclear Information System (INIS)
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, Km, 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
The enzyme kinetics of the NADP-malic enzyme from tobacco leaves
Czech Academy of Sciences Publication Activity Database
Ryšlavá, H.; Doubnerová, V.; Müller, Karel; Baťková, Petra; Schnablová, Renáta; Liberda, J.; Synková, Helena; Čeřovská, Noemi
2007-01-01
Roč. 72, č. 10 (2007), s. 1420-1434. ISSN 0010-0765 R&D Projects: GA ČR GA206/03/0310 Grant ostatní: Grantová agentura Univerzity Karlovy(CZ) 428/2004/B-Ch/PrF Institutional research plan: CEZ:AV0Z50380511 Source of funding: V - iné verejné zdroje ; V - iné verejné zdroje Keywords : oxidoreductases * enzyme kinetics * NADP-malic enzyme * divalent metal ions * Nicotiana tabacum L. Subject RIV: CE - Biochemistry Impact factor: 0.879, year: 2007
Angiotensin-converting enzyme kinetics in an endothelial cell column
International Nuclear Information System (INIS)
The kinetics of saturable endothelial metabolic functions have been assessed in vivo by transient (indicator-dilution) measurements and in culture by steady-state measurements, but comparisons between the two are difficult. Therefore, we used indicator-dilution methods to assess the kinetics of angiotensin-converting enzyme (ACE) activity in cultured endothelium. Bovine fetal aortic endothelial cells were grown to confluence on microcarrier beads. Cell-covered beads were poured into polypropylene columns and perfused with serum-free culture medium. Six injections, containing [3H]benzol-Phe-Ala-Pro [( 3H]BPAP, an ACE substrate) and varying amounts of unlabeled BPAP, were applied to each column and effluent was collected in serial samples. The apparent kinetics of BPAP metabolism were determined by four models used previously to determine pulmonary endothelial ACE kinetics in vivo, the most useful model incorporating transit time heterogeneity. The Km averaged 5 microM, which is close to values determined previously in vivo and in vitro. The Amax (Vmax.reaction volume) and Amax/Km averaged 6 nmol/min and 1.5 ml/min, respectively, which are lower than estimates in vivo. In conclusion, we have developed a new method for investigating saturable metabolic activity in cultured endothelium, which after further exploration should also enable better comparisons of endothelial metabolic functions in vivo and in culture
Kinetic controlled affinity labeling of target enzyme with thioester chemistry.
Tomohiro, Takenori; Nakabayashi, Masahiro; Sugita, Yuka; Morimoto, Shota
2016-08-01
High specificity has been an important feature in affinity labeling for target profiling. Especially, to label targets via rapidly progressing reactions with consumption of ligand (probe), high specificity of reaction with common functional groups of target protein should be achieved without reactions with similar groups of non-target proteins. Herein, we demonstrate the kinetic controlled affinity labeling of acyl CoA synthetase using a fatty acid analogue containing a phenylthioester linkage. High specificity was attained by accelerating the labeling rate in the binding pocket. This approach could be useful for profiling a series of target enzymes and transporters in signal transduction pathways. PMID:27298000
Quantum Corrections to Classical Kinetics: the Weight of Rotation
Chafin, Clifford
2016-01-01
Hydrodynamics of gases in the classical domain are examined from the perspective that the gas has a well-defined wavefunction description at all times. Specifically, the internal energy and volume exclusion of decorrelated vortex structures are included so that quantum corrections and modifications to Navier-Stokes behavior can be derived. This leads to a small deviation in rigid body rotation for a cylindrically bound gas and the internal energy changes associated with vorticity give deviations in the Reynolds' transport theorem. Some macroscopic observable features arising from this include variations in the specific heat, an anisotropic correction to thermal conductivity and a variation in optical scattering as a function of the declination from the axis of local vorticity. The improvements in magneto-optical traps suggests some interesting experiments to be done in higher temperature regimes where they are not usually employed. It is argued that the finite lifetime of observed vortices in ultracold bosoni...
Using Trypsin & Soybean Trypsin Inhibitor to Teach Principles of Enzyme Kinetics
Howard, David R.; Herr, Julie; Hollister, Rhiannon
2006-01-01
Trypsin and soybean trypsin inhibitor (Kunitz inhibitor) can be used in a relatively simple and inexpensive student exercise to demonstrate the usefulness of enzyme kinetics. The study of enzyme kinetics is essential to biology because enzymes play such a crucial role in the biochemical pathways of all living organisms. The data from enzyme…
Kumar, Ashutosh; Dua, Arti
2015-01-01
Recent fluorescence spectroscopy measurements of the turnover time distribution of single-enzyme turnover kinetics of $\\beta$-galactosidase provide evidence of Michaelis-Menten kinetics at low substrate concentration. However, at high substrate concentrations, the dimensionless variance of the turnover time distribution shows systematic deviations from the Michaelis-Menten prediction. This difference is attributed to conformational fluctuations in both the enzyme and the enzyme-substrate complex and to the possibility of both parallel and off-pathway kinetics. Here, we use the chemical master equation to model the kinetics of a single fluctuating enzyme that can yield a product through either parallel or off-pathway mechanisms. An exact expression is obtained for the turnover time distribution from which the mean turnover time and randomness parameters are calculated. The parallel and off-pathway mechanisms yield strikingly different dependences of the mean turnover time and the randomness parameter on the su...
Classic hydrodynamic and kinetic formalism as averaging of delta-functional particle images
Kuz'menkov, L S
2014-01-01
Critical analyses of well-known methods of derivation of kinetic and hydrodynamic equations is presented. Another method of derivation of kinetic and hydrodynamic equations from classic mechanics is described. It is shown that equations of classic hydrodynamics can be derived directly from microscopic picture of motion, without using of kinetic equations as an intermediate step. New method of derivation of equation of macroscopic motion includes explicit averaging of microscopic motion on infinitesimally small piece of medium. This averaging leads to presence of electric dipole, magnetic dipole, and higher moments along with the charge density and the current density in hydrodynamic equations. The method under consideration allows to derive equations of evolution for new quantities.
Measurement of Enzyme Kinetics by Use of a Blood Glucometer: Hydrolysis of Sucrose and Lactose
Heinzerling, Peter; Schrader, Frank; Schanze, Sascha
2012-01-01
An alternative analytical method for measuring the kinetic parameters of the enzymes invertase and lactase is described. Invertase hydrolyzes sucrose to glucose and fructose and lactase hydrolyzes lactose to glucose and galactose. In most enzyme kinetics studies, photometric methods or test strips are used to quantify the derivates of the…
Nonrelativistic Quantum Mechanics with Spin in the Framework of a Classical Subquantum Kinetics
G. Kaniadakis
2002-01-01
Recently it has been shown that the spinnless one particle quantum mechanics can be obtained in the framework of entirely classical subquantum kinetics. In the present paper we argue that, within the same scheme and without any extra assumption, it is possible to obtain both the non relativistic quantum mechanics with spin, in the presence of an arbitrary external electromagnetic field, as well as the nonlinear quantum mechanics. Pacs: 03.65.Ta, 05.20.Dd KEY WORDS: monads, subquantum physics,...
A Simulation Game for the Study of Enzyme Kinetics and Inhibition.
Chayoth, Reuben; Cohen, Annette
1996-01-01
Presents a simulation game that facilitates understanding of the concepts of enzyme kinetics and inhibition. The first part of the game deals with the relationship between enzyme activity and substrate concentration while the second part deals with characterization of competitive and noncompetitive inhibition of enzyme activity. (JRH)
A Continuous Kinetic Assay for Adenylation Enzyme Activity and Inhibition
Daniel J. Wilson; Aldrich, Courtney C.
2010-01-01
Adenylation/adenylate-forming enzymes catalyze the activation of a carboxylic acid at the expense of ATP to form an acyl-adenylate intermediate and pyrophosphate (PPi). In a second half-reaction, adenylation enzymes catalyze the transfer of the acyl moiety of the acyl-adenylate onto an acceptor molecule, which can be either a protein or a small molecule. We describe the design, development, and validation of a coupled continuous spectrophotometric assay for adenylation enzymes that employs hy...
Determining Enzyme Kinetics for Systems Biology with Nuclear Magnetic Resonance Spectroscopy
Eicher, Johann J.; Snoep, Jacky L.; Rohwer, Johann M.
2012-01-01
Enzyme kinetics for systems biology should ideally yield information about the enzyme’s activity under in vivo conditions, including such reaction features as substrate cooperativity, reversibility and allostery, and be applicable to enzymatic reactions with multiple substrates. A large body of enzyme-kinetic data in the literature is based on the uni-substrate Michaelis–Menten equation, which makes unnatural assumptions about enzymatic reactions (e.g., irreversibility), and its application i...
Emergence of Dynamic Cooperativity in the Stochastic Kinetics of Fluctuating Enzymes
Kumar, Ashutosh; Nandi, Mintu; Dua, Arti
2016-01-01
Dynamic cooperativity 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 cooperativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative cooperativity. For fewer enzymes, dynamic cooperativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, how...
Eu, Byung Chan
2010-01-01
In the kinetic theory of dense fluids the many-particle collision bracket integral is given in terms of a classical collision operator defined in the phase space. To find an algorithm to compute the collision bracket integrals, we revisit the eigenvalue problem of the Liouville operator and re-examine the method previously reported[Chem. Phys. 20, 93(1977)]. Then we apply the notion and concept of the eigenfunctions of the Liouville operator and knowledge acquired in the study of the eigenfun...
Non-classical nuclei and growth kinetics of Cr precipitates in FeCr alloys during ageing
International Nuclear Information System (INIS)
In this manuscript, we have quantitatively calculated the thermodynamic properties of the critical nuclei of Cr precipitates in FeCr alloys. The concentration profiles of the critical nuclei and nucleation energy barriers were predicted by the constrained shrinking dimer dynamics method. It is found that Cr concentration distribution in the critical nuclei strongly depends on the overall Cr concentration as well as on the temperature. The critical nuclei are non-classical because the concentration in the nuclei is smaller than the thermodynamic equilibrium value. These results are in agreement with atomic probe observation. The growth kinetics of both classical and non-classical nuclei was investigated by the phase-field approach. The simulations of critical nucleus evolution showed a number of interesting phenomena: (1) a critical classical nucleus first shrinks toward its non-classical nucleus and then grows; (2) a non-classical nucleus has much slower growth kinetics at its earlier growth stage compared to the diffusion-controlled growth kinetics and (3) a critical classical nucleus grows faster at the earlier growth stage than does a non-classical nucleus. All of these results demonstrate that it is critical to introduce the correct critical nuclei in order to correctly capture the kinetics of precipitation. (paper)
KINETIC STUDY OF THE ENZYME CONVERSION OF STEAM EXPLODED PAULOWNIA TOMENTOSA TO GLUCOSE
Greta Radeva,; Ivo Valchev; Stoiko Petrin,; Eva Valcheva,; Petya Tsekova
2011-01-01
Paulownia Tomentosa was pretreated by steam explosion. The cellulase complex NS 50013 and the β-glucosidase NS 50010 of Novozymes AS were used for the enzymatic conversion of cellulose to glucose. The kinetics of enzyme conversion was studied using the exponential kinetic equation valid for processes taking place at uniformly inhomogeneous surfaces. The kinetic coefficient of inhomogeneity accounts for the energy and entropy inhomogeneity of the system and depends on the temperature. It was e...
The Nuts and Bolts of Michaelis-Menten Enzyme Kinetics: Suggestions and Clarifications
Silverstein, Todd
2011-01-01
Matthew Junker's recent article describes a useful and effective enzyme kinetics application and analogy in which students simulate enzyme activity by unscrewing nut-bolt "substrate molecules", thus, converting them into separate nuts and bolts "products". A number of suggestions and corrections are presented that improve the clarity and accuracy…
Studies on Enzyme Kinetics by Microchip and Related Techniques
Institute of Scientific and Technical Information of China (English)
James J. Bao; WANG Huai-Feng; ZHOU Da-Wei; Ken R. Wehmeyer
2004-01-01
Both conventional and microchip-based capillary electrophoresis(CE) technologies have been used for the analysis of enzymes. Practical procedures of using CE to determine the Km and Vmax values of an enzyme have been developed. By studying the inhibition to the enzyme, it is possible to select a suitable drug candidate. When compared with the conventional CE method, single lane microchip-based method can improve the speed for the assay three times. By using multiple lane-based microchip, the speed can be further increased.
More Nuts and Bolts of Michaelis-Menten Enzyme Kinetics
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.)
Bioethanol from lignocellulose - pretreatment, enzyme immobilization and hydrolysis kinetics
Tsai, Chien Tai; Anne S. Meyer; Johansen, Katja Salomon
2012-01-01
Forbehandling og enzymatisk hydrolyse er to af processerne involveret i produktionen af cellulosebaseret ethanol. Adskillige forbehandlings-strategier er foreslået, hvor nye forbehandlings-strategier udvikles til at øge effektiviteten af den enzymatiske hydrolyse. Prisen på enzymer er til stadighed en flaskehals i den enzymatiske hydrolyse, hvor genanvendelse af enzymerne er en mulig strategi for at reducere enzym-tilførslen i processen. Fra proces-ingeniørens synspunkt, er kinetikken bag enz...
An Enzyme Kinetics Experiment for the Undergraduate Organic Chemistry Laboratory
Olsen, Robert J.; Olsen, Julie A.; Giles, Greta A.
2010-01-01
An experiment using [superscript 1]H NMR spectroscopy to observe the kinetics of the acylase 1-catalyzed hydrolysis of "N"-acetyl-DL-methionine has been developed for the organic laboratory. The L-enantiomer of the reactant is hydrolyzed completely in less than 2 h, and [superscript 1]H NMR spectroscopic data from a single sample can be worked up…
Chaudhury, Srabanti
2014-09-01
We consider a generic stochastic model to describe the kinetics of single-molecule enzyme inhibition reactions in which the turnover events correspond to conversion of substrate into a product by a single enzyme molecule in the presence of an inhibitor. We observe that slow fluctuations between the active and inhibited state of the enzyme or the enzyme substrate complex can induce dynamic disorder, which is manifested in the measurement of the Poisson indicator and the Fano factor as functions of substrate concentrations for different inhibition reactions. For a single enzyme molecule inhibited by the product, we derive a single-molecule Michaelis-Menten equation for the reaction rate, which shows a dependence on the substrate concentration similar to the ensemble enzymatic catalysis rate as obtained from bulk experimental results. The measurement of Fano factor is shown to be able to discriminate reactions following different inhibition mechanisms and also extract kinetic rates. PMID:25122511
Universal Bound on the Fano Factor in Enzyme Kinetics
Barato, Andre C.; Seifert, Udo
2015-01-01
The Fano factor, an observable quantifying fluctuations of product generation by a single enzyme, can reveal information about the underlying reaction scheme. A lower bound on this Fano factor that depends on the thermodynamic affinity driving the transformation from substrate to product constrains the number of intermediate states of an enzymatic cycle. So far, this bound has been proven only for a unicyclic network of states. We show that the bound can be extended to arbitrary multicyclic n...
Kinetic theory of the shear viscosity of a strongly coupled classical one-component plasma
International Nuclear Information System (INIS)
We present an approximation to the linearized collision operator or memory function of the exact kinetic equation obeyed by the correlation function of the phase-space density of a classical one-component plasma. This approximate collision operator generalizes the well known Balescu-Guernsey-Lenard (BGL) operator to finite wavelengths, finite frequencies, and finite coupling constants. It, moreover, satisfies the necessary symmetry relations, leads to appropriate conservation laws, and fulfills its first sum rule exactly. Next we use this operator to compute the shear viscosity eta for a series of coupling constants spanning the whole fluid phase. For weak coupling we make contact with the BGL theory, while for strong coupling we confirm, at least qualitatively, the results of Vieillefosse and Hansen, who predicted a minimum in eta as a function of temperature. We also demonstrate the important role played by the sum rules in the quantitative evaluation of a transport coefficient such as eta
Universal bound on the Fano factor in enzyme kinetics.
Barato, Andre C; Seifert, Udo
2015-06-01
The Fano factor, an observable quantifying fluctuations of product generation by a single enzyme, can reveal information about the underlying reaction scheme. A lower bound on this Fano factor that depends on the thermodynamic affinity driving the transformation from substrate to product constrains the number of intermediate states of an enzymatic cycle. So far, this bound has been proven only for a unicyclic network of states. We show that the bound can be extended to arbitrary multicyclic networks, with the Fano factor constraining the largest value of the effective length, which is the ratio between the number of states and the number of products, among all cycles. PMID:25965813
Universal Bound on the Fano Factor in Enzyme Kinetics
Barato, Andre C
2015-01-01
The Fano factor, an observable quantifying fluctuations of product generation by a single enzyme, can reveal information about the underlying reaction scheme. A lower bound on this Fano factor that depends on the thermodynamic affinity driving the transformation from substrate to product constrains the number of intermediate states of an enzymatic cycle. So far, this bound has been proven only for a unicyclic network of states. We show that the bound can be extended to arbitrary multicyclic networks, with the Fano factor constraining the largest value of the effective length, which is the ratio between the number of states and the number of products, among all cycles.
The renneting of milk. A kinetic study of the enzymic and aggregation reactions.
Hooydonk, van, V.E.
1987-01-01
The rennet-induced clotting of milk was studied under various conditions. The kinetics of the enzymic and aggregation reactions was analysed separately and, where possible, related to the physico-chemical properties of the casein micelle and its environment.The effects of important variables, such as temperature, pH, divalent cations, ionic strength, casein concentration and pre-heat treatment of milk, are given and discussed in relation to the reaction kinetics and to the implications for th...
Dubois, F.; Goudeau, A
1988-01-01
The kinetics of delta antigen (HDAg) and anti-delta antibody (anti-HD) was analyzed in 22 acute delta hepatitis infections (11 coinfections and 11 superinfections), with an enzyme immunoassay developed by Organon Teknika and with two commercially available assays: Deltassay, a test for HDAg from Noctech and Abbott anti-delta enzyme immunoassay, a test for anti-HD from Abbott Laboratories. In seven cases, HDAg was detected with the Organon assay but not with Deltassay. These discrepancies were...
Bioethanol from lignocellulose - pretreatment, enzyme immobilization and hydrolysis kinetics
DEFF Research Database (Denmark)
Tsai, Chien Tai
Pretreatment and enzymatic hydrolysis are two of the processes involved in the production of cellulosic ethanol. Several pretreatment methods were proposed, however new pretreatment strategies to increase enzymetic hydrolysis efficiency are still under investigation. For enzymatic hydrolysis, the...... economic considerations, barley straw can be pretreated under 150°C for 50 min with dry matter of 20% (w/w). Glucose yield can be up to 70% after enzymatic hydrolysis. (2) Immobilization of ß-glucosidase (BG), which was done during 2010. One of the major bottlenecks in production of ethanol from...... different product inhibitors such as glucose, cellobiose and xylose) to test the hydrolysis and product inhibition mechanism of the model. Nonlinear least squares methodwas used to identify the model and estimate kinetic parameters based on the experimental data. The analysis showed that transglycosylation...
Directory of Open Access Journals (Sweden)
Kelath Murali Manoj
Full Text Available Many heme enzymes show remarkable versatility and atypical kinetics. The fungal extracellular enzyme chloroperoxidase (CPO characterizes a variety of one and two electron redox reactions in the presence of hydroperoxides. A structural counterpart, found in mammalian microsomal cytochrome P450 (CYP, uses molecular oxygen plus NADPH for the oxidative metabolism (predominantly hydroxylation of substrate in conjunction with a redox partner enzyme, cytochrome P450 reductase. In this study, we employ the two above-mentioned heme-thiolate proteins to probe the reaction kinetics and mechanism of heme enzymes. Hitherto, a substrate inhibition model based upon non-productive binding of substrate (two-site model was used to account for the inhibition of reaction at higher substrate concentrations for the CYP reaction systems. Herein, the observation of substrate inhibition is shown for both peroxide and final substrate in CPO catalyzed peroxidations. Further, analogy is drawn in the "steady state kinetics" of CPO and CYP reaction systems. New experimental observations and analyses indicate that a scheme of competing reactions (involving primary product with enzyme or other reaction components/intermediates is relevant in such complex reaction mixtures. The presence of non-selective reactive intermediate(s affords alternate reaction routes at various substrate/product concentrations, thereby leading to a lowered detectable concentration of "the product of interest" in the reaction milieu. Occam's razor favors the new hypothesis. With the new hypothesis as foundation, a new biphasic treatment to analyze the kinetics is put forth. We also introduce a key concept of "substrate concentration at maximum observed rate". The new treatment affords a more acceptable fit for observable experimental kinetic data of heme redox enzymes.
Single Molecule Simulation of Diffusion and Enzyme Kinetics.
Pérez-Rodríguez, Gael; Gameiro, Denise; Pérez-Pérez, Martín; Lourenço, Anália; Azevedo, Nuno F
2016-04-28
This work presents a molecular-scale agent-based model for the simulation of enzymatic reactions at experimentally measured concentrations. The model incorporates stochasticity and spatial dependence, using diffusing and reacting particles with physical dimensions. We developed strategies to adjust and validate the enzymatic rates and diffusion coefficients to the information required by the computational agents, i.e., collision efficiency, interaction logic between agents, the time scale associated with interactions (e.g., kinetics), and agent velocity. Also, we tested the impact of molecular location (a source of biological noise) in the speed at which the reactions take place. Simulations were conducted for experimental data on the 2-hydroxymuconate tautomerase (EC 5.3.2.6, UniProt ID Q01468) and the Steroid Delta-isomerase (EC 5.3.3.1, UniProt ID P07445). Obtained results demonstrate that our approach is in accordance to existing experimental data and long-term biophysical and biochemical assumptions. PMID:27049044
Validation and characterization of uninhibited enzyme kinetics performed in multiwell plates.
Perdicakis, Basil; Montgomery, Heather J; Guillemette, J Guy; Jervis, Eric
2004-09-01
Several systematic errors may occur during the analysis of uninhibited enzyme kinetic data using commercially available multiwell plate reader software. A MATLAB program is developed to remove these systematic errors from the data analysis process for a single substrate-enzyme system conforming to Michaelis-Menten kinetics. Three experimental designs that may be used to validate a new enzyme preparation or assay methodology and to characterize an enzyme-substrate system, while capitalizing on the ability of multiwell plate readers to perform multiple reactions simultaneously, are also proposed. These experimental designs are used to (i) test for enzyme inactivation and the quality of data obtained from an enzyme assay using Selwyn's test, (ii) calculate the limit of detection of the enzyme assay, and (iii) calculate Km and Vm values. If replicates that reflect the overall error in performing a measurement are used, the latter two experiments may be performed with internal estimation of the error structure. The need to correct for the systematic errors discussed and the utility of the proposed experimental designs were confirmed by numerical simulation. The proposed experiments were conducted using recombinant inducible nitric oxide synthase preparations and the oxyhemoglobin assay. PMID:15301957
Appreciating Formal Similarities in the Kinetics of Homogeneous, Heterogeneous, and Enzyme Catalysis
Ashby, Michael T.
2007-01-01
Because interest in catalysts is widespread, the kinetics of catalytic reactions have been investigated by widely diverse groups of individuals, including chemists, engineers, and biologists. This has lead to redundancy in theories, particularly with regard to the topics of homogeneous, heterogeneous, and enzyme catalysis. From a pedagogical…
Enzyme catalyzed oxidative gelation of sugar beet pectin: Kinetics and rheology
DEFF Research Database (Denmark)
Abang Zaidel, Dayang Norulfairuz; Chronakis, Ioannis S.; Meyer, Anne S.
2012-01-01
Sugar beet pectin (SBP) is a marginally utilized co-processing product from sugar production from sugar beets. In this study, the kinetics of oxidative gelation of SBP, taking place via enzyme catalyzed cross-linking of ferulic acid moieties (FA), was studied using small angle oscillatory measure...
Czech Academy of Sciences Publication Activity Database
Müller, Stefan; Regensburger, G.; Steuer, Ralf
2014-01-01
Roč. 347, APR 2014 (2014), s. 182-190. ISSN 0022-5193 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : metabolic optimization * enzyme kinetics * oriented matroid * elementary vector * conformal sum Subject RIV: EI - Biotechnology ; Bionics Impact factor: 2.116, year: 2014
Müller, Stefan; Regensburger, Georg; Steuer, Ralf
2014-04-21
The survival and proliferation of cells and organisms require a highly coordinated allocation of cellular resources to ensure the efficient synthesis of cellular components. In particular, the total enzymatic capacity for cellular metabolism is limited by finite resources that are shared between all enzymes, such as cytosolic space, energy expenditure for amino-acid synthesis, or micro-nutrients. While extensive work has been done to study constrained optimization problems based only on stoichiometric information, mathematical results that characterize the optimal flux in kinetic metabolic networks are still scarce. Here, we study constrained enzyme allocation problems with general kinetics, using the theory of oriented matroids. We give a rigorous proof for the fact that optimal solutions of the non-linear optimization problem are elementary flux modes. This finding has significant consequences for our understanding of optimality in metabolic networks as well as for the identification of metabolic switches and the computation of optimal flux distributions in kinetic metabolic networks. PMID:24295962
Kinetics and regulation of hepatoma mitochondrial NAD(P) malic enzyme.
Teller, J K; Fahien, L A; Davis, J W
1992-05-25
Kinetic studies of Morris 7777 hepatoma mitochondrial NAD(P) malic enzyme were consistent with an ordered mechanism where NAD adds to the enzyme before malate and dissociation of NADH from the enzyme is rate-limiting. In addition to its active site, malate apparently also associates with a lower affinity with an activator site. The activator fumarate competes with malate at the activator site and facilitates dissociation of NADH from the enzyme. The ratio of NAD(P) malic enzyme to malate dehydrogenase activity in the hepatoma mitochondrial extract was found to be too low, even in the presence of known inhibitors of malate dehydrogenase, to account for the known ability of NAD(P) malic enzyme to intercept exogenous malate from malate dehydrogenase in intact tumor mitochondria (Moreadith, R.W., and Lehninger, A.L. (1984) J. Biol. Chem. 259, 6215-6221). However, NAD(P) malic enzyme may be able to intercept exogenous malate because according to the present results, it can associate with the pyruvate dehydrogenase complex, which could localize NAD(P) malic enzyme in the vicinity of the inner mitochondrial membrane. The activity levels of some key metabolic enzymes were found to be different in Morris 7777 mitochondria than in liver or mitochondria of other rapidly dividing tumors. These results are discussed in terms of differences among tumors in their ability to utilize malate, glutamate, and citrate as respiratory fuels. PMID:1587826
Cremaschini, Claudio; 10.1140/epjp/i2011-11063-3
2012-01-01
A notorious difficulty in the covariant dynamics of classical charged particles subject to non-local electromagnetic (EM) interactions arising in the EM radiation-reaction (RR) phenomena is due to the definition of the related non-local Lagrangian and Hamiltonian systems. The lack of a standard Lagrangian/Hamiltonian formulation in the customary asymptotic approximation for the RR equation may inhibit the construction of consistent kinetic and fluid theories. In this paper the issue is investigated in the framework of Special Relativity. It is shown that, for finite-size spherically-symmetric classical charged particles, non-perturbative Lagrangian and Hamiltonian formulations in standard form can be obtained, which describe particle dynamics in the presence of the exact EM RR self-force. As a remarkable consequence, based on axiomatic formulation of classical statistical mechanics, the covariant kinetic theory for systems of charged particles subject to the EM RR self-force is formulated in Hamiltonian form....
Determining Enzyme Kinetics for Systems Biology with Nuclear Magnetic Resonance Spectroscopy
Directory of Open Access Journals (Sweden)
Johann J. Eicher
2012-11-01
Full Text Available Enzyme kinetics for systems biology should ideally yield information about the enzyme’s activity under in vivo conditions, including such reaction features as substrate cooperativity, reversibility and allostery, and be applicable to enzymatic reactions with multiple substrates. A large body of enzyme-kinetic data in the literature is based on the uni-substrate Michaelis–Menten equation, which makes unnatural assumptions about enzymatic reactions (e.g., irreversibility, and its application in systems biology models is therefore limited. To overcome this limitation, we have utilised NMR time-course data in a combined theoretical and experimental approach to parameterize the generic reversible Hill equation, which is capable of describing enzymatic reactions in terms of all the properties mentioned above and has fewer parameters than detailed mechanistic kinetic equations; these parameters are moreover defined operationally. Traditionally, enzyme kinetic data have been obtained from initial-rate studies, often using assays coupled to NAD(PH-producing or NAD(PH-consuming reactions. However, these assays are very labour-intensive, especially for detailed characterisation of multi-substrate reactions. We here present a cost-effective and relatively rapid method for obtaining enzyme-kinetic parameters from metabolite time-course data generated using NMR spectroscopy. The method requires fewer runs than traditional initial-rate studies and yields more information per experiment, as whole time-courses are analyzed and used for parameter fitting. Additionally, this approach allows real-time simultaneous quantification of all metabolites present in the assay system (including products and allosteric modifiers, which demonstrates the superiority of NMR over traditional spectrophotometric coupled enzyme assays. The methodology presented is applied to the elucidation of kinetic parameters for two coupled glycolytic enzymes from Escherichia coli
A generalized cellular automata approach to modeling first order enzyme kinetics
Indian Academy of Sciences (India)
Abhishek Dutta; Saurajyoti Kar; Advait Apte; Ingmar Nopens; Denis Constales
2015-04-01
Biochemical processes occur through intermediate steps which are associated with the formation of reaction complexes. These enzyme-catalyzed biochemical reactions are inhibited in a number of ways such as inhibitors competing for the binding site directly, inhibitors deforming the allosteric site or inhibitors changing the structure of active substrate. Using an in silico approach, the concentration of various reaction agents can be monitored at every single time step, which are otherwise difficult to analyze experimentally. Cell-based models with discrete state variables, such as Cellular Automata (CA) provide an understanding of the organizational principles of interacting cellular systems to link the individual cell (microscopic) dynamics wit a particular collective (macroscopic) phenomenon. In this study, a CA model representing a first order enzyme kinetics with inhibitor activity is formulated. The framework of enzyme reaction rules described in this study is probabilistic. An extended von Neumann neighborhood with periodic boundary condition is implemented on a two-dimensional (2D) lattice framework. The effect of lattice-size variation is studied followed by a sensitivity analysis of the model output to the probabilistic parameters which represent various kinetic reaction constants in the enzyme kinetic model. This provides a deeper insight into the sensitivity of the CA model to these parameters. It is observed that cellular automata can capture the essential features of a discrete real system, consisting of space, time and state, structured with simple local rules without making complex implementations but resulting in complex but explainable patterns.
Directory of Open Access Journals (Sweden)
Simon Brown
2010-06-01
Full Text Available The behavior of enzyme-catalyzed reactions is not made clear to many students by the standard mathematical description of enzyme kinetics. An enzyme-machine analogy is described that has made the details of the Michaelis-Menten mechanism and the associated kinetics more accessible with minimal use of mathematics. Students taught using the analogy appear to have fewer of the misconceptions than those taught using a more mathematical approach.
Fundamental study of the mechanism and kinetics of cellulose hydrolysis by acids and enzymes
Gong, C. S.; Chang, M.
1981-02-01
There are three basic enzymes e.g., endoglucanase (C/sub x/), exoglucanase (C1) and cellobiase comprising the majority of extracellular cellulase enzymes produced by the cellulolytic mycelial fungi, Trichoderma reesei, and other cellulolytic microorganisms. The kinetics of cellobiase were developed on the basis of applying the pseudo-steady state assumption to hydrolyze cellobiose to glucose. The results indicated that cellobiase was bjected to end-product inhibition by glucose. The kinetic modeling of exoglucanase (C1) with respect to cellodextrins was studied. Both glucose and cellobiose were found to be inhibitors of this enzyme with cellobiose being a stronger inhibitor than glucose. Similarly, endoglucanase (C/sub x) is subject to end-product inhibition by glucose. Crystallinity of the cellulose affects the rate of hydrolysis by cellulases. Hence, the changes in crystallinity of cellulose in relation to chemical pretreatment and enzyme hydrolysis was compared. The study of cellulase biosynthesis resulted in the conclusion that exo-and endo-glucanases are coinduced while cellobiase is synthesized independent of the other two enzymes.
Zakharov, A Yu
2016-01-01
The exact closed equation of motion for microscopic distribution function of classical many-body system with account of interactions retardation between particles is derived. It is shown that interactions retardation leads to irreversible behaviour of many-body systems.
The kinetics of cellulose enzymatic hydrolysis : Implications of the synergism between enzymes
Väljamäe, Priit
2002-01-01
The hydrolysis kinetics of bacterial cellulose and its derivatives by Trichoderma reesei cellulases was studied. The cellulose surface erosion model was introduced to explain the gradual and strong retardation of the rate of enzymatic hydrolysis of cellulose. This model identifies the decrease in apparent processivity of cellobiohydrolases during the hydrolysis as a major contributor to the decreased rates. Both enzyme-related (non-productive binding) and substrate-related (erosion of cellulo...
Directory of Open Access Journals (Sweden)
Michael E.G. Lyons
2003-01-01
Full Text Available A detailed kinetic analysis of the pertinent physical processes underlying the operation of enzyme electrodes immobilized within alkane thiol self assembled monolayers is developed. These electrodes utilize a soluble mediator, which partitions into the monolayer, regenerates the active catalytic form of the enzyme and is re-oxidized at the underlying support electrode surface giving rise to a current which reflects kinetic events at the enzyme surface. Both the enzyme/substrate and enzyme mediator kinetics have been quantified fully in terms of a ping-pong mechanism for the former and Michaelis-Menten kinetics for the latter. The effect of substrate and mediator diffusion in solution have also been specifically considered and the latter processes have been shown to result in a complex expression for the reaction flux. Four limiting kinetic cases have been enumerated and simple expressions for the reaction flux in each of these rate limiting situations have been developed. Kinetic case diagrams have been presented as an aid to mechanistic diagnosis. The complicating effects of diffusive loss of reduced mediator from the enzyme layer have also been examined and the relation between the observed flux corresponding to reduced mediator oxidation at the support electrode and the substrate reaction flux in the enzyme layer have been quantified in terms of an efficiency factor. Results extracted from recently published practical realizations of immobilized monolayer enzyme systems have been discussed in the context of the proposed model analysis.
Wilson, Kerry A.; Finch, Craig A.; Anderson, Phillip; Vollmer, Frank; Hickman, James J.
2014-01-01
Understanding protein adsorption and resultant conformation changes on modified and unmodified silicon dioxide surfaces is a subject of keen interest in biosensors, microfluidic systems and for medical diagnostics. However, it has been proven difficult to investigate the kinetics of the adsorption process on these surfaces as well as understand the topic of the denaturation of proteins and its effect on enzyme activity. A highly sensitive optical whispering gallery mode (WGM) resonator was used to study a catalytic enzyme’s adsorption processes on different silane modified glass substrates (plain glass control, DETA, 13F, and SiPEG). The WGM sensor was able to obtain high resolution kinetic data of glucose oxidase (GO) adsorption with sensitivity of adsorption better than that possible with SPR. The kinetic data, in combination with a functional assay of the enzyme activity, was used to test hypotheses on adsorption mechanisms. By fitting numerical models to the WGM sensograms for protein adsorption, and by confirming numerical predictions of enzyme activity in a separate assay, we were able to identify mechanisms for GO adsorption on different alkylsilanes and infer information about the adsorption of protein on nanostructured surfaces. PMID:25453976
KINETIC STUDY OF THE ENZYME CONVERSION OF STEAM EXPLODED PAULOWNIA TOMENTOSA TO GLUCOSE
Directory of Open Access Journals (Sweden)
Greta Radeva,
2011-11-01
Full Text Available Paulownia Tomentosa was pretreated by steam explosion. The cellulase complex NS 50013 and the β-glucosidase NS 50010 of Novozymes AS were used for the enzymatic conversion of cellulose to glucose. The kinetics of enzyme conversion was studied using the exponential kinetic equation valid for processes taking place at uniformly inhomogeneous surfaces. The kinetic coefficient of inhomogeneity accounts for the energy and entropy inhomogeneity of the system and depends on the temperature. It was established that both the activation energy and the pre-exponential factor increase simultaneously with increasing of conversion degree. A compensation effect between pre-exponential factor and activation energy was observed. The energetic hindrances established cannot be completely compensated by the positive effect of the pre-exponential factor increase. Hence, the activation energy has a determining influence on how quickly the rate of hydrolysis decreases.
Gelis, F.; Jeon, S.; Venugopalan, R.
2007-01-01
We develop the formalism discussed previously in hep-ph/0601209 and hep-ph/0605246 to construct a kinetic theory that provides insight into the earliest ``Glasma'' stage of a high energy heavy ion collision. Particles produced from the decay of classical fields in the Glasma obey a Boltzmann equation whose novel features include an inhomogeneous source term and new contributions to the collision term. We discuss the power counting associated with the different terms in the Boltzmann equation ...
Pedruzzi, Israel; da Silva, Eduardo A Borges; Rodrigues, Alírio E
2011-07-10
In this work, we have investigated the kinetics of the biotechnological production of lactobionic acid (LBA) and sorbitol by the catalytic action of glucose-fructose oxidoreductase (GFOR) and glucono-δ-lactonase (GL) enzymes. The cells of bacterium Zymomonas mobilis ATCC 29191 containing this enzymatic complex were submitted to permeabilization and reticulation procedures. The effect of the concentration of substrates on the rate of product formation using a mobilized cell system was investigated. The application of higher fructose concentration seems to not affect the initial rate of formation of the bionic acid. Under conditions of low initial concentration of lactose, the experimental kinetic data of the bi-substrate reaction were modelled by assuming a rate equation of the classical ping-pong mechanism. The found kinetic parameters displayed a low affinity of the GFOR enzyme for both substrates. The enzymatic system did not exhibit normal Michaelis-Menten kinetics in response to a change of concentration of lactose, when fructose was held constant, presenting a sigmoid relationship between initial velocity and substrate concentration. A rate equation based on Hill kinetics was used to describe the kinetic behaviour of this enzyme-substituted reaction at higher lactose concentrations. The results from batch experiments using immobilized cells within Ca-alginate beads revealed that there is no pronounced occurrence of mass transfer limitations on LBA production for beads with 1.2 mm in average diameter. This discussion aids for defining the best operating conditions to maximize the productivity for LBA and sorbitol in this bioconversion and also for reducing the complexity of downstream separation processes. PMID:22112407
Ward, Keeran; Xi, Jingshu; Stuckey, David C
2016-05-01
This study seeks to examine the ability of non-ionic/non-polar Colloidial Liquid Aphrons (CLAs) to preserve enzyme functionality upon immobilization and release. CLAs consisting of micron-sized oil droplets surrounded by a thin aqueous layer stabilized by a mixture of surfactants, were formulated by direct addition (pre-manufacture addition) using 1% Tween 80/mineral oil and 1% Tween 20 and the enzymes lipase, aprotinin and α-chymotrypsin. The results of activity assays for both lipase and α-chymotrypsin showed that kinetic activity increased upon immobilization by factors of 7 and 5.5, respectively, while aprotinin retained approximately 85% of its native activity. The conformation of the enzymes released through desorption showed no significant alterations compared to their native state. Changes in pH and temperature showed that optimum conditions did not change after immobilization, while analysis of activation energy for the immobilized enzyme showed an increase in activity at higher temperatures. Furthermore, the effect of bound water within the aphron structure allowed for some degree of enzyme hydration, and this hydration was needed for an active conformation with results showing a decrease in ΔH* for the immobilized system compared to its native counterpart. Biotechnol. Bioeng. 2016;113: 970-978. © 2015 Wiley Periodicals, Inc. PMID:26497856
Archelas, Alain; Zhao, Wei; Faure, Bruno; Iacazio, Gilles; Kotik, Michael
2016-02-01
A detailed kinetic study based on steady-state and pre-steady-state measurements is described for the highly enantioselective epoxide hydrolase Kau2. The enzyme, which is a member of the α/β-hydrolase fold family, preferentially reacts with the (S,S)-enantiomer of trans-stilbene oxide (TSO) with an E value of ∼200. The enzyme follows a classical two-step catalytic mechanism with formation of an alkyl-enzyme intermediate in the first step and hydrolysis of this intermediate in a rate-limiting second step. Tryptophan fluorescence quenching during TSO conversion appears to correlate with alkylation of the enzyme. The steady-state data are consistent with (S,S) and (R,R)-TSO being two competing substrates with marked differences in kcat and KM values. The high enantiopreference of the epoxide hydrolase is best explained by pronounced differences in the second-order alkylation rate constant (k2/KS) and the alkyl-enzyme hydrolysis rate k3 between the (S,S) and (R,R)-enantiomers of TSO. Our data suggest that during conversion of (S,S)-TSO the two active site tyrosines, Tyr(157) and Tyr(259), serve mainly as electrophilic catalysts in the alkylation half-reaction, polarizing the oxirane oxygen of the bound epoxide through hydrogen bond formation, however, without fully donating their hydrogens to the forming alkyl-enzyme intermediate. PMID:26714303
An Integrated Circuit for Chip-Based Analysis of Enzyme Kinetics and Metabolite Quantification.
Cheah, Boon Chong; Macdonald, Alasdair Iain; Martin, Christopher; Streklas, Angelos J; Campbell, Gordon; Al-Rawhani, Mohammed A; Nemeth, Balazs; Grant, James P; Barrett, Michael P; Cumming, David R S
2016-06-01
We have created a novel chip-based diagnostic tools based upon quantification of metabolites using enzymes specific for their chemical conversion. Using this device we show for the first time that a solid-state circuit can be used to measure enzyme kinetics and calculate the Michaelis-Menten constant. Substrate concentration dependency of enzyme reaction rates is central to this aim. Ion-sensitive field effect transistors (ISFET) are excellent transducers for biosensing applications that are reliant upon enzyme assays, especially since they can be fabricated using mainstream microelectronics technology to ensure low unit cost, mass-manufacture, scaling to make many sensors and straightforward miniaturisation for use in point-of-care devices. Here, we describe an integrated ISFET array comprising 2(16) sensors. The device was fabricated with a complementary metal oxide semiconductor (CMOS) process. Unlike traditional CMOS ISFET sensors that use the Si3N4 passivation of the foundry for ion detection, the device reported here was processed with a layer of Ta2O5 that increased the detection sensitivity to 45 mV/pH unit at the sensor readout. The drift was reduced to 0.8 mV/hour with a linear pH response between pH 2-12. A high-speed instrumentation system capable of acquiring nearly 500 fps was developed to stream out the data. The device was then used to measure glucose concentration through the activity of hexokinase in the range of 0.05 mM-231 mM, encompassing glucose's physiological range in blood. Localised and temporal enzyme kinetics of hexokinase was studied in detail. These results present a roadmap towards a viable personal metabolome machine. PMID:26742138
Purification, kinetic behavior, and regulation of NAD(P)+ malic enzyme of tumor mitochondria.
Moreadith, R W; Lehninger, A L
1984-05-25
The purification and kinetic characterization of an NAD(P)+-malic enzyme from 22aH mouse hepatoma mitochondria are described. The enzyme was purified 328-fold with a final yield of 51% and specific activity of 38.1 units/mg of protein by employing DEAE-cellulose chromatography and an ATP affinity column. Sephadex G-200 chromatography yielded a native Mr = 240,000. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a major subunit with Mr = 61,000, suggesting a tetrameric structure, and also showed that the preparation contained less than 10% polypeptide impurities. Use of the ATP affinity column required the presence of MnCl2 and fumarate (an allosteric activator) in the elution buffers. In the absence of fumarate, the Michaelis constants for malate, NAD+, and NADP+ were 3.6 mM, 55 microM, and 72 microM, respectively; in the presence of fumarate (2 mM), the constants were 0.34 mM, 9 microM, and 13 microM, respectively. ATP was shown to be an allosteric inhibitor, competitive with malate. However, the inhibition by ATP displayed hyperbolic competitive kinetics with a KI (ATP) of 80 microM (minus fumarate) and 0.5 mM (plus 2 mM fumarate). The allosteric properties of the enzyme are integrated into a rationale for its specific role in the pathways of malate and glutamate oxidation in tumor mitochondria. PMID:6725250
A new multi-wavelength model-based method for determination of enzyme kinetic parameters
Indian Academy of Sciences (India)
Mohammad-Hossein Sorouraddin; Kaveh Amini; Abdolhossein Naseri; Javad Vallipour; Jalal Hanaee; Mohammad-Reza Rashidi
2010-09-01
Lineweaver–Burk plot analysis is the most widely used method to determine enzyme kinetic parameters. In the spectrophotometric determination of enzyme activity using the Lineweaver–Burk plot, it is necessary to find a wavelength at which only the substrate or the product has absorbance without any spectroscopic interference of the other reaction components. Moreover, in this method, different initial concentrations of the substrate should be used to obtain the initial velocities required for Lineweaver–Burk plot analysis. In the present work, a multi-wavelength model-based method has been developed and validated to determine Michaelis–Menten constants for some enzyme reactions. In this method, a selective wavelength region and several experiments with different initial concentrations of the substrate are not required. The absorbance data of the kinetic assays are fitted by non-linear regression coupled to the numeric integration of the related differential equation. To indicate the applicability of the proposed method, the Michaelis–Menten constants for the oxidation of phenanthridine, 6-deoxypenciclovir and xanthine by molybdenum hydroxylases were determined using only a single initial concentration of the substrate, regardless of any spectral overlap.
Steady-state analysis of kinetic isotope effects in enzymic reactions
International Nuclear Information System (INIS)
The decrease in the rate of bond cleavage resulting from the presence of heavy isotopes is expressed to a greater or lesser extent as an isotope effect on steady-state kinetic parameters of enzyme-catalyzed reactions, depending upon complex relationships between individual rate constants. This paper describes these relationships and derives general kinetic expressions which allow the determination of the limits of the relative contribution of different reaction components to V/sub max/ and V/sub max//K/sub m/. The value of the true isotope effect on a carbon-hydrogen bond breaking step, the rate of this step, and its percentage of partial rate limitation of the overall reaction, plus the dissociation constant of the enzyme-substrate complex, can be determined from the derived expressions by comparing deuterium and tritium isotope effects on V/sub max//K/sub m/. In the absence of a measure of the true isotope effect, the lower limit of primary isotope effects of deuterium which may be interpreted as identifying the slowest or ''rate-determining'' step in an enzyme-catalyzed reaction is found to be k/sub H//k/sub D/ = 8, and not k/sub H//k/sub D/ = 2 as is currently supposed. (U.S.)
Wypijewska, Anna; Bojarska, Elzbieta; STEPINSKI, JANUSZ; Jankowska-Anyszka, Marzena; Jemielity, Jacek; Davis, Richard E.; Darzynkiewicz, Edward
2010-01-01
The activity of C. elegans scavenger decapping enzyme (DcpS) on its natural substrates and dinucleotide cap analogues modified in the nucleoside’s base or ribose moiety, has been examined. All tested dinucleotides were specifically cleaved between β and γ phosphate groups in the triphosphate chain. The kinetic parameters of enzymatic hydrolysis (Km, Vmax) were determined using fluorescence and HPLC methods, as complementary approaches for the kinetic studies of C. elegans DcpS. From the kinet...
Large-scale ruthenium- and enzyme-catalyzed dynamic kinetic resolution of (rac-1-phenylethanol
Directory of Open Access Journals (Sweden)
Bäckvall Jan-E
2007-12-01
Full Text Available Abstract The scale-up of the ruthenium- and enzyme-catalyzed dynamic kinetic resolution (DKR of (rac-1-phenylethanol (2 is addressed. The immobilized lipase Candida antarctica lipase B (CALB was employed for the resolution, which shows high enantioselectivity in the transesterification. The ruthenium catalyst used, (η 5-C5Ph5RuCl(CO2 1, was shown to possess very high reactivity in the "in situ" redox racemization of 1-phenylethanol (2 in the presence of the immobilized enzyme, and could be used in 0.05 mol% with high efficiency. Commercially available isopropenyl acetate was employed as acylating agent in the lipase-catalyzed transesterifications, which makes the purification of the product very easy. In a successful large-scale DKR of 2, with 0.05 mol% of 1, (R-1-phenylethanol acetate (3 was obtained in 159 g (97% yield in excellent enantiomeric excess (99.8% ee.
Application of A Microfluidic Tool for the Determination of Enzyme Kinetics
DEFF Research Database (Denmark)
Ringborg, Rolf H.
aim. All the limitations surround the reactor of a process,and with the performance of this being unknown, it is almost impossible to direct development. A focal point must therefore lie in the determination of kinetic models and howkinetic data can be obtained in a robust and generic way. Models for...... analysis of aqueous solutions on‐line. Furthermore, the use of a size exclusion column enables the simultaneous detection of enzymes and UV/VISactive compounds. The size exclusion chromatography does not provide baseline separated results, nor is this required. The application of chemometric tools enable...... detection of compounds in the collected retention time wavelength data. A major improvement over traditional techniques is the quantification of enzyme concentration and this makes it possible to use specific activities for model fitting. The setup takes advantage of microfluidic featuresand delivers semi...
Determination Of Enzyme Kinetic Parameters on Sago Starch Hydrolysis By Linearized Graphical Methods
International Nuclear Information System (INIS)
Amyloglucosidase (E.C. 3.2.1.3) from Aspergillus niger was used to hydrolyze the sago (Metro xylon sagu) starch into reducing sugars. The experiment was conducted at constant temperature, 55 degree Celsius; pH, 4.5 and enzyme amount, 0.2 U/ ml, respectively. In this investigation, the substrate concentration was varied ranging from 1.0 - 7.0 g/ L. The obtained data were then fixed into linearized plots namely Lineweaver-Burk and Langmuir models to calculate enzyme kinetic parameters, Km and Vmax. Both of the Km and Vmax (mM, mol/min) values from each plot were: Lineweaver-Burk (26.53, 3.31) and Langmuir (13.52, 2.35). Among the linearized models, Km and Vmax values acquired from Langmuir plot was chosen. (author)
Dzierlenga, Michael; Antoniou, Dimitri; Schwartz, Steven
2015-03-01
The mechanisms involved in enzymatic hydride transfer have been studies for years but questions remain, due to the difficulty in determining the participation of protein dynamics and quantum effects, especially hydrogen tunneling. In this study, we use transition path sampling (TPS) with normal mode centroid molecular dynamics (CMD) to calculate the barrier to hydride transfer in yeast alcohol dehydrogenase (YADH) and lactate dehydrogenase (LDH). Calculation of the work applied to the hydride during the reaction allows for observation of the change in barrier height due to inclusion of quantum effects. Additionally, the same calculations were performed using deuterium as the transferring particle to validate our methods with experimentally measured kinetic isotope effects. The change in barrier height in YADH upon inclusion of quantum effects is indicative of a zero-point energy contribution, and is evidence that the protein mediates a near-barrierless transfer of the rate-limiting hydride. Calculation of kinetic isotope effects using the average difference in barrier between hydride and deuteride agreed well with experimental results. The authors acknowledge the support of the National Institutes of Health Grants GM068036 and GM102226.
Dzierlenga, Michael W; Antoniou, Dimitri; Schwartz, Steven D
2015-04-01
The mechanisms involved in enzymatic hydride transfer have been studied for years, but questions remain due, in part, to the difficulty of probing the effects of protein motion and hydrogen tunneling. In this study, we use transition path sampling (TPS) with normal mode centroid molecular dynamics (CMD) to calculate the barrier to hydride transfer in yeast alcohol dehydrogenase (YADH) and human heart lactate dehydrogenase (LDH). Calculation of the work applied to the hydride allowed for observation of the change in barrier height upon inclusion of quantum dynamics. Similar calculations were performed using deuterium as the transferring particle in order to approximate kinetic isotope effects (KIEs). The change in barrier height in YADH is indicative of a zero-point energy (ZPE) contribution and is evidence that catalysis occurs via a protein compression that mediates a near-barrierless hydride transfer. Calculation of the KIE using the difference in barrier height between the hydride and deuteride agreed well with experimental results. PMID:26262969
Löppmann, Sebastian; Blagodatskaya, Evgenia; Kuzyakov, Yakov
2014-05-01
Rhizosphere and detritusphere are soil microsites with very high resource availability for microorganisms affecting their biomass, composition and functions. In the rhizosphere low molecular compounds occur with root exudates and low available polymeric compounds, as belowground plant senescence. In detritusphere the substrate for decomposition is mainly a polymeric material of low availability. We hypothesized that microorganisms adapted to contrasting quality and availability of substrates in the rhizosphere and detritusphere are strongly different in affinity of hydrolytic enzymes responsible for decomposition of organic compounds. According to common ecological principles easily available substrates are quickly consumed by microorganisms with enzymes of low substrate affinity (i.e. r-strategists). The slow-growing K-strategists with enzymes of high substrate affinity are better adapted for growth on substrates of low availability. Estimation of affinity of enzyme systems to the substrate is based on Michaelis-Menten kinetics, reflecting the dependency of decomposition rates on substrate amount. As enzymes-mediated reactions are substrate-dependent, we further hypothesized that the largest differences in hydrolytic activity between the rhizosphere and detritusphere occur at substrate saturation and that these differences are smoothed with increasing limitation of substrate. Affected by substrate limitation, microbial species follow a certain adaptation strategy. To achieve different depth gradients of substrate availability 12 plots on an agricultural field were established in the north-west of Göttingen, Germany: 1) 4 plots planted with maize, reflecting lower substrate availability with depth; 2) 4 unplanted plots with maize litter input (0.8 kg m-2 dry maize residues), corresponding to detritusphere; 3) 4 bare fallow plots as control. Maize litter was grubbed homogenously into the soil at the first 5 cm to ensure comparable conditions for the herbivore and
Hoeven, Robin; Heyes, Derren J; Hay, Sam; Scrutton, Nigel S
2015-08-01
The temperature dependence of kinetic isotope effects (KIEs) has emerged as the main experimental probe of enzymatic H-transfer by quantum tunnelling. Implicit in the interpretation is a presumed role for dynamic coupling of H-transfer chemistry to the protein environment, the so-called 'promoting motions/vibrations hypothesis'. This idea remains contentious, and others have questioned the importance and/or existence of promoting motions/vibrations. New experimental methods of addressing this problem are emerging, including use of mass-modulated enzymes and time-resolved spectroscopy. The pressure dependence of KIEs has been considered as a potential probe of quantum tunnelling reactions, because semi-classical KIEs, which are defined by differences in zero-point vibrational energy, are relatively insensitive to kbar changes in pressure. Reported combined pressure and temperature (p-T) dependence studies of H-transfer reactions are, however, limited. Here, we extend and review the available p-T studies that have utilized well-defined experimental systems in which quantum mechanical tunnelling is established. These include flavoproteins, quinoproteins, light-activated enzymes and chemical model systems. We show that there is no clear general trend between the p-T dependencies of the KIEs in these systems. Given the complex nature of p-T studies, we conclude that computational simulations using determined (e.g. X-ray) structures are also needed alongside experimental measurements of reaction rates/KIEs to guide the interpretation of p-T effects. In providing new insight into H-transfer/environmental coupling, combined approaches that unite both atomistic understanding with experimental rate measurements will require careful evaluation on a case-by-case basis. Although individually informative, we conclude that p-T studies do not provide the more generalized insight that has come from studies of the temperature dependence of KIEs. PMID:25581554
Sequence diversity of NanA manifests in distinct enzyme kinetics and inhibitor susceptibility
Xu, Zhongli; von Grafenstein, Susanne; Walther, Elisabeth; Fuchs, Julian E.; Liedl, Klaus R.; Sauerbrei, Andreas; Schmidtke, Michaela
2016-04-01
Streptococcus pneumoniae is the leading pathogen causing bacterial pneumonia and meningitis. Its surface-associated virulence factor neuraminidase A (NanA) promotes the bacterial colonization by removing the terminal sialyl residues from glycoconjugates on eukaryotic cell surface. The predominant role of NanA in the pathogenesis of pneumococci renders it an attractive target for therapeutic intervention. Despite the highly conserved activity of NanA, our alignment of the 11 NanAs revealed the evolutionary diversity of this enzyme. The amino acid substitutions we identified, particularly those in the lectin domain and in the insertion domain next to the catalytic centre triggered our special interest. We synthesised the representative NanAs and the mutagenized derivatives from E. coli for enzyme kinetics study and neuraminidase inhibitor susceptibility test. Via molecular docking we got a deeper insight into the differences between the two major variants of NanA and their influence on the ligand-target interactions. In addition, our molecular dynamics simulations revealed a prominent intrinsic flexibility of the linker between the active site and the insertion domain, which influences the inhibitor binding. Our findings for the first time associated the primary sequence diversity of NanA with the biochemical properties of the enzyme and with the inhibitory efficiency of neuraminidase inhibitors.
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Z. R. Yelebe
2014-03-01
Full Text Available This paper addresses the challenge of estimating various kinetic parameters for the design of an optimized enzyme catalysed batch bioreactor of high efficiency and yield. Mathematical models were developed to describe the batch reaction time in relation to the substrate, enzyme and product concentration. The results obtained from the plots generated were: 35.50gmol/l.hr for the velocity of reaction of the enzymes (Vmax, 0.10049hr-1 for the maximum specific growth rate (µmax 826.45gmol/l for the Michaelis-Menten constant (Km, 0.005402577 for maintenance coefficient (Ms, 10.104kgCx/kgCs for yield of cell weight per unit weight of substrate (Ycx/CS, 0.05436kgCp/kgCs for yield of product weight per unit weight of substrate utilized (Ycp/CS and 0.01416 for endogenous decay coefficient (Kd for the design of the batch biochemical reactor. Hence, they are useful parameters for predicting the most appropriate batch reaction conditions and the efficiency of the bioreactor. The mathematical model predictions showed that it can be considered as a good complimentary tool to real system since the simulation results of the mathematical model agrees with experimental data reported in literature.
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Zahra Ghobadi Nejad
2014-01-01
Full Text Available Due to great commercial application of protease, it is necessary to study kinetic characterization of this enzyme in order to improve design of enzymatic reactors. In this study, mathematical modeling of protease enzyme production kinetics which is derived from Bacillus licheniformis BBRC 100053 was studied (at 37°C, pH 10 after 73 h in stationary phase, and 150 rpm. The aim of the present paper was to determine the best kinetic model and kinetic parameters for production of protease and calculating Ki (inhibition constant of different inhibitors to find the most effective one. The kinetic parameters Km (Michaelis-Menten constant and Vm (maximum rate were calculated 0.626 mM and 0.0523 mM/min. According to the experimental results, using DFP (diisopropyl fluorophosphate and PMSF (phenylmethanesulfonyl fluoride as inhibitors almost 50% of the enzyme activity could be inhibited when their concentrations were 0.525 and 0.541 mM, respectively. Ki for DFP and PMSF were 0.46 and 0.56 mM, respectively. Kinetic analysis showed that the Lineweaver-Burk model was the best fitting model for protease production kinetics DFP was more effective than PMSF and both of them should be covered in the group of noncompetitive inhibitors.
Enzymes are complex proteins that cause a specific chemical change in all parts of the body. For ... use them. Blood clotting is another example of enzymes at work. Enzymes are needed for all body ...
Kinetics of Circulating Plasma Cell-Free DNA in Paediatric Classical Hodgkin Lymphoma
Primerano, Simona; Burnelli, Roberta; Carraro, Elisa; Pillon, Marta; Elia, Caterina; Farruggia, Piero; Sala, Alessandra; Vinti, Luciana; Buffardi, Salvatore; Basso, Giuseppe; Mascarin, Maurizio; Mussolin, Lara
2016-01-01
Levels of plasma cell-free DNA (cfDNA) of a large series of children with classical Hodgkin lymphoma (cHL) were evaluated and analyzed at diagnosis and during chemotherapy treatment in relation with clinical characteristics. CfDNA levels in cHL patients were significantly higher compared with controls (p=0.002). CfDNA at diagnosis was correlated with presence of B symptoms (p=0.027) and high erythrocyte sedimentation rate (p=0.049). We found that the increasing of plasma cfDNA after first che...
A Numerical Procedure for Model Identifiability Analysis Applied to Enzyme Kinetics
DEFF Research Database (Denmark)
Daele, Timothy, Van; Van Hoey, Stijn; Gernaey, Krist;
2015-01-01
structure evaluation by assessing the local identifiability characteristics of the parameters. Moreover, such a procedure should be generic to make sure it can be applied independent from the structure of the model. We hereby apply a numerical identifiability approach which is based on the work of Walter...... and Pronzato (1997) and which can be easily set up for any type of model. In this paper the proposed approach is applied to the forward reaction rate of the enzyme kinetics proposed by Shin and Kim(1998). Structural identifiability analysis showed that no local structural model problems were occurring....... In contrast, the practical identifiability analysis revealed that high values of the forward rate parameter Vf led to identifiability problems. These problems were even more pronounced athigher substrate concentrations, which illustrates the importance of a proper experimental designto avoid...
Cao, Yuansheng; Gong, Zongping; Quan, H. T.
2015-06-01
Motivated by the recent proposed models of the information engine [Proc. Natl. Acad. Sci. USA 109, 11641 (2012), 10.1073/pnas.1204263109] and the information refrigerator [Phys. Rev. Lett. 111, 030602 (2013), 10.1103/PhysRevLett.111.030602], we propose a minimal model of the information pump and the information eraser based on enzyme kinetics. This device can either pump molecules against the chemical potential gradient by consuming the information to be encoded in the bit stream or (partially) erase the information initially encoded in the bit stream by consuming the Gibbs free energy. The dynamics of this model is solved exactly, and the "phase diagram" of the operation regimes is determined. The efficiency and the power of the information machine is analyzed. The validity of the second law of thermodynamics within our model is clarified. Our model offers a simple paradigm for the investigating of the thermodynamics of information processing involving the chemical potential in small systems.
Novel approach for predicting the joint effects based on the enzyme-catalyzed kinetics.
Zheng, Min; Yao, Zhifeng; Lin, Zhifen; Fang, Shuxia; Song, Chunlei; Liu, Ying
2016-04-15
Organisms are exposed to mixtures of multiple contaminants and it is necessary to build prediction models for the joint effects, considering the high expense and the complexity of the traditional toxicity testing and the flood occurrence of environmental chemical pollutants. In this study, a new method for predicting the joint effects was developed and corresponding prediction models were constructed based on the kinetic models of enzyme-catalyzed reactions. While, we utilized Vibrio fischeri, Escherichia coli and Bacillus subtilis as model organisms and determined the chronic toxicity of the binary mixtures of sulfonamides (SAs) and sulfonamide potentiators (SAPs) (SA+SAP), the mixtures of two kinds of sulfonamides (SA+SA) and the binary mixtures of sulfonamide potentiators (SAPs) and tetracyclines (TCs) (SAP+TC) respectively. Finally, corresponding mixture toxicity data was utilized to fit and verify the prediction models for different joint effects. PMID:26826939
International Nuclear Information System (INIS)
We prove the detailed and integral multivariable fluctuation theorems in the steady-state cycle kinetics of single enzyme with competing substrates for any arbitrary time interval [0, t]. It is shown that the moment generating function for the stochastic number of each enzymatic cycle follows the multivariable fluctuation theorems in the form of Kurchan–Lebowitz–Spohn-type symmetry. These symmetry relations associated with different variables are independent of each other, which may help experimentally determine the thermodynamic affinities from the sample trajectories separately. Furthermore, we also obtain the Kawasaki equalities for the fluctuating chemical work done within each enzymatic cycle. The derivation here is directly based on the generalized Haldane equalities, which say that the forward and backward conditional dwell times for each enzymatic cycle have identical distributions. These symmetries are independent of each other, which may help experimentally determine the thermodynamic affinities from the sample trajectories separately. (paper)
Cao, Yuansheng; Gong, Zongping; Quan, H T
2015-06-01
Motivated by the recent proposed models of the information engine [Proc. Natl. Acad. Sci. USA 109, 11641 (2012)] and the information refrigerator [Phys. Rev. Lett. 111, 030602 (2013)], we propose a minimal model of the information pump and the information eraser based on enzyme kinetics. This device can either pump molecules against the chemical potential gradient by consuming the information to be encoded in the bit stream or (partially) erase the information initially encoded in the bit stream by consuming the Gibbs free energy. The dynamics of this model is solved exactly, and the "phase diagram" of the operation regimes is determined. The efficiency and the power of the information machine is analyzed. The validity of the second law of thermodynamics within our model is clarified. Our model offers a simple paradigm for the investigating of the thermodynamics of information processing involving the chemical potential in small systems. PMID:26172671
Parametric constraints on the dynamic behavior of immobilized enzyme kinetics in a microreactor
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Pratap R Patnaik
2011-08-01
Full Text Available Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} The observed kinetics of reactions catalyzed by immobilized enzymes in microreactors may differ from their kinetics in well-mixed solution-phase reactors. While the steady-state differences have been analyzed before, the time-dependent differences have not been explored. In the present study, therefore, an initial feasibility analysis has been conducted to identify permissible regions for the kinetic parameters for dynamics solutions to exist. For a reaction catalyzed by alkaline phosphatase, it has been shown that the choices of the values of three vital parameters are inter-related and restricted to certain nonlinear loci. These limits add to the limits imposed by thermodynamic requirements, and they are important in determining dynamic behavior.
Kinetics of Circulating Plasma Cell-Free DNA in Paediatric Classical Hodgkin Lymphoma
Primerano, Simona; Burnelli, Roberta; Carraro, Elisa; Pillon, Marta; Elia, Caterina; Farruggia, Piero; Sala, Alessandra; Vinti, Luciana; Buffardi, Salvatore; Basso, Giuseppe; Mascarin, Maurizio; Mussolin, Lara
2016-01-01
Levels of plasma cell-free DNA (cfDNA) of a large series of children with classical Hodgkin lymphoma (cHL) were evaluated and analyzed at diagnosis and during chemotherapy treatment in relation with clinical characteristics. CfDNA levels in cHL patients were significantly higher compared with controls (p=0.002). CfDNA at diagnosis was correlated with presence of B symptoms (p=0.027) and high erythrocyte sedimentation rate (p=0.049). We found that the increasing of plasma cfDNA after first chemotherapy cycle seems to be associated with a worse prognosis (p=0.049). Levels of plasma cfDNA might constitute an interesting non-invasive tool in cHL patients' management. PMID:26918050
Kinetics of Circulating Plasma Cell-Free DNA in Paediatric Classical Hodgkin Lymphoma.
Primerano, Simona; Burnelli, Roberta; Carraro, Elisa; Pillon, Marta; Elia, Caterina; Farruggia, Piero; Sala, Alessandra; Vinti, Luciana; Buffardi, Salvatore; Basso, Giuseppe; Mascarin, Maurizio; Mussolin, Lara
2016-01-01
Levels of plasma cell-free DNA (cfDNA) of a large series of children with classical Hodgkin lymphoma (cHL) were evaluated and analyzed at diagnosis and during chemotherapy treatment in relation with clinical characteristics. CfDNA levels in cHL patients were significantly higher compared with controls (p=0.002). CfDNA at diagnosis was correlated with presence of B symptoms (p=0.027) and high erythrocyte sedimentation rate (p=0.049). We found that the increasing of plasma cfDNA after first chemotherapy cycle seems to be associated with a worse prognosis (p=0.049). Levels of plasma cfDNA might constitute an interesting non-invasive tool in cHL patients' management. PMID:26918050
Mapping of the classical kinetic balance equations onto the Pauli equation
Pesci, Adriana I.; Goldstein, Raymond E.; Uys, Hermann
2005-01-01
Here we find a mapping onto the Pauli equation of the first two balance equations derived from the classical Boltzmann equation. The essence of this mapping, which we previously used to obtain the particular case of the Sturm-Liouville operator known as Schrödinger's equation, consists of applying a Fourier transform to the momentum coordinate of the distribution function. This procedure introduces a natural parameter η with units of angular momentum. The main difference between the two cases is the conditions imposed on the probability distribution function, a difference most clearly understood at the level of the hydrodynamic equations generated in the first steps of the mapping. The case leading to the Sturm-Liouville operator corresponds to an irrotational flow, while here the ansatz leading to the Pauli equation corresponds to a fluid with non-zero vorticity. In the context of fluid dynamics, the magnitude of the angular momentum associated with the vorticity is η/2. To perform the mapping we follow the standard technique common in hydrodynamic problems, namely writing the Lagrangian for the Euler equations with the corresponding constraints expressed in terms of the Clebsch variables.
Alkema, WBL; de Vries, E; Floris, R; Janssen, DB
2003-01-01
Penicillin acylase catalyses the hydrolysis and synthesis of semisynthetic beta-lactam antibiotics via formation of a covalent acyl-enzyme intermediate. The kinetic and mechanistic aspects of these reactions were studied. Stopped-flow experiments with the penicillin and ampicillin analogues 2-nitro-
Chaudhury, Srabanti; Cao, Jianshu; Sinitsyn, Nikolai A
2013-01-17
We consider a generic stochastic model of ion transport through a single channel with arbitrary internal structure and kinetic rates of transitions between internal states. This model is also applicable to describe kinetics of a class of enzymes in which turnover events correspond to conversion of substrate into product by a single enzyme molecule. We show that measurement of statistics of single molecule transition time through the channel contains only restricted information about internal structure of the channel. In particular, the most accessible flux fluctuation characteristics, such as the Poisson indicator (P) and the Fano factor (F) as function of solute concentration, depend only on three parameters in addition to the parameters of the Michaelis-Menten curve that characterizes average current through the channel. Nevertheless, measurement of Poisson indicator or Fano factor for such renewal processes can discriminate reactions with multiple intermediate steps as well as provide valuable information about the internal kinetic rates. PMID:23198705
Enzyme Kinetics: A critique of the quasi-steady-state approximation
Bhattacharyya, Kamal
2013-01-01
The standard two-step model of homogeneous-catalyzed reactions had been theoretically analyzed at various levels of approximations from time to time. The primary aim was to check the validity of the quasi-steady-state approximation, and hence emergence of the Michaelis-Menten kinetics, with various substrate-enzyme ratios. But, conclusions vary. We solve here the desired set of coupled nonlinear differential equations by invoking a new set of dimensionless variables. Approximate solutions are obtained via the power-series method aided by Pade approximants. The scheme works very successfully in furnishing the initial dynamics at least up to the region where existence of any steady state can be checked. A few conditions for its validity are put forward and tested against the findings. Temporal profiles of the substrate and the product are analyzed in addition to that of the complex to gain further insights into legitimacy of the above approximation. Some recent observations like the reactant stationary approxim...
Energy Technology Data Exchange (ETDEWEB)
Toshihiro, Toshihiro [Fukushima National College of Technology, Fukushima (Japan). Department of Chemistry; Ajiri, Tadafumi; Arai, Kunio [Tohoku University, Miyagi (Japan). Department of Chemical Engineering
1999-03-10
This paper presents a method to evaluate kinetics for an immobilized enzyme with nonuniform activity distribution. Kinetic studies were conducted for esterification of caproic acid with methanol by immobilized lipase (Lysozyme) at 40 degree C. Effective diffusivity (D{sub e}) and Michaelis constant (K{sub m}) were determined independently and then the activity distribution was determined by analysing the relationship between the reaction rate and the substrate concentration. first D{sub e} was determined by step response experiments that were conducted in a packed-bed column using carbonic acid as a tracer and hexane as a solvent. In the analysis of the response curves, intraparticle mass transfer, D{sub e}, and adsorption of tracer in the particles was taken into account. The adsorption constant, K{sub a}, was evaluated by adsorption experiments. Then, K{sub m} was determined by analysing the relationship between the reaction rate and the substrate concentration under chemical reaction control. The final step was the evaluation of active enzyme distribution in the particles using D{sub e}, K{sub m} and K{sub a}. The enzyme activity was observed only in the vicinity of the surface of the support. By using these evaluated constants and considering the nonuniform activity distribution of the immobilized enzyme, kinetics of the raction could by successfully described over a wide range of concentrations and particle sizes. (author)
Lee, H.; Angus, R. H.; Storer, A. C.; Carey, P. R.
1989-12-01
Resonance Raman (RR) spectroscopy is used to probe the structure of the substrate in the substrate-enzyme complex N-pentafluorobenzoyl) glycine (dithioacyl) papain (C 6F 5C(=O) NHCH 2C(=S)S-papain). This system was chosen since the high electron withdrawing capacity of the C 6F 5 group markedly affects electron density of the -NH- moiety which, in turn, is known to change catalytic activity. The RR spectrum of the enzyme-substrate complex is interpreted by reference to the model compound N-(pentafluorobenzoyl) glycine ethyl dithioester (C 6F 5(CO))NHCH 2C(=S)SC 2H 5. The RR spectra of this compound in aqueous or organic solvents can be understood in terms of the known conformational states of N-acylglycine dithioesters. Comparison of model with enzyme-substrate RR spectra shows that the substrate is binding in the active site in a conformer known as conformer B characterized by a small-NHCH 2CS(thiol) torsional angle and close N-to-S (thiol) contact. Kinetic rate-structure correlations are developed involving k3, the rate constant for deacylation, and the strength of the N-to-S (thiol) interaction. N-(Pentafluorobenzoyl) glycine dithioacyl papain fits the rate-structure correlation whereas the corresponding pentafluorobenzoyl glycine thiol intermediate does not. It is proposed that the difference in the size of the CS compared to the CO group brings about a small change in the dithioacyl papain compared to the thiolacyl papain conformation such that enzyme-substrate contacts involving ortho and meta F atoms in the thiol acyl enzyme case are weakened or removed in the case of the dithioacyl papain.
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Karatzos Sergios
2012-08-01
Full Text Available Abstract Background Effective pretreatment is key to achieving high enzymatic saccharification efficiency in processing lignocellulosic biomass to fermentable sugars, biofuels and value-added products. Ionic liquids (ILs, still relatively new class of solvents, are attractive for biomass pretreatment because some demonstrate the rare ability to dissolve all components of lignocellulosic biomass including highly ordered (crystalline cellulose. In the present study, three ILs, 1-butyl-3-methylimidazolium chloride ([C4mim]Cl, 1-ethyl-3-methylimidazolium chloride ([C2mim]Cl, 1-ethyl-3-methylimidazolium acetate ([C2mim]OAc are used to dissolve/pretreat and fractionate sugarcane bagasse. In these IL-based pretreatments the biomass is completely or partially dissolved in ILs at temperatures greater than 130°C and then precipitated by the addition of an antisolvent to the IL biomass mixture. For the first time mass balances of IL-based pretreatments are reported. Such mass balances, along with kinetics data, can be used in process modelling and design. Results Lignin removals of 10% mass of lignin in bagasse with [C4mim]Cl, 50% mass with [C2mim]Cl and 60% mass with [C2mim]OAc, are achieved by limiting the amount of water added as antisolvent to 0.5 water:IL mass ratio thus minimising lignin precipitation. Enzyme saccharification (24 h, 15FPU yields (% cellulose mass in starting bagasse from the recovered solids rank as: [C2mim]OAc(83% > >[C2mim]Cl(53% = [C4mim]Cl(53%. Composition of [C2mim]OAc-treated solids such as low lignin, low acetyl group content and preservation of arabinosyl groups are characteristic of aqueous alkali pretreatments while those of chloride IL-treated solids resemble aqueous acid pretreatments. All ILs are fully recovered after use (100% mass as determined by ion chromatography. Conclusions In all three ILs regulated addition of water as an antisolvent effected a polysaccharide enriched precipitate since some of the lignin
Blázquez, J.S.; Conde, C. F.; Conde, A.
2014-01-01
The classical theory of Johnson–Mehl–Avrami–Kolmogorov (JMAK) is widely used to describe the kinetics of crystallization even when the premises required for its application are not strictly fulfilled. In this paper we propose a procedure to obtain the JMAK parameters of the independent transformations that simultaneously occur during a crystallization process (e.g. leading to the formation of several crystalline phases). The predictions of the analysis have been used to describe the crystalli...
Estimating the turnover number in enzyme kinetic reactions using transient and stationary state data
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Sibel Uludag-Demirer
2009-12-01
Full Text Available Substrate and product concentration data obtained by simulating enzyme-substrate reaction rate equations were used to test two proposed kinetic rate constant estimation techniques in this study. In the first technique, the turnover number, k3, was calculated using early transient time domain data, which are difficult to obtain experimentally. The technique used an iterative approach to calculate k3 with a pair of data and the value of k3 could be retrieved with 35% error. The second technique calculated k3 using stationary domain data and the value of k3 could be retrieved with less than 5% error. This second technique also offered internal consistency in the calculation of k3 by calculating k3 both from the intercept and the slope of the linear plot derived in this study. A series of sensitivity analyses was conducted to understand the robustness of the second technique in estimating k3 from simulated data to the changes in the reaction rate constants (k1, k2, and k3 and the initial concentration of enzyme used for simulation. It was found that the second technique generally worked well in the estimation of k3 except for the simulated data for fast substrate conversions such as in the large k3 and [E]0 cases . This latter method, thus, shows promise for the use of late time experimental substrate/product concentration data to obtain k3. Exclusively using late time data avoids the need for difficult and expensive rapid early time measurement techniques for estimating k3. Once a reasonable estimate for k3 is obtained, the initial enzyme value can easily be determined from the maximum velocity constant established from fitting the Michaelis-Menten or Briggs-Haldane equations to substrate and product stationary state domain (late time data. While the first technique can estimate k3 with only one point in the transient domain, it is suggested that the second method generally be favored since it only requires late-time stationary domain data and
Romero, J J; Zarate, M A; Queiroz, O C M; Han, J H; Shin, J H; Staples, C R; Brown, W F; Adesogan, A T
2013-09-01
The objectives were to compare the effect of exogenous fibrolytic enzyme (Biocellulase A20) or anhydrous ammonia (4% DM) treatment on the nutritive value, voluntary intake, and digestion kinetics of bermudagrass (Cynodon dactylon cultivar Coastal) hay harvested after 2 maturities (5- and 13-wk regrowths). Six individually housed, ruminally cannulated Brangus steers (BW 325 ± 10 kg) were used in an experiment with a 6 × 6 Latin square design with a 3 (additives) × 2 (maturities) factorial arrangement of treatments. Each period consisted of 14 d of adaptation and 7, 4, 1, 1, and 4 d for measuring in vivo digestibility, in situ degradability, no measurements, rumen liquid fermentation and passage indices, and rate of solid passage, respectively. Steers were fed hay for ad libitum intake and supplemented with sugarcane molasses and distillers grain (supplement total of 2.88 kg DM/d). Enzyme did not affect the nutritional composition of hay but ammonia treatment decreased hay NDF, hemicellulose, and ADL concentrations and increased the CP concentration particularly for the mature lignified 13-wk hay. The enzyme increased NDF and hemicellulose digestibility of the 5-wk hay but decreased those of the 13-wk hay. Ammoniation decreased intake of hay but increased digestibility of DM, OM, NDF, hemicellulose, ADF, and cellulose and increased the ruminal in situ soluble and potentially digestible fractions and the rate of DM degradation of the 13-wk hay. Also, ammoniation increased the concentrations of ruminal NH3, total VFA, acetate, and butyrate but enzyme treatment did not. Neither enzyme addition nor ammoniation affected rate of liquid and solid passage. In conclusion, ammoniation decreased the concentration of most fiber fractions, decreased the intake of hays, and increased their CP concentration, in vivo digestibility, and in situ degradability at both maturities whereas enzyme application increased fiber digestibility of the 5-wk hay but decreased it in the case of
Purification of SUMO conjugating enzymes and kinetic analysis of substrate conjugation
Yunus, Ali A.; Lima, Christopher D.
2009-01-01
SUMO conjugation to protein substrates requires the concerted action of a dedicated E2 ubiquitin conjugation enzyme (Ubc9) and associated E3 ligases. Although Ubc9 can directly recognize and modify substrate lysine residues that occur within a consensus site for SUMO modification, E3 ligases can redirect specificity and enhance conjugation rates during SUMO conjugation in vitro and in vivo. In this chapter, we will describe methods utilized to purify SUMO conjugating enzymes and model substra...
C.M. Van Gelder (Carin)
2013-01-01
textabstract__Abstract__ The introduction of enzyme-replacement therapy (ERT) in 2006 has dramatically increased the interest in Pompe disease. In the three decades following the discovery of acid a-glucosidase deficiency as cause of the disease by H.G. Hers in 1963 only very few research laborator
On the dynamics of immobilized enzyme kinetics in a microreactor: A study of AP-catalyzed reactions
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Pratap R Patnaik
2011-11-01
Full Text Available Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin-top:0in; mso-para-margin-right:0in; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0in; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} The kinetics of immobilized enzyme-catalyzed reactions in microreactors differ from those in macro-scale reactors. Recognizing this, a recent study (Patnaik 2011 based on a new interpretation of the kinetics of AP-catalyzed reactions showed that dynamic behavior is feasible only certain loci relating key kinetic parameters. That work has been extended here, and the kinetic parameters have now been related to bulk phase concentrations, thereby providing a link with the reaction system per se. It has also been shown that under certain conditions the reaction may become self-quenching but either monotonically or as damped oscillations. These two studies thus establish the importance of understanding kinetic dynamics in microreactors and in selecting feasible operating conditions.
Kinetics of enzyme-catalyzed cross-linking of feruloylated arabinan from sugar beet
DEFF Research Database (Denmark)
Abang Zaidel, Dayang Norulfairuz; Arnous, Anis; Holck, Jesper;
2011-01-01
the kinetics of HRP catalyzed cross-linking of FA esterified to α-(1,5)-linked arabinans are affected by the length of the arabinan chains carrying the feruloyl substitutions. The kinetics of the HRP-catalyzed cross-linking of four sets of arabinan samples from sugar beet pulp, having different...... molecular weights and hence different degrees of polymerization, were monitored by the disappearance of FA absorbance at 316 nm. MALDI-TOF/TOF-MS analysis confirmed that the sugar beet arabinans were feruloyl-substituted, and HPLC analysis verified that the amounts of diFAs increased when FA levels...
Kinetic studies of Thermobifida fusca Cel9A active site mutant enzymes.
Zhou, Weilin; Irwin, Diana C; Escovar-Kousen, Jose; Wilson, David B
2004-08-01
Thermobifida fusca Cel9A-90, an unusual family 9 enzyme, is a processive endoglucanase containing a catalytic domain closely linked to a family 3c cellulose binding domain (Cel9A-68) followed by a fibronectin III-like domain and a family 2 cellulose binding domain. To study its catalytic mechanism, 12 mutant genes with changes in five conserved residues of Cel9A-68 were constructed, cloned, and expressed in Escherichia coli. The purified mutant enzymes were assayed for their activities on (carboxymethyl)cellulose, phosphoric acid-swollen cellulose, bacterial microcrystalline cellulose, and 2,4-dinitrophenyl beta-D-cellobioside. They were also tested for ligand binding, enzyme processivity, and thermostability. The results clearly show that E424 functions as the catalytic acid, D55 and D58 are both required for catalytic base activity, and Y206 plays an important role in binding, catalysis, and processivity, while Y318 plays an important role in binding of crystalline cellulose substrates and is required for processivity. Several amino acids located in a loop at the end of the catalytic cleft (T245-L251) were deleted from Cel9A-68, and this enzyme showed slightly improved filter paper activity and binding to BMCC but otherwise behaved like the wild-type enzyme. The FnIII-like domain was deleted from Cel9A-90, reducing BMCC activity to 43% of the wild type. PMID:15274620
Deacylation Mechanism and Kinetics of Acyl-Enzyme Complex of Class C β-Lactamase and Cephalothin.
Tripathi, Ravi; Nair, Nisanth N
2016-03-17
Understanding the molecular details of antibiotic resistance by the bacterial enzymes β-lactamases is vital for the development of novel antibiotics and inhibitors. In this spirit, the detailed mechanism of deacylation of the acyl-enzyme complex formed by cephalothin and class C β-lactamase is investigated here using hybrid quantum-mechanical/molecular-mechanical molecular dynamics methods. The roles of various active-site residues and substrate in the deacylation reaction are elucidated. We identify the base that activates the hydrolyzing water molecule and the residue that protonates the catalytic serine (Ser64). Conformational changes in the active sites and proton transfers that potentiate the efficiency of the deacylation reaction are presented. We have also characterized the oxyanion holes and other H-bonding interactions that stabilize the reaction intermediates. Together with the kinetic and mechanistic details of the acylation reaction, we analyze the complete mechanism and the overall kinetics of the drug hydrolysis. Finally, the apparent rate-determining step in the drug hydrolysis is scrutinized. PMID:26918257
Giardina, Bennett J; Chiang, Hui-Ling
2013-01-01
In Saccharomyces cerevisia, the key gluconeogenic enzyme fructose-1,6-bisphosphatase is secreted into the periplasm during prolonged glucose starvation and is internalized into Vid/endosomes following glucose re-feeding. Fructose-1,6-bisphosphatase does not contain signal sequences required for the classical secretory and endocytic pathways. Hence, the secretion and internalization are mediated via the non-classical pathways.
Fleischmann, Peter; Studer, Kerstin; Winterhalter, Peter
2002-03-13
For the first time, a cytosolic carotenoid cleavage enzyme isolated from quince (Cydonia oblonga) fruit is described. The enzyme was partially purified by using centrifugation, acetone precipitation, ultrafiltration (300 kD, 50 kD), isoelectric focusing (pH 3-10), and sodium dodecyl sulfate polyacrylamide gel electrophoresis (7.5%). In this way, an enzymatically active protein fraction was obtained that contained three similar proteins, all exhibiting molecular weights in the range of 20 kD. Using beta-carotene as substrate, the enzyme activity was detected spectrophotometrically at a wavelength of 505 nm. The time constant of the reaction was 8.2 min, the Michaelis constant (K(m)) was 11.0 micromol x L(-1), and the maximum velocity (v(max)) was 0.083 micromol x L(-1) x min(-1) x mg(protein)(-1). The optimum temperature was above 50 degrees C. PMID:11879057
Hardee, John R.; Delgado, Bryan; Jones, Wray
2011-01-01
The kinetic parameters for the conversion of alpha-D-glucose to beta-D-glucose were measured using a blood glucometer. The reaction order, rate constant, and Arrhenius activation energy are reported for the noncatalyzed reaction and turnover number and Michaelis constant are reported for the reaction catalyzed by porcine kidney mutarotase. The…
Mazur, Anna; Lichti, Cheryl F.; Prather, Paul L.; Zielinska, Agnieszka K.; Bratton, Stacie M.; Gallus-Zawada, Anna; Finel, Moshe; Miller, Grover P.; Radomińska-Pandya, Anna; Moran, Jeffery H.
2009-01-01
Tetrahydrocannabinol (Δ9-THC), the primary psychoactive ingredient in marijuana, is subject to cytochrome P450 oxidation and subsequent UDP-glucuronosyltransferase (UGT)-dependent glucuronidation. Many studies have shown that CYP2C9 and CYP3A4 are the primary enzymes responsible for these cytochrome P450-dependent oxidations, but little work has been done to characterize phase II metabolic pathways. In this study, we test the hypothesis that there are specific human UG...
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Harvey F. Fisher
2013-07-01
Full Text Available Much of our understanding of the mechanisms of enzyme-catalyzed reactions is based on steady-state kinetic studies. Experimentally, this approach depends solely on the measurement of rates of free product appearance (d[P]/dt, a mechanistically and mathematically complex entity. Despite the ambiguity of this observed parameter, the method’s success is due in part to the elaborate rigorously derived algebraic theory on which it is based. Transient-state kinetics, on the other hand, despite its ability to observe the formation of intermediate steps in real time, has contributed relatively little to the subject due in, some measure, to the lack of such a solid mathematical basis. Here we discuss the current state of existing transient-state theory and the difficulties in its realistic application to experimental data. We describe a basic analytic theory of transient-state kinetic isotope effects in the form of three novel fundamental rules. These rules are adequate to define an extended mechanism, locating the isotope-sensitive step and identifying missing steps from experimental data. We demonstrate the application of these rules to resolved component time courses of the phenylalanine dehydrogenase reaction, extending the previously known reaction by one new prehydride transfer step and two new post hydride transfer steps. We conclude with an assessment of future directions in this area.
International Nuclear Information System (INIS)
The rapid development of biogas production will result in increased use of biogas residues as organic fertilizers. However, control of microbial activity by organic fertilizers remains a challenge for modern land use, especially with respect to mitigating greenhouse effects and increasing C sequestration in soil. To address this issue, we compared CO2 emissions, microbial growth and extracellular enzyme activities in agricultural soil amended with biogas residues (BGR) versus maize straw (MST). Over a 21 day incubation period, 6.4% of organic C added was mineralised and evolved as CO2 with BGR and 30% with MST. As shown by the substrate-induced growth respiration approach, BGR and MST significantly decreased the specific microbial growth rate (μ) and increased the microbial biomass C in the soil, indicating a clear shift in the microbial community to slower-growing microorganisms. Because of the reduced availability of C associated with the less labile C and more lignin in biogas residues, observed μ values and microbial biomass C were lower after BGR application than after MST application. After 21 days incubation, BGR had no effect on the activity of three extracellular enzymes: β-glucosidase and cellobiohydrolase, both of which are involved in cellulose decomposition; and xylanase, which is involved in hemicellulose decomposition. In contrast, MST significantly increased the activity of these three enzymes. The application of biogas residues in short-term experiment leads to a 34% increase in soil C content and slower C turnover as compared to common maize residues. -- Highlights: ► Biogas residues (BGR) applied to soil as organic fertilizers were decomposed 2.5 times slower as compared to maize straw. ► BGR application stimulated mainly slow-growing soil microorganisms. ► In contrast to maize straw the BGR did not increase the activity of cellulose-degrading soil enzymes. ► BGR leads to slower C turnover and a 34% increase in C sequestration versus
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Roberta Besio
Full Text Available Prolidase is the only human enzyme responsible for the digestion of iminodipeptides containing proline or hydroxyproline at their C-terminal end, being a key player in extracellular matrix remodeling. Prolidase deficiency (PD is an intractable loss of function disease, characterized by mutations in the prolidase gene. The exact causes of activity impairment in mutant prolidase are still unknown. We generated three recombinant prolidase forms, hRecProl-231delY, hRecProl-E412K and hRecProl-G448R, reproducing three mutations identified in homozygous PD patients. The enzymes showed very low catalytic efficiency, thermal instability and changes in protein conformation. No variation of Mn(II cofactor affinity was detected for hRecProl-E412K; a compromised ability to bind the cofactor was found in hRecProl-231delY and Mn(II was totally absent in hRecProl-G448R. Furthermore, local structure perturbations for all three mutants were predicted by in silico analysis. Our biochemical investigation of the three causative alleles identified in perturbed folding/instability, and in consequent partial prolidase degradation, the main reasons for enzyme inactivity. Based on the above considerations we were able to rescue part of the prolidase activity in patients' fibroblasts through the induction of Heath Shock Proteins expression, hinting at new promising avenues for PD treatment.
Energy Technology Data Exchange (ETDEWEB)
Gong, C.S.; Chang, M.
1981-02-01
There are three basic enzymes (e.g., endoglucanase (C/sub x/), exoglucanase (C/sub 1/) and cellobiase) comprising the majority of extracellular cellulase enzymes produced by the cellulolytic mycelial fungi, Trichoderma reesei, and other cellulolytic microorganisms. The enzymes exhibited different mode of actions in respect to the hydrolysis of cellulose and cellulose derived oligosaccharides. In combination, these enzymes complimented each other to hydrolyze cellulose to its basic constituent, glucose. The kinetics of cellobiase were developed on the basis of applying the pseudo-steady state assumption to hydrolyze cellobiose to glucose. The results indicated that cellobiase was subjected to end-product inhibition by glucose. The kinetic modeling of exoglucanase (C/sub 1/) with respect to cellodextrins was studied. Both glucose and cellobiose were found to be inhibitors of this enzyme with cellobiose being a stronger inhibitor than glucose. Similarly, endoglucanase (C/sub x/) is subject to end-product inhibition by glucose. Crystallinity of the cellulose affects the rate of hydrolysis by cellulases. Hence, the changes in crystallinity of cellulose in relation to chemical pretreatment and enzyme hydrolysis was compared. The study of cellulase biosynthesis resulted in the conclusion that exo- and endo-glucanases are co-induced while cellobiase is synthesized independent of the other two enzymes. The multiplicity of cellulase enzymes are the end results of post-translational modification during and/or after the secretion of enzymes into growth environment.
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Mohammad Shakil
2015-01-01
Full Text Available Many problems of enzyme kinetics can be described by a function known as the Michaelis-Menten (M-M function. In this paper, motivated by the importance of Michaelis-Menten function in biochemistry and other biological phenomena, we have introduced a new class of generalized Pearson distribution arising from Michaelis-Menten function. Various properties of this distribution are derived, for example, its probability density function (pdf, cumulative distribution function (cdf, moment, entropy function, and relationships with some well-known continuous probability distributions. The graphs of the pdf and cdf of our new distribution are provided for some selected values of the parameters. It is observed that our new distribution is positively skewed and unimodal. We hope that the findings of this paper will be useful in many applied research problems. 2000 Mathematics Subject Classification: 60E05, 62E10, 62E15.
Weis, David D; Nardozzi, Jonathan D
2005-04-15
The rate of the alkaline phosphatase-catalyzed hydrolysis of 4-methylumbelliferone phosphate was measured in acoustically levitated droplets of aqueous tris (50 mM) at pH 8.5 at 22 +/- 2 degrees C and in supercooled solution at -6 +/- 2 degrees C. At 22 degrees C, the rate of product formation was in excellent agreement with the rate observed in bulk solution in a cuvette, indicating that the acoustic levitation process does not alter the enzyme activity. The rate of the reaction decreased 6-fold in supercooled solution at -6 +/- 2 degrees C. The acoustic levitator apparatus is described in detail. PMID:15828793
Mechanistic and Kinetic Analysis of the DcpS Scavenger Decapping Enzyme*
Liu, Shin-Wu; Rajagopal, Vaishnavi; Smita S Patel; Kiledjian, Megerditch
2008-01-01
Decapping is an important process in the control of eukaryotic mRNA degradation. The scavenger decapping enzyme DcpS functions to clear the cell of cap structure following decay of the RNA body by catalyzing the hydrolysis of m7GpppN to m7Gp and ppN. Structural analysis has revealed that DcpS is a dimeric protein with a domain-swapped amino terminus. The protein dimer contains two cap binding/hydrolysis sites and displays a symmetric structure with both binding sites i...
Single-enzyme kinetics with branched pathways: exact theory and series expansion
Garai, Ashok
2014-01-01
The progress of the successive rounds of catalytic conversion of substrates into product(s) by a single enzyme is characterized by the distribution of turnover times. Establishing the most general form of dependence of this distribution on the substrate concentration [S] is one of the fundamental challenges in single molecule enzymology. The distribution of the times of dwell of a molecular motor at the successive positions on its track is an analogous quantity. We derive approximate series expansions for the [ATP]-dependence of the first two moments of the dwell time distributions of motors that catalyze hydrolysis of ATP to draw input energy. Comparison between our results for motors with branched pathways and the corresponding expressions reported earlier for linear enzymatic pathways provides deep insight into the effects of the branches. Such insight is likely to help in discovering the most general form of [S]-dependence of these fundamental distributions.
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María Francisca eAguayo
2015-02-01
Full Text Available Polyols are enzymatically-produced plant compounds which can act as compatible solutes during periods of abiotic stress. NAD+-dependent SORBITOL DEHYDROGENASE (SDH, E.C. 1.1.1.14 from Arabidopsis thaliana L. (AtSDH is capable of oxidizing several polyols including sorbitol, ribitol and xylitol. In the present study, enzymatic assays using recombinant AtSDH demonstrated a higher specificity constant for xylitol compared to sorbitol and ribitol, all of which are C2 (S and C4 (R polyols. Enzyme activity was reduced by preincubation with ethylenediaminetetraacetic acid (EDTA, indicating a requirement for zinc ions. In humans, it has been proposed that sorbitol becomes part of a pentahedric coordination sphere of the catalytic zinc during the reaction mechanism. In order to determine the validity of this pentahedric coordination model in a plant SDH, homology modeling and Molecular Dynamics simulations of AtSDH ternary complexes with the three polyols were performed using crystal structures of human and Bemisia argentifolii (Genn. (Hemiptera: Aleyrodidae SDHs as scaffolds. The results indicate that the differences in interaction with structural water molecules correlate very well with the observed enzymatic parameters, validate the proposed pentahedric coordination of the catalytic zinc ion in a plant SDH, and provide an explanation for why AtSDH shows a preference for polyols with a chirality of C2 (S and C4 (R.
Field, Christopher Ryan
2009-01-01
Developments in analytical chemistry were made using acoustically levitated small volumes of liquid to study enzyme reaction kinetics and by detecting volatile organic compounds in the gas phase using single-walled carbon nanotubes. Experience gained in engineering, electronics, automation, and software development from the design and…
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…
International Nuclear Information System (INIS)
We have investigated the effect of a range of 2-nitroimidazoles on CCNU metabolism, using an in vitro mouse liver microsomal preparation. CCNU is hydroxylated to at least 5 monohydroxylated metabolites. For the major metabolite, cis-4-hydroxy CCNU, values of Km and Vmax were 0.026 mM and 1.92 nmol/min/mg protein, respectively. MISO and other 2-nitroimidazoles inhibited the hydroxylation of CCNU in a dose-dependent manner and their potencies as inhibitors were governed by their lipophilicities. In order of increasing potency I50 values were 15.5, 6.4, 5.8, 1.4, 0.4, and 0.37 mM for SR 2508, Ro 03-8799, MISO, Ro 07-1902, Ro 07-1127, and BENZO, respectively. Chemosensitization potency correlated well with the extent of inhibition at achieved plasma concentrations in mice, suggesting a causal relationship between enzyme inhibition and chemosensitization. All the nitroimidazoles exhibited type II optical difference spectra with phenobarbitone-induced mouse liver microsomes. However, with increasing lipophilicity of the nitroimidazole both the wavelength at maximum absorbance (lambda max) and the isosbestic point of the type II spectrum were shifted to longer wavelengths, suggesting that a type I binding component may become more significant. Our previous work has shown that changes in CCNU pharmacokinetics contribute to chemosensitization by nitroimidazoles in mice, and that altered pharmacokinetics also occur in man. The present results provide strong evidence that the mechanism involves binding to liver microsomal cytochrome P-450, leading to inhibition of CCNU metabolism
New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies.
Liu, Yao; Rodrigues, João P G L M; Bonvin, Alexandre M J J; Zaal, Esther A; Berkers, Celia R; Heger, Michal; Gawarecka, Katarzyna; Swiezewska, Ewa; Breukink, Eefjan; Egmond, Maarten R
2016-07-15
Phospho-MurNAc-pentapeptide translocase (MraY) catalyzes the synthesis of Lipid I, a bacterial peptidoglycan precursor. As such, MraY is essential for bacterial survival and therefore is an ideal target for developing novel antibiotics. However, the understanding of its catalytic mechanism, despite the recently determined crystal structure, remains limited. In the present study, the kinetic properties of Bacillus subtilis MraY (BsMraY) were investigated by fluorescence enhancement using dansylated UDP-MurNAc-pentapeptide and heptaprenyl phosphate (C35-P, short-chain homolog of undecaprenyl phosphate, the endogenous substrate of MraY) as second substrate. Varying the concentrations of both of these substrates and fitting the kinetics data to two-substrate models showed that the concomitant binding of both UDP-MurNAc-pentapeptide-DNS and C35-P to the enzyme is required before the release of the two products, Lipid I and UMP. We built a model of BsMraY and performed docking studies with the substrate C35-P to further deepen our understanding of how MraY accommodates this lipid substrate. Based on these modeling studies, a novel catalytic role was put forward for a fully conserved histidine residue in MraY (His-289 in BsMraY), which has been experimentally confirmed to be essential for MraY activity. Using the current model of BsMraY, we propose that a small conformational change is necessary to relocate the His-289 residue, such that the translocase reaction can proceed via a nucleophilic attack of the phosphate moiety of C35-P on bound UDP-MurNAc-pentapeptide. PMID:27226570
Nielsen, S L; Sørensen, I; Andersen, H K
1988-01-01
Antibody-capture enzyme-linked immunosorbent assay (ELISA) using enzyme-labeled cytomegalovirus (CMV) nuclear antigen is a reliable and easily performed test suitable for routine use. As the serologic response to CMV infection may, however, vary considerably among patients, we have studied the kinetics of CMV-specific immunoglobulin M (IgM), IgE, IgA, and IgG antibodies in 352 sera from 61 patients by using antibody-capture ELISA and complement fixation (CF) tests. In a CMV mononucleosis grou...
DEFF Research Database (Denmark)
Bieniasz, Leslaw K.; Østerby, Ole; Britz, Dieter
1995-01-01
We extend the analysis of the stepwise numerical stability of the classic explicit, fully implicit and Crank-Nicolson finite difference algorithms for electrochemical kinetic simulations, to the multipoint gradient approximations at the electrode. The discussion is based on the matrix method of...
DEFF Research Database (Denmark)
Uttenthal, Åse; Storgaard, Torben; Oleksiewicz, M.B.;
2003-01-01
We performed experimental infection in 10-week-old pigs with the Paderborn isolate of classical swine fever virus (CSFV). Despite being epidemiologically linked to the major CSFV outbreak in The Netherlands in 1997, the in vivo replication kinetics of this isolate have to our knowledge not been...
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Xiaolian Fan
Full Text Available Heparin acetyl-CoA:alpha-glucosaminide N-acetyltransferase (N-acetyltransferase, EC 2.3.1.78 is an integral lysosomal membrane protein containing 11 transmembrane domains, encoded by the HGSNAT gene. Deficiencies of N-acetyltransferase lead to mucopolysaccharidosis IIIC. We demonstrate that contrary to a previous report, the N-acetyltransferase signal peptide is co-translationally cleaved and that this event is required for its intracellular transport to the lysosome. While we confirm that the N-acetyltransferase precursor polypeptide is processed in the lysosome into a small amino-terminal alpha- and a larger ß- chain, we further characterize this event by identifying the mature amino-terminus of each chain. We also demonstrate this processing step(s is not, as previously reported, needed to produce a functional transferase, i.e., the precursor is active. We next optimize the biochemical assay procedure so that it remains linear as N-acetyltransferase is purified or protein-extracts containing N-acetyltransferase are diluted, by the inclusion of negatively charged lipids. We then use this assay to demonstrate that the purified single N-acetyltransferase protein is both necessary and sufficient to express transferase activity, and that N-acetyltransferase functions as a monomer. Finally, the kinetic mechanism of action of purified N-acetyltransferase was evaluated and found to be a random sequential mechanism involving the formation of a ternary complex with its two substrates; i.e., N-acetyltransferase does not operate through a ping-pong mechanism as previously reported. We confirm this conclusion by demonstrating experimentally that no acetylated enzyme intermediate is formed during the reaction.
International Nuclear Information System (INIS)
We have measured the temperature-dependent kinetics for the reactions of OH+ with H2 and D2 using a selected ion flow tube apparatus. Reaction occurs via atom abstraction to result in H2O+/HDO+ + H/D. Room temperature rate coefficients are in agreement with prior measurements and resulting temperature dependences are T0.11 for the hydrogen and T0.25 for the deuterated reactions. This work is prompted in part by recent theoretical work that mapped a full-dimensional global potential energy surface of H3O+ for the OH+ + H2 → H + H2O+ reaction [A. Li and H. Guo, J. Phys. Chem. A 118, 11168 (2014)], and reported results of quasi-classical trajectory calculations, which are extended to a wider temperature range and initial rotational state specification here. Our experimental results are in excellent agreement with these calculations which accurately predict the isotope effect in addition to an enhancement of the reaction rate constant due to the molecular rotation of OH+. The title reaction is of high importance to astrophysical models, and the temperature dependence of the rate coefficients determined here should now allow for better understanding of this reaction at temperatures more relevant to the interstellar medium
Knight, Kirsty; Scrutton, Nigel S
2002-01-01
The reduction by NADPH of the FAD and FMN redox centres in the isolated flavin reductase domain of calmodulin-bound rat neuronal nitric oxide synthase (nNOS) has been studied by anaerobic stopped-flow spectroscopy using absorption and fluorescence detection. We show by global analysis of time-dependent photodiode array spectra, single wavelength absorption and NADPH fluorescence studies, that at least four resolvable steps are observed in stopped-flow studies with NADPH and that flavin reduction is reversible. The first reductive step represents the rapid formation of an equilibrium between an NADPH-enzyme charge-transfer species and two-electron-reduced enzyme bound to NADP(+). The second and third steps represent further reduction of the enzyme flavins and NADP(+) release. The fourth step is attributed to the slow accumulation of an enzyme species that is inferred not to be relevant catalytically in steady-state reactions. Stopped-flow flavin fluorescence studies indicate the presence of slow kinetic phases, the timescales of which correspond to the slow phase observed in absorption and NADPH fluorescence transients. By analogy with stopped-flow studies of cytochrome P450 reductase, we attribute these slow fluorescence and absorption changes to enzyme disproportionation and/or conformational change. Unlike for the functionally related cytochrome P450 reductase, transfer of the first hydride equivalent from NADPH to nNOS reductase does not generate the flavin di-semiquinoid state. This indicates that internal electron transfer is relatively slow and is probably gated by NADP(+) release. Release of calmodulin from the nNOS reductase does not affect the kinetics of inter-flavin electron transfer under stopped-flow conditions, although the observed rate of formation of the equilibrium between the NADPH-oxidized enzyme charge-transfer species and two-electron-reduced enzyme bound to NADP(+) is modestly slower in calmodulin-depleted enzyme. Our studies indicate the
Cuccioloni, Massimiliano; Mozzicafreddo, Matteo; Ali, Ishtiaq; Bonfili, Laura; Cecarini, Valentina; Eleuteri, Anna Maria; Angeletti, Mauro
2016-12-15
Alpha-amylase/trypsin bi-functional inhibitors (ATIs) are non-gluten protein components of wheat and other cereals that can hypersensitise the human gastrointestinal tract, eventually causing enteropathies in predisposed individuals. These inhibitory proteins can act both directly by targeting specific pro-inflammatory receptors, and indirectly by impairing the activity of digestive enzymes, the latter event causing the accumulation of undigested peptides with potential immunogenic properties. Herein, according to a concerted approach based on in vitro and in silico methods we characterized kinetics, equilibrium parameters and modes of binding of the complexes formed between wheat ATI and two representative mammalian digestive enzymes, namely trypsin and alpha-amylase. Interestingly, we demonstrated ATI to target both enzymes with independent binding sites and with moderately high affinity. PMID:27451220
Narwal, Rajesh Kumari; Bhushan, Bharat; Pal, Ajay; Malhotra, Sarla Popli; Kumar, Satish; Saharan, Vinod
2016-10-01
Milk clotting enzyme (MCE) was immobilized in alginate-pectate interwoven gel with the yield of 73%. The encapsulated enzyme retained most of the protein load while soluble enzyme lost major proportion of activity after few hours. The immobilized enzyme showed high operational stability by retaining 40% activity even after 10 uses. The narrow optimal working pH of soluble enzyme changed to a broader range after encapsulation and a shift in optimum temperature from 45 to 50°C was also recorded for encapsulated enzyme. Studies on isokinetic temperature showed that immobilized enzyme is more thermo-stable at higher temperature. Immobilization, therefore, not only improved the catalytic properties and stability but also its suitability in food processes like cheese preparation with reduced cost and time. PMID:27174906
International Nuclear Information System (INIS)
In the last decade, many environmental organizations have devoted their efforts to identifying renewable biosystems, which could provide sustainable fuels and thus enhance energy security. Amidst the myriad of possibilities, some biofuels make use of different types of waste biomasses, and enzymes are often employed to hydrolyze these biomasses and produce sugars that will be subsequently converted into ethanol. In this project, we aimed to bridge nanotechnology and biofuel production: here we report on the activity and structure of the enzyme amyloglucosidase (AMG), physically adsorbed or covalently immobilized onto single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs). In fact, carbon nanotubes (CNTs) present several properties that render them ideal support systems, without the diffusion limitations displayed by porous material and with the advantage of being further functionalizable at their surface. Chemical ligation was achieved both on oxidized nanotubes (via carbodiimide chemistry), as well as on amino-functionalized nanotubes (via periodate-oxidized AMG). Results showed that AMG retained a certain percentage of its specific activity for all enzyme-carbon nanotubes complexes prepared, with the physically adsorbed samples displaying better catalytic efficiency than the covalently immobilized samples. Analysis of the enzyme's structure through circular dichroism (CD) spectroscopy revealed significant structural changes in all samples, the degree of change being consistent with the activity profiles. This study proves that AMG interacts differently with carbon nanotubes depending on the method employed. Due to the higher activity reported by the enzyme physically adsorbed onto CNTs, these samples demonstrated a vast potential for further development. At the same time, the possibility of inducing magnetic properties into CNTs offers the opportunity to easily separate them from the original solution. Hence, substances to which they
Energy Technology Data Exchange (ETDEWEB)
Cang-Rong, Jason Teng; Pastorin, Giorgia [Department of Pharmacy, National University of Singapore, 117543 (Singapore)], E-mail: jasonteng@nus.edu.sg, E-mail: phapg@nus.edu.sg
2009-06-24
In the last decade, many environmental organizations have devoted their efforts to identifying renewable biosystems, which could provide sustainable fuels and thus enhance energy security. Amidst the myriad of possibilities, some biofuels make use of different types of waste biomasses, and enzymes are often employed to hydrolyze these biomasses and produce sugars that will be subsequently converted into ethanol. In this project, we aimed to bridge nanotechnology and biofuel production: here we report on the activity and structure of the enzyme amyloglucosidase (AMG), physically adsorbed or covalently immobilized onto single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs). In fact, carbon nanotubes (CNTs) present several properties that render them ideal support systems, without the diffusion limitations displayed by porous material and with the advantage of being further functionalizable at their surface. Chemical ligation was achieved both on oxidized nanotubes (via carbodiimide chemistry), as well as on amino-functionalized nanotubes (via periodate-oxidized AMG). Results showed that AMG retained a certain percentage of its specific activity for all enzyme-carbon nanotubes complexes prepared, with the physically adsorbed samples displaying better catalytic efficiency than the covalently immobilized samples. Analysis of the enzyme's structure through circular dichroism (CD) spectroscopy revealed significant structural changes in all samples, the degree of change being consistent with the activity profiles. This study proves that AMG interacts differently with carbon nanotubes depending on the method employed. Due to the higher activity reported by the enzyme physically adsorbed onto CNTs, these samples demonstrated a vast potential for further development. At the same time, the possibility of inducing magnetic properties into CNTs offers the opportunity to easily separate them from the original solution. Hence, substances to which
Sener, N.; Kilic-Apar, D.; DEMIRHAN, E.; Ozbek, B.
2008-01-01
The present investigation describes the effects of the process quantities on enzymatic hydrolysis of milk lactose and enzyme stability. The lactose hydrolysis reactions were carried out in 250 mL of milk by using a commercial β-galactosidase produced from Kluyveromyces marxianus lactis. The residual lactose mass concentration (g L-1) and residual enzyme activity (%) against time were investigated vs. process variables such as temperature, impeller speed and enzyme concentration. Optimum condi...
Barlough, J E; Jacobson, R H; Downing, D R; Lynch, T J; Scott, F. W.
1987-01-01
The computer-assisted, kinetics-based enzyme-linked immunosorbent assay for coronavirus antibodies in cats was calibrated to the conventional indirect immunofluorescence assay by linear regression analysis and computerized interpolation (generation of "immunofluorescence assay-equivalent" titers). Procedures were developed for normalization and standardization of kinetics-based enzyme-linked immunosorbent assay results through incorporation of five different control sera of predetermined ("ex...
Study on the kinetics of saccharifying enzymes of Luzhou-flavor daqu%浓香型大曲糖化动力学研究
Institute of Scientific and Technical Information of China (English)
任飞; 张晓宇
2013-01-01
In order to study on the kinetics of saccharifying enzymes of Luzhou-flavor Daqu, using the enzymes of 5% Daqu hydrolyzed soluble starch, at pH 4. 6, 30℃ , an Michaelis-Menten equation was deduced. The optimum pH value for the catalysis of saccharifying enzymes of Luzhou-flavor Daqu was 6. 0. Studying the catalytic reaction rate under different temperatures, the calculation results showed that the activation energy of the enzyme catalytic reaction was 40. 966 kJ/mol. The kinetics of saccharifying enzymes of Luzhou-fla-vor Daqu was similar to a single enzyme, During the production of Luzhou-flavor liquor, it will contribute to manage the saccharification and fermentation process simultaneously by controlling the conditions of pits input into the cellar, such as the concentration of starch and starter, initial acidity and temperature.%为研究浓香型大曲的糖化动力学,用5％的大曲浸出液水解可溶性淀粉,在pH4.6、30℃的条件下,用菲林试剂法测定还原糖的含量,得出米氏方程；浓香型大曲糖化反应的最适pH值为6.0；在不同温度下测定糖化反应速率,计算得到活化能E为40.966 kJ/mol.试验证明,浓香型大曲糖化酶类的糖化反应动力学与单一酶相似.通过控制淀粉浓度(投粮量)、用曲量、入窖酸度和温度可以使浓香型大曲酒的糖化、发酵过程协调进行.
The kinetic characteristics of two Rhizopus oryzae exo-polygalacturonases acting on galacturonic acid oligomers (GalpA) were determined using isothermal titration calorimetry (ITC). RPG15 hydrolyzing (GalpA)2 demonstrated a Km of 55 uM and kcat of 10.3 s^-1^ while RPG16 was shown to have greater af...
Energy Technology Data Exchange (ETDEWEB)
Ahmad, Mustaq, E-mail: mushtaq213@yahoo.com [University of Science and Technology, Bannu, (Pakistan). Department of Biotechnology; Weber, Andrea D.; Zanon, Graciane; Tavares, Luciana de C.; Ilha, Vinicius; Dalcol, Ionara I.; Morel, Ademir F., E-mail: ademirfariasm@gmail.com [Universidade Federal de Santa Maria, RS (Brazil). Dept. de Quimica
2014-01-15
The in vitro activity of chelerythrine and lupeol, two metabolites isolated from Zanthoxylum rhoifolium were studied against the venom of the snake Bungarus sindanus (Elapidae). The venom, which is highly toxic to humans, consists mainly by the enzyme acetylcholinesterase (AChE). Both compounds showed activity against the venom, and the alkaloid chelerythrine presented higher activity than did triterpene lupeol. (author)
Bogaards, J.J.P.; Hissink, E.M.; Briggs, M.; Weaver, R.; Jochemsen, R.; Jackson, P.; Bertrand, M.; Bladeren, P. van
2000-01-01
A strategy is presented to predict interindividual variation in drug plasma levels in vivo by the use of physiologically based pharmacokinetic modeling and human in vitro metabolic parameters, obtained through the combined use of microsomes containing single cytochrome P450 enzymes and a human liver
International Nuclear Information System (INIS)
The in vitro activity of chelerythrine and lupeol, two metabolites isolated from Zanthoxylum rhoifolium were studied against the venom of the snake Bungarus sindanus (Elapidae). The venom, which is highly toxic to humans, consists mainly by the enzyme acetylcholinesterase (AChE). Both compounds showed activity against the venom, and the alkaloid chelerythrine presented higher activity than did triterpene lupeol. (author)
Jittam, Piyachat; Boonsiri, Patcharee; Promptmas, Chamras; Sriwattanarothai, Namkang; Archavarungson, Nattinee; Ruenwongsa, Pintip; Panijpan, Bhinyo
2009-01-01
Haloperoxidase enzymes are of interest for basic and applied bioscientists because of their increasing importance in pharmaceutical industry and environmental cleanups. In a guided inquiry-based laboratory experiment for life-science, agricultural science, and health science undergraduates, the bromoperoxidase from a red seaweed was used to…
Wu, Yue; Jiang, Ying; Jiao, Jiaguo; Liu, Manqiang; Hu, Feng; Griffiths, Bryan S; Li, Huixin
2014-02-01
Laccases play an important role in the degradation of soil phenol or phenol-like substance and can be potentially used in soil remediation through immobilization. Iron and aluminum minerals can adsorb extracellular enzymes in soil environment. In the present study, we investigated the adsorptive interaction of laccase, from the white-rot fungus Trametes versicolor, with soil iron and aluminum minerals and characterized the properties of the enzyme after adsorption to minerals. Results showed that both soil iron and aluminum minerals adsorbed great amount of laccase, independent of the mineral specific surface areas. Adsorbed laccases retained 26-64% of the activity of the free enzyme. Compared to the free laccase, all adsorbed laccases showed higher Km values and lower Vmax values, indicating a reduced enzyme-substrate affinity and a lower rate of substrate conversion in reactions catalyzed by the adsorbed laccase. Adsorbed laccases exhibited increased catalytic activities compared to the free laccase at low pH, implying the suitable application of iron and aluminum mineral-adsorbed T. versicolor laccase in soil bioremediation, especially in acid soils. In terms of the thermal profiles, adsorbed laccases showed decreased thermal stability and higher temperature sensitivity relative to the free laccase. Moreover, adsorption improved the resistance of laccase to proteolysis and extended the lifespan of laccase. Our results implied that adsorbed T. versicolor laccase on soil iron and aluminum minerals had promising potential in soil remediation. PMID:24225344
Energy Technology Data Exchange (ETDEWEB)
Costella, J.P.; McKellar, B.H.J.; Rawlinson, A.A.
1997-03-01
We review how antiparticles may be introduced in classical relativistic mechanics, and emphasize that many of their paradoxical properties can be more transparently understood in the classical than in the quantum domain. (authors). 13 refs., 1 tab.
Classical galactosaemia revisited
A.M. Bosch
2006-01-01
Classical galactosaemia (McKusick 230400) is an: autosomal recessive disorder of galactose metabolism, caused by a deficiency of the enzyme galactose-1-phosphate uridyltransferase (GALT; EC 2.7.712). Most patients present in the neonatal period, after ingestion of galactose, with jaundice, hepatospl
DEFF Research Database (Denmark)
Bieniasz, Leslaw K.; Østerby, Ole; Britz, Dieter
1995-01-01
The stepwise numerical stability of the classic explicit, fully implicit and Crank-Nicolson finite difference discretizations of example diffusional initial boundary value problems from electrochemical kinetics has been investigated using the matrix method of stability analysis. Special attention...... has been paid to the effect of the discretization of the mixed, linear boundary condition with time-dependent coefficients on stability, assuming the two-point forward-difference approximations for the gradient at the left boundary (electrode). Under accepted assumptions one obtains the usual...
PVA降解酶催化反应的动力学方程%Kinetic Equation on the Catalytic Reaction of PVA-Degradation Enzyme
Institute of Scientific and Technical Information of China (English)
郭雅妮; 段士然; 周明; 崔双科
2012-01-01
The properties and catalytic reaction kinetics of PVA-degradation enzyme from a newly selected mixed strain that is able to fully degrade PVA were studied for its actual use. Through the determination of changes in enzymatic activities in the course of the PVA degradation process, a catalysis kinetic equation was assumed first and then verified. The results indicated that the enzymatic activities would get lower along with the PVA degradation efficiency rising when PVA was not yet completely degraded. After the degradation was completed, the enzymatic activities tended to keep at certain level. As the PVA concentration increased, the enzymatic activities enhanced gradually. Michaelis constant Kr, of PVA-degradation enzyme was 2.06×10^-3 mol/L and the highest reaction rate Vr~,x was 19.5 units per minute. Thus, the kinetic equation on the catalytic reaction could be obtained as V=19.5 [S] / (2.06×10^-3+[S]).%筛选了1种能够完全降解PVA的混合菌系,对其所生产的PVA降解酶的降解性质及其酶催化反应动力学进行了研究。通过测定在PVA降解过程中酶活的变化,采用＂先假设-后验证＂的方法研究酶催化动力学方程。结果表明,在PVA未完全降解时,该降解酶的酶活随着PVA降解效率的提高而降低;在完全降解后,其酶活趋于一定。随着PVA浓度的升高,酶活逐渐提高。该酶的米氏常数Km=2.06×10^-3mol/L,最大反应速率Vmax=19.5U/min,得到该酶对PVA的催化反应动力学方程,为V=19.5[S]/（2.06×10^-3＋[S]）,从而为混合菌系的实际应用提供理论依据。
Energy Technology Data Exchange (ETDEWEB)
Parker, Lorien J.; Ciccone, Sarah; Italiano, Louis C.; Primavera, Alessandra; Oakley, Aaron J.; Morton, Craig J.; Hancock, Nancy C.; Bello, Mario Lo; Parker, Michael W. (SVIMR-A); (Melbourne); (Rome)
2008-08-04
The commonly used anti-cancer drug chlorambucil is the primary treatment for patients with chronic lymphocytic leukaemia. Chlorambucil has been shown to be detoxified by human glutathione transferase Pi (GST P1-1), an enzyme that is often found over-expressed in cancer tissues. The allelic variants of GST P1-1 are associated with differing susceptibilities to leukaemia and differ markedly in their efficiency in catalysing glutathione (GSH) conjugation reactions. Here, we perform detailed kinetic studies of the allelic variants with the aid of three representative co-substrates. We show that the differing catalytic properties of the variants are highly substrate-dependent. We show also that all variants exhibit the same temperature stability in the range 10 C to 45 C. We have determined the crystal structures of GST P1-1 in complex with chlorambucil and its GSH conjugate for two of these allelic variants that have different residues at positions 104 and 113. Chlorambucil is found to bind in a non-productive mode to the substrate-binding site (H-site) in the absence of GSH. This result suggests that under certain stress conditions where GSH levels are low, GST P1-1 can inactivate the drug by sequestering it from the surrounding medium. However, in the presence of GSH, chlorambucil binds in the H-site in a productive mode and undergoes a conjugation reaction with GSH present in the crystal. The crystal structure of the GSH-chlorambucil complex bound to the *C variant is identical with the *A variant ruling out the hypothesis that primary structure differences between the variants cause structural changes at the active site. Finally, we show that chlorambucil is a very poor inhibitor of the enzyme in contrast to ethacrynic acid, which binds to the enzyme in a similar fashion but can act as both substrate and inhibitor.
Energy Technology Data Exchange (ETDEWEB)
Chen, C.Y.; Harris, B.G.; Cook, P.F.
1988-01-12
Isotope partitioning studies beginning with E-(/sup 14/C)NAD, E-(/sup 14/C) malate, E-(/sup 14/C) NAD-Mg/sup 2 +/, and E-Mg-(/sup 14/C)malate suggest a steady-state random mechanism for the NAD-malic enzyme. Isotope trapping beginning with E-(/sup 14/C)NAD and with varying concentrations of Mg/sup 2 +/ and malate in the chase solution indicates that Mg/sup 2 +/ is added in rapid equilibrium and must be added prior to malate for productive ternary complex formation. Equal percentage trapping from E-(/sup 14/C)NAD-Mg and E-Mg-(/sup 14/C) malate indicates the mechanism is steady-state random with equal off-rates for NAD and malate from E-NAD-Mg-malate. The off-rates for both do not change significantly in the ternary E-Mg-malate and E-NAD-Mg complexes, nor does the off-rate change for NAD from E-NAD. No trapping of malate was obtained from E-(/sup 14/C) malate, suggesting that this complex is nonproductive. A quantitative analysis of the data allows an estimation of values for a number of the rate constants along the reaction pathway.
International Nuclear Information System (INIS)
Isotope partitioning studies beginning with E-[14C]NAD, E-[14C] malate, E-[14C] NAD-Mg2+, and E-Mg-[14C]malate suggest a steady-state random mechanism for the NAD-malic enzyme. Isotope trapping beginning with E-[14C]NAD and with varying concentrations of Mg2+ and malate in the chase solution indicates that Mg2+ is added in rapid equilibrium and must be added prior to malate for productive ternary complex formation. Equal percentage trapping from E-[14C]NAD-Mg and E-Mg-[14C] malate indicates the mechanism is steady-state random with equal off-rates for NAD and malate from E-NAD-Mg-malate. The off-rates for both do not change significantly in the ternary E-Mg-malate and E-NAD-Mg complexes, nor does the off-rate change for NAD from E-NAD. No trapping of malate was obtained from E-[14C] malate, suggesting that this complex is nonproductive. A quantitative analysis of the data allows an estimation of values for a number of the rate constants along the reaction pathway
Gao, Wen-Li; Li, Ning; Zong, Min-Hua
2013-03-10
Enzymatic regioselective acylation of pyrimidine nucleosides was mediated by immobilized lipase from Penicillium expansum in 2-methyltetrahydrofuran (MeTHF), a bio-solvent derived from biomass. Despite of the moderate dissolution ability of MeTHF toward nucleosides, the initial enzymatic reaction rate was much higher in this eco-friendly solvent than in other commonly used organic solvents. This could be explained by the lower apparent activation energy of the enzymatic reaction (24.5 vs. 43.3-57.1kJ/mol) and the higher catalytic efficiency of the enzyme (Vmax/Km, 5.8 vs. 1.1-2.9h(-1)) in MeTHF. The enzymatic acylation of a group of ribonucleosides afforded the desirable 5'-esters with the conversions of 96-99% and 5'-regioselectivities of 96 to >99%. In enzymatic acylation of 2'-deoxynucleosides, however, 5'-regioselectivities showed a clear dependence on the 5-substituents present in the base moiety although the substrate conversions reached >98% within 1-3h. In the cases of 2',3'-dideoxynucleoside analogs, the reaction rate decreased markedly due to the lack of 3'-hydroxyl. PMID:23337886
DEFF Research Database (Denmark)
Jensen, Kaj Frank; Hansen, Michael Riis; Jensen, Kristine Steen;
2015-01-01
The adenine phosphoribosyltransferase (APRTase) encoded by the open reading frame SSO2342 of Sulfolobus solfataricus P2, was subjected to crystallographic, kinetic and ligand binding analyses. The enzyme forms dimers in solution and in the crystals, and binds one molecule of the reactants 5...
Bernacchi, Carl J; Portis, Archie R; Nakano, Hiromi; von Caemmerer, Susanne; Long, Stephen P
2002-12-01
CO(2) transfer conductance from the intercellular airspaces of the leaf into the chloroplast, defined as mesophyll conductance (g(m)), is finite. Therefore, it will limit photosynthesis when CO(2) is not saturating, as in C3 leaves in the present atmosphere. Little is known about the processes that determine the magnitude of g(m). The process dominating g(m) is uncertain, though carbonic anhydrase, aquaporins, and the diffusivity of CO(2) in water have all been suggested. The response of g(m) to temperature (10 degrees C-40 degrees C) in mature leaves of tobacco (Nicotiana tabacum L. cv W38) was determined using measurements of leaf carbon dioxide and water vapor exchange, coupled with modulated chlorophyll fluorescence. These measurements revealed a temperature coefficient (Q(10)) of approximately 2.2 for g(m), suggesting control by a protein-facilitated process because the Q(10) for diffusion of CO(2) in water is about 1.25. Further, g(m) values are maximal at 35 degrees C to 37.5 degrees C, again suggesting a protein-facilitated process, but with a lower energy of deactivation than Rubisco. Using the temperature response of g(m) to calculate CO(2) at Rubisco, the kinetic parameters of Rubisco were calculated in vivo from 10 degrees C to 40 degrees C. Using these parameters, we determined the limitation imposed on photosynthesis by g(m). Despite an exponential rise with temperature, g(m) does not keep pace with increased capacity for CO(2) uptake at the site of Rubisco. The fraction of the total limitations to CO(2) uptake within the leaf attributable to g(m) rose from 0.10 at 10 degrees C to 0.22 at 40 degrees C. This shows that transfer of CO(2) from the intercellular air space to Rubisco is a very substantial limitation on photosynthesis, especially at high temperature. PMID:12481082
Enzyme efficiency: An open reaction system perspective
Energy Technology Data Exchange (ETDEWEB)
Banerjee, Kinshuk, E-mail: kb36@rice.edu [Department of Chemistry, University of Calcutta, Rajabazar Science College Campus, Kolkata 700 009 (India); Bhattacharyya, Kamal, E-mail: pchemkb@gmail.com [Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Kolkata 700 009 (India)
2015-12-21
A measure of enzyme efficiency is proposed for an open reaction network that, in suitable form, applies to closed systems as well. The idea originates from the description of classical enzyme kinetics in terms of cycles. We derive analytical expressions for the efficiency measure by treating the network not only deterministically but also stochastically. The latter accounts for any significant amount of noise that can be present in biological systems and hence reveals its impact on efficiency. Numerical verification of the results is also performed. It is found that the deterministic equation overestimates the efficiency, the more so for very small system sizes. Roles of various kinetics parameters and system sizes on the efficiency are thoroughly explored and compared with the standard definition k{sub 2}/K{sub M}. Study of substrate fluctuation also indicates an interesting efficiency-accuracy balance.
Enzyme efficiency: An open reaction system perspective
International Nuclear Information System (INIS)
A measure of enzyme efficiency is proposed for an open reaction network that, in suitable form, applies to closed systems as well. The idea originates from the description of classical enzyme kinetics in terms of cycles. We derive analytical expressions for the efficiency measure by treating the network not only deterministically but also stochastically. The latter accounts for any significant amount of noise that can be present in biological systems and hence reveals its impact on efficiency. Numerical verification of the results is also performed. It is found that the deterministic equation overestimates the efficiency, the more so for very small system sizes. Roles of various kinetics parameters and system sizes on the efficiency are thoroughly explored and compared with the standard definition k2/KM. Study of substrate fluctuation also indicates an interesting efficiency-accuracy balance
Torrielli, Alessandro
2016-08-01
We review some essential aspects of classically integrable systems. The detailed outline of the sections consists of: 1. Introduction and motivation, with historical remarks; 2. Liouville theorem and action-angle variables, with examples (harmonic oscillator, Kepler problem); 3. Algebraic tools: Lax pairs, monodromy and transfer matrices, classical r-matrices and exchange relations, non-ultralocal Poisson brackets, with examples (non-linear Schrödinger model, principal chiral field); 4. Features of classical r-matrices: Belavin–Drinfeld theorems, analyticity properties, and lift of the classical structures to quantum groups; 5. Classical inverse scattering method to solve integrable differential equations: soliton solutions, spectral properties and the Gel’fand–Levitan–Marchenko equation, with examples (KdV equation, Sine-Gordon model). Prepared for the Durham Young Researchers Integrability School, organised by the GATIS network. This is part of a collection of lecture notes.
Crevillén, Pedro; Ballicora, Miguel A; Mérida, Angel; Preiss, Jack; Romero, José M
2003-08-01
ADP-glucose pyrophosphorylase catalyzes the first and limiting step in starch biosynthesis and is allosterically regulated by the levels of 3-phosphoglycerate and phosphate in plants. ADP-glucose pyrophosphorylases from plants are heterotetramers composed of two types of subunits (small and large). In this study, the six Arabidopsis thaliana genes coding for ADP-glucose pyrophosphorylase isoforms (two small and four large subunits) have been cloned and expressed in an Escherichia coli mutant deficient in ADP-glucose pyrophosphorylase activity. The co-expression of the small subunit APS1 with the different Arabidopsis large subunits (APL1, APL2, APL3, and APL4) resulted in heterotetramers with different regulatory and kinetic properties. Heterotetramers composed of APS1 and APL1 showed the highest sensitivity to the allosteric effectors as well as the highest apparent affinity for the substrates (glucose-1-phosphate and ATP), whereas heterotetramers formed by APS1 and APL2 showed the lower response to allosteric effectors and the lower affinity for the substrates. No activity was detected for the second gene coding for a small subunit isoform (APS2) annotated in the Arabidopsis genome. This lack of activity is possibly due to the absence of essential amino acids involved in catalysis and/or in the binding of glucose-1-phosphate and 3-phosphoglycerate. Kinetic and regulatory properties of the different heterotetramers, together with sequence analysis has allowed us to make a distinction between sink and source enzymes, because the combination of different large subunits would provide a high plasticity to ADP-glucose pyrophosphorylase activity and regulation. This is the first experimental data concerning the role that all the ADP-glucose pyrophosphorylase isoforms play in a single plant species. This phenomenon could have an important role in vivo, because different large subunits would confer distinct regulatory properties to ADP-glucose pyrophosphorylase according
Cohn, A G; Rabinowitz, Mario
2003-01-01
A classical representation of an extended body over barriers of height greater than the energy of the incident body is shown to have many features in common with quantum tunneling as the center-of-mass literally goes through the barrier. It is even classically possible to penetrate any finite barrier with a body of arbitrarily low energy if the body is sufficiently long. A distribution of body lengths around the de Broglie wavelength leads to reasonable agreement with the quantum transmission coefficient.
Cohn, Arthur; Rabinowitz, Mario
2003-01-01
A classical representation of an extended body over barriers of height greater than the energy of the incident body is shown to have many features in common with quantum tunneling as the center-of-mass literally goes through the barrier. It is even classically possible to penetrate any finite barrier with a body of arbitrarily low energy if the body is sufficiently long. A distribution of body lengths around the de Broglie wavelength leads to reasonable agreement with the quantum transmission...
Mould, Richard A
2003-01-01
Preciously given rules allow conscious systems to be included in quantum mechanical systems. There rules are derived from the empirical experience of an observer who witnesses a quantum mechanical interaction leading to the capture of a single particle. In the present paper it is shown that purely classical changes experienced by an observer are consistent with these rules. Three different interactions are considered, two of which combine classical and quantum mechanical changes. The previous...
Directory of Open Access Journals (Sweden)
Lisa M. Bishop
2010-09-01
Full Text Available We develop the stochastic, chemical master equation as a unifying approach to the dynamics of biochemical reaction systems in a mesoscopic volume under a living environment. A living environment provides a continuous chemical energy input that sustains the reaction system in a nonequilibrium steady state with concentration fluctuations. We discuss the linear, unimolecular single-molecule enzyme kinetics, phosphorylation-dephosphorylation cycle (PdPC with bistability, and network exhibiting oscillations. Emphasis is paid to the comparison between the stochastic dynamics and the prediction based on the traditional approach based on the Law of Mass Action. We introduce the difference between nonlinear bistability and stochastic bistability, the latter has no deterministic counterpart. For systems with nonlinear bistability, there are three different time scales: (a individual biochemical reactions, (b nonlinear network dynamics approaching to attractors, and (c cellular evolution. For mesoscopic systems with size of a living cell, dynamics in (a and (c are stochastic while that with (b is dominantly deterministic. Both (b and (c are emergent properties of a dynamic biochemical network; We suggest that the (c is most relevant to major cellular biochemical processes such as epi-genetic regulation, apoptosis, and cancer immunoediting. The cellular evolution proceeds with transitions among the attractors of (b in a “punctuated equilibrium” manner.
Qian, Hong; Bishop, Lisa M
2010-01-01
We develop the stochastic, chemical master equation as a unifying approach to the dynamics of biochemical reaction systems in a mesoscopic volume under a living environment. A living environment provides a continuous chemical energy input that sustains the reaction system in a nonequilibrium steady state with concentration fluctuations. We discuss the linear, unimolecular single-molecule enzyme kinetics, phosphorylation-dephosphorylation cycle (PdPC) with bistability, and network exhibiting oscillations. Emphasis is paid to the comparison between the stochastic dynamics and the prediction based on the traditional approach based on the Law of Mass Action. We introduce the difference between nonlinear bistability and stochastic bistability, the latter has no deterministic counterpart. For systems with nonlinear bistability, there are three different time scales: (a) individual biochemical reactions, (b) nonlinear network dynamics approaching to attractors, and (c) cellular evolution. For mesoscopic systems with size of a living cell, dynamics in (a) and (c) are stochastic while that with (b) is dominantly deterministic. Both (b) and (c) are emergent properties of a dynamic biochemical network; We suggest that the (c) is most relevant to major cellular biochemical processes such as epi-genetic regulation, apoptosis, and cancer immunoediting. The cellular evolution proceeds with transitions among the attractors of (b) in a "punctuated equilibrium" manner. PMID:20957107
DEFF Research Database (Denmark)
Christensen, Peter Møller; Gunnarsson, Thomas Gunnar Petursson; Thomassen, Martin;
2015-01-01
perturbation during INT. Pulmonary V˙O2 kinetics was determined in eight trained male cyclists (V˙O2-max: 59 ± 4 (means ± SD) mL min(-1) kg(-1)) during MOD (205 ± 12 W ~65% V˙O2-max) and INT (286 ± 17 W ~85% V˙O2-max) exercise before and after a 7-week HIT period (30-sec sprints and 4-min intervals) with a 50......The present study examined if high intensity training (HIT) could increase the expression of oxidative enzymes in fast-twitch muscle fibers causing a faster oxygen uptake (V˙O2) response during intense (INT), but not moderate (MOD), exercise and reduce the V˙O2 slow component and muscle metabolic...... between MOD and INT. Muscle creatine phosphate was lower (42 ± 15 vs. 66 ± 17 mmol kg DW(-1)) and muscle lactate was higher (40 ± 18 vs. 14 ± 5 mmol kg DW(-1)) at 6 min of INT (P < 0.05) after compared to before HIT. A period of intensified training with a volume reduction did not increase the content of...
Perrella, F W
1988-11-01
EZ-FIT, an interactive microcomputer software package, has been developed for the analysis of enzyme kinetic and equilibrium binding data. EZ-FIT was designed as a user-friendly menu-driven package that has the facility for data entry, editing, and filing. Data input permits the conversion of cpm, dpm, or optical density to molar per minute per milligram protein. Data can be fit to any of 14 model equations including Michaelis-Menten, Hill, isoenzyme, inhibition, dual substrate, agonist, antagonist, and modified integrated Michaelis-Menten. The program uses the Nelder-Mead simplex and Marquardt nonlinear regression algorithms sequentially. A report of the results includes the parameter estimates with standard errors, a Student t test to determine the accuracy of the parameter values, a Runs statistic test of the residuals, identification of outlying data, an Akaike information criterion test for goodness-of-fit, and, when the experimental variance is included, a chi 2 statistic test for goodness-of-fit. Several different graphs can be displayed: an X-Y, a Scatchard, an Eadie-Hofstee, a Lineweaver-Burk, a semilogarithmic, and a residual plot. A data analysis report and graphs are designed to evaluate the goodness-of-fit of the data to a particular model. PMID:3239747
Mould, R A
2003-01-01
Preciously given rules allow conscious systems to be included in quantum mechanical systems. There rules are derived from the empirical experience of an observer who witnesses a quantum mechanical interaction leading to the capture of a single particle. In the present paper it is shown that purely classical changes experienced by an observer are consistent with these rules. Three different interactions are considered, two of which combine classical and quantum mechanical changes. The previously given rules support all of these cases. Key Words: brain states, conscious observer, detector, measurement, probability current, state reduction, von Neumann, wave collapse.
Subedi, Bishnu P; Corder, Andra L; Zhang, Siai; Foss, Frank W; Pierce, Brad S
2015-01-20
MiaE [2-methylthio-N(6)-isopentenyl-adenosine(37)-tRNA monooxygenase] isolated from Salmonella typhimurium is a unique non-heme diiron enzyme that catalyzes the O2-dependent post-transcriptional allylic hydroxylation of a hypermodified nucleotide (ms(2)i(6)A37) at position 37 of selected tRNA molecules to produce 2-methylthio-N(6)-(4-hydroxyisopentenyl)-adenosine(37). In this work, isopentenylated tRNA substrates for MiaE were produced from small RNA oligomers corresponding to the anticodon stem loop (ACSL) region of tRNA(Trp) using recombinant MiaA and dimethylallyl pyrophosphate. Steady-state rates for MiaE-catalyzed substrate hydroxylation were determined using recombinant ferredoxin (Fd) and ferredoxin reductase (FdR) to provide a catalytic electron transport chain (ETC) using NADPH as the sole electron source. As with previously reported peroxide-shunt assays, steady-state product formation retains nearly stoichiometric (>98%) E stereoselectivity. MiaE-catalyzed i(6)A-ACSL(Trp) hydroxylation follows Michaelis-Menten saturation kinetics with kcat, KM, and V/K determined to be 0.10 ± 0.01 s(-1), 9.1 ± 1.5 μM, and ∼11000 M(-1) s(-1), respectively. While vastly slower, MiaE-catalyzed hydroxylation of free i(6)A nucleoside could also be observed using the (Fd/FdR)-ETC assay. By comparison to the V/K determined for i(6)A-ACSL substrates, an ∼6000-fold increase in enzymatic efficiency is imparted by ACSL(Trp)-MiaE interactions. The impact of substrate tRNA-MiaE interactions on protein secondary structure and active site electronic configuration was investigated using circular dichroism, dual-mode X-band electron paramagnetic resonance, and Mössbauer spectroscopies. These studies demonstrate that binding of tRNA to MiaE induces a protein conformational change that influences the electronic structure of the diiron site analogous to what has been observed for various bacterial multicomponent diiron monooxygenases upon titration with their corresponding effector
Luo, Yuzi; Li, Lin; Austermann-Busch, Sophia; Dong, Mei; Xu, Jingjing; Shao, Lina; Lei, Jianlin; Li, Na; He, Wen-Rui; Zhao, Bibo; Li, Su; Li, Yongfeng; Liu, Lihong; Becher, Paul; Sun, Yuan; Qiu, Hua-Ji
2015-09-15
Classical swine fever (CSF), caused by classical swine fever virus (CSFV), is a devastating disease of swine worldwide. Although a mandatory vaccination with the modified live vaccine C-strain has been implemented in China for decades, CSF remains a serious threat to the swine industry. To facilitate the control and eradication of CSF in China, the E2-based marker vaccine rAdV-SFV-E2, an adenovirus-delivered, alphavirus replicon-vectored vaccine, has been developed. Accordingly, an accompanying discriminatory test that allows differentiating infected from vaccinated animals (DIVA) is required. Here, the enhanced expression of E(rns) protein of CSFV was achieved in the methyltropic yeast Pichia pastoris by codon-optimization of the E(rns) gene, and an indirect enzyme-linked immunosorbent assay (iELISA) based on the yeast-expressed E(rns) (yE(rns)) was developed and evaluated. The optimized iELISA was able to detect CSFV-specific antibodies in the serum samples from the CSFV-infected pigs as early as 6 days post-infection, and discriminate the CSFV-infected pigs from those vaccinated with rAdV-SFV-E2. The iELISA was evaluated using a panel of swine sera, and showed comparable sensitivity (94.6%) and specificity (97.1%), and the consistence rates with the virus neutralization test were 96.8% for CSFV-infected swine sera, 83.3% for C-strain-vaccinated swine sera, and 95.0% for field swine sera. In addition, the iELISA showed higher sensitivity (90.4%) compared with PrioCHECK CSFV E(rns) (59.6%). Taken together, the yE(rns)-based iELISA is specific and sensitive, representing a promising DIVA test for E2-based marker vaccines against CSF. PMID:26005003
Danforth, Douglas G.
2001-01-01
Classical systems can be entangled. Entanglement is defined by coincidence correlations. Quantum entanglement experiments can be mimicked by a mechanical system with a single conserved variable and 77.8% conditional efficiency. Experiments are replicated for four particle entanglement swapping and GHZ entanglement.
Gallavotti, Giovanni
1999-01-01
This is the English version of a friendly graduate course on Classical Mechanics, containing about 80% of the material I covered during the January-June 1999 semester at IFUG in the Mexican city of Leon. For the Spanish version, see physics/9906066
Hurwitz, Selwyn J; Asif, Ghazia; Kivel, Nancy M; Schinazi, Raymond F
2008-12-01
In vitro selection studies and data from large genotype databases from clinical studies have demonstrated that tenofovir disoproxil fumarate and abacavir sulfate select for the K65R mutation in the human immunodeficiency virus type 1 polymerase region. Furthermore, other novel non-thymine nucleoside reverse transcriptase (RT) inhibitors also select for this mutation in vitro. Studies performed in vitro and in humans suggest that viruses containing the K65R mutation remained susceptible to zidovudine (ZDV) and other thymine nucleoside antiretroviral agents. Therefore, ZDV could be coformulated with these agents as a "resistance repellent" agent for the K65R mutation. The approved ZDV oral dose is 300 mg twice a day (b.i.d.) and is commonly associated with bone marrow toxicity thought to be secondary to ZDV-5'-monophosphate (ZDV-MP) accumulation. A simulation study was performed in silico to optimize the ZDV dose for b.i.d. administration with K65R-selecting antiretroviral agents in virtual subjects using the population pharmacokinetic and cellular enzyme kinetic parameters of ZDV. These simulations predicted that a reduction in the ZDV dose from 300 to 200 mg b.i.d. should produce similar amounts of ZDV-5'-triphosphate (ZDV-TP) associated with antiviral efficacy (>97% overlap) and reduced plasma ZDV and cellular amounts of ZDV-MP associated with toxicity. The simulations also predicted reduced peak and trough amounts of cellular ZDV-TP after treatment with 600 mg ZDV once a day (q.d.) rather than 300 or 200 mg ZDV b.i.d., indicating that q.d. dosing with ZDV should be avoided. These in silico predictions suggest that 200 mg ZDV b.i.d. is an efficacious and safe dose that could delay the emergence of the K65R mutation. PMID:18838591
Institute of Scientific and Technical Information of China (English)
吴梅芬; 王晓岗; 刘亚菲; 许新华
2015-01-01
通过严格的化学反应动力学推导,得到了a-糜蛋白酶催化三甲基乙酸对硝基苯酯水解反应相关的动力学参数的表达式,包括表观米氏常数 KM、酶-底物络合物稳定常数 K 、催化速率常数 kcat 、以及基元反应步骤速率常 k2和 k3等.实验在25℃,pH ＝8．5的三羟基氨基甲烷缓冲液中进行,用分光光度法测定反应的动力学曲线.数据经过非线性拟合和线性拟合,得到相关的动力学参数,该参数与理论预测一致.该实验酶制剂价格低廉,活性稳定,实验方法简单,可作为本科物理化学实验课程中复杂反应动力学测量的一个很好的实例,加深学生对化学反应动力学相关理论和概念的理解和掌握.%The mechanism of a-chymotrypsin-catalyzed hydrolysis of 4-nitrophenyl trimethylacetate includes the following steps:the reversible enzyme-substrate binding and the enzyme acylation and enzyme deacylation.This mechanism is quite different from the conventional Michaelis-Menten mechanism for enzyme-catalyzed reactions.The corresponding kinetic parameters can be expressed precisely on the basis of chemical kinetics theory,such as Michaelis constant KM ,equilibrium constant K,catalytic rate constant kcat ,and the rate constants of the elementary reactions k 2 and k 3 .The reaction is carried out at 25 °C in a pH = 8.5 buffer of tris(hydroxymethyl)aminomethane (TRIS)by means of spectrophotometry.The kinetic curves are fitted linearly and non-linearly.The kinetic parameters are in agreement with the theoretical prediction.The enzyme product used in this experiment is cheap and the activity is stable. The experimental method is simple enough to be applied in undergraduate physical chemistry laboratory courses.As an ideal model of complex reaction,the experiment will help the students to enhance the understanding and knowledge of chemical kinetics theories.
Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects
DEFF Research Database (Denmark)
Wedberg, Nils Hejle Rasmus Ingemar
This thesis describes the development of a molecular simulation methodology to study properties of enzymes in non-aqueous media at fixed thermodynamic water activities. The methodology is applied in a molecular dynamics study of the industrially important enzyme Candida antarctica lipase B (CALB...... of enzyme kinetics in non-aqueous media, it has been a fruitful approach to fix the enzyme hydration level by controlling the water activity of the medium. In this work, a protocol is therefore developed for determining the water activity in non-aqueous protein simulations. The method relies on determining...... the system size of the simulation box generally used in simulation. Therefore, a method is developed for extending the RDFs to arbitrary distances so that the integrals can be evaluated. The method, which was first used in the classical study of the Lennard-Jones fluid by Verlet (Verlet (1968), Phys. Rev...
International Nuclear Information System (INIS)
Photoreactivating enzymes (PRE) also called photolyases (EC 4.1.99.3) catalyze the light 300 to 600 nm)-dependent monomerization of cyclobutyl pyrimidine dimers, formed between adjacent pyrimidines on the same DNA strand, upon exposure to ultraviolet (uv) irradiation (220 to 320 nm). Although much is known about the substrate and product of these unusual enzymes, their identification required the development and synthesis of such fields as photochemistry, biochemistry, and microbiology. Photoreactivation was first known as a biological recovery phenomenon: cells exposed to visible light following uv irradiation showed higher survival than those kept in the dark. Early investigators examined the photoreactivability of an enormous range of cellular damage in both prokaryotes and eukaryotes. This review article discusses the purification and properties of PRE, the kinetics of photoreactivation and the biological role of this repair process
Oikawa, P. Y.; Jenerette, D.; Knox, S. H.; Sturtevant, C. S.; Verfaillie, J. G.; Baldocchi, D. D.
2014-12-01
Under California's Cap-and-Trade program, companies are looking to invest in land-use practices that will reduce greenhouse gas (GHG) emissions. The Sacramento-San Joaquin River Delta is a drained cultivated peatland system and a large source of CO2. To slow soil subsidence and reduce CO2 emissions, there is growing interest in converting drained peatlands to wetlands. However, wetlands are large sources of CH4 that could offset CO2-based GHG reductions. The goal of our research is to provide accurate measurements and model predictions of the changes in GHG budgets that occur when drained peatlands are restored to wetland conditions. We have installed a network of eddy covariance towers across multiple land use types in the Delta and have been measuring CO2 and CH4 ecosystem exchange for multiple years. In order to upscale these measurements through space and time we are using these data to parameterize and validate a process-based biogeochemical model. To predict gross primary productivity (GPP), we are using a simple light use efficiency (LUE) model which requires estimates of light, leaf area index and air temperature and can explain 90% of the observed variation in GPP in a mature wetland. To predict ecosystem respiration we have adapted the Dual Arrhenius Michaelis-Menten (DAMM) model. The LUE-DAMM model allows accurate simulation of half-hourly net ecosystem exchange (NEE) in a mature wetland (r2=0.85). We are working to expand the model to pasture, rice and alfalfa systems in the Delta. To predict methanogenesis, we again apply a modified DAMM model, using simple enzyme kinetics. However CH4 exchange is complex and we have thus expanded the model to predict not only microbial CH4 production, but also CH4 oxidation, CH4 storage and the physical processes regulating the release of CH4 to the atmosphere. The CH4-DAMM model allows accurate simulation of daily CH4 ecosystem exchange in a mature wetland (r2=0.55) and robust estimates of annual CH4 budgets. The LUE
Pannhorst, Katrin; Fröhlich, Andreas; Staubach, Christoph; Meyer, Denise; Blome, Sandra; Becher, Paul
2015-07-01
Infections with Classical swine fever virus (CSFV) are a major economic threat to pig production. To combat CSF outbreaks and to maintain trade, new marker vaccines were developed that allow differentiation of infected from vaccinated animals (DIVA principle). The chimeric pestivirus CP7_E2alf was shown to be safe and efficacious. Its DIVA strategy is based on the detection of CSFV E(rns)-specific antibodies that are only developed on infection. However, for the new marker vaccine to be considered a valuable control tool, a validated discriminatory assay is needed. One promising candidate is the already commercially available enzyme-linked immunosorbent assay, PrioCHECK CSFV E(rns) ELISA (Prionics BV, Lelystad, The Netherlands). Four laboratories of different European Union member states tested 530 serum samples and country-specific field sera from domestic pigs and wild boar. The ELISA displayed a good robustness. However, based on its reproducibility and repeatability, ranges rather than single values for diagnostic sensitivity and specificity were defined. The ELISA displayed a sensitivity of 90-98% with sera from CSFV-infected domestic pigs. A specificity of 89-96% was calculated with sera from domestic pigs vaccinated once with CP7_E2alf. The ELISA detected CSFV infections in vaccinated domestic pigs with a sensitivity of 82-94%. The sensitivity was lower with sera taken ≤21 days post-challenge indicating that the stage of CSFV infection had a considerable influence on testing. Taken together, the PrioCHECK CSFV E(rns) ELISA can be used for detection of CSFV infections in CP7_E2alf-vaccinated and nonvaccinated domestic pig populations, but should only be applied on a herd basis by testing a defined number of animals. PMID:26179095
International Nuclear Information System (INIS)
A review of tachyons, with particular attention to their classical theory, is presented. The extension of Special Relativity to tachyons in two dimensional is first presented, an elegant model-theory which allows a better understanding also of ordinary physics. Then, the results are extended to the four-dimensional case (particular on tachyon mechanics) that can be derived without assuming the existence of Super-luminal reference-frames. Localizability and the unexpected apparent shape of tachyonic objects are discussed, and it is shown (on the basis of tachyon kinematics) how to solve the common causal paradoxes. In connection with General Relativity, particularly the problem of the apparent superluminal expansions in astrophysics is reviewed. The problem (still open) of the extension of relativitic theories to tachyons in four dimensions is tackled, and the electromagnetic theory of tachyons, a topic that can be relevant also for the experimental side, is reviewed. (Author)
Shivakumar, Srividya; Karmali, Anika Nayak; Ruhimbana, Charles
2014-01-01
A new alkalophilic low-molecular-mass chitinase of 14 kD from the potent biocontrol agent Bacillus subtilis JN032305 was partially purified and enzymology of the chitinase was studied. The enzyme showed optimal pH of 9.0 and temperature of 50°C. The enzyme was found stable during the 60-min incubation at 50 °C. The chitinase was inhibited by group specific agents like IAA, DAN, TLCK, and SDS and metal ions Mg(2+), Ca(2+), Fe(2+), Mn(2+), Ba(2+), and Hg(2+), whereas Zn(2+) did not show significant inhibitory effect against the chitinase. PMSF partially inhibited the enzyme. Substrates specificity tests indicated that the enzyme showed 75% of relative activity on glycol chitin, 58% on carboxymethylcellulose (CMC), 33% on chitin flakes, and 166% laminarin compared to that on colloidal chitin. The enzyme also hydrolyzed 4-methylumbelliferyl-N-acetyl-D-glucosaminide, indicating its chitobiase activity. The chitinase of this study has broad specificity, which could hydrolyze not only the glycosidic bond in GlcNAc-GlcNAc but also that of related carbohydrates with glycosidic linkages. The partially purified chitinase not only showed antifungal activity against Rhizoctonia solani and Colletotrichum gloeosporioides, two potent phytopathogens of chilli, but also increased the germination of chilli seeds when infected with the two potent phytopathogenic fungi. PMID:24499366
Institute of Scientific and Technical Information of China (English)
杨明莉; 任建敏
2001-01-01
With the King-Altman plot, the kinetics equation of a single substrate enzyme-catalyzed reaction inhibited by a reversible inhibitor was attained. With the help of the general kinetics equation from an enzyme-catalyzed reaction obeying partially reversible inhibiting mechanism, the reaction mechanisms and the characteristics for partially and fully competitive inhibition, partially and fully noncompetitive inhibition, partially and fully uncompetitive inhibition were discussed.% 本文用King-Altman作图法推导了可逆抑制酶促单底物反应动力学方程，并借助于部分可逆抑制单底物酶促反应动力学方程对完全与部分的竞争性抑制作用(PC与FC)、完全与部分非竞争性抑制作用(FNC与PNC)、完全与部分反竞争性抑制作用(FUC与PUC)和完全与部分混合抑制作用(FM与PM)的动力学机理与特点进行了讨论。
A staphylolytic fusion protein (K-L) was created, harboring three unique lytic activities comprised of the LysK CHAP endopeptidase, and amidase domains, and the lysostaphin glycyl-glycine endopeptidase domain. To assess the potential of possible therapeutic applications, the kinetic behavior of K-L...
Hoag, Matthew R; Roman, Joseph; Beaupre, Brett A; Silvaggi, Nicholas R; Moran, Graham R
2015-06-23
Despite a lack of convincing in vitro evidence and a number of sound refutations, it is widely accepted that renalase is an enzyme unique to animals that catalyzes the oxidative degradation of catecholamines in blood in order to lower vascular tone. Very recently, we identified isomers of β-NAD(P)H as substrates for renalase (Beaupre, B. A. et al. (2015) Biochemistry, 54, 795-806). These molecules carry the hydride equivalent on the 2 or 6 position of the nicotinamide base and presumably arise in nonspecific redox reactions of nicotinamide dinucleotides. Renalase serves to rapidly oxidize these isomers to form β-NAD(P)⁺ and then pass the electrons to dioxygen, forming H₂O₂. We have also shown that these substrate molecules are highly inhibitory to dehydrogenase enzymes and thus have proposed an intracellular metabolic role for this enzyme. Here, we identify a renalase from an organism without a circulatory system. This bacterial form of renalase has the same substrate specificity profile as that of human renalase but, in terms of binding constant (K(d)), shows a marked preference for substrates derived from β-NAD⁺. 2-dihydroNAD(P) substrates reduce the enzyme with rate constants (k(red)) that greatly exceed those for 6-dihydroNAD(P) substrates. Taken together, k(red)/K(d) values indicate a minimum 20-fold preference for 2DHNAD. We also offer the first structures of a renalase in complex with catalytically relevant ligands β-NAD⁺ and β-NADH (the latter being an analogue of the substrate(s)). These structures show potential electrostatic repulsion interactions with the product and a unique binding orientation for the substrate nicotinamide base that is consistent with the identified activity. PMID:26016690
Haataja, Tatu J.K.; Koski, M. Kristian; Hiltunen, J. Kalervo; Glumoff, Tuomo
2011-01-01
Abstract All the peroxisomal ?-oxidation pathways characterized thus far house at least one multifunctional enzyme (MFE) catalyzing two out of four reactions of the spiral. MFE type 2 proteins from various species display great variation in domain composition and predicted substrate preference. The gene CG3415 encodes for D. melanogaster MFE-2 (DmMFE-2), complements the S. cerevisiae MFE-2 deletion strain, and the recombinant protein displays both MFE-2 enzymatic activities in vitr...
Price, Nigel T; Jackson, Vicky N; van der Leij, Feike R; Cameron, Jacqueline M; Travers, Maureen T; Bartelds, Beatrijs; Huijkman, Nicolette C; Zammit, Victor A
2003-01-01
The nucleotide sequence data reported will appear in DDBJ, EMBL, GenBank(R) and GSDB Nucleotide Sequence Databases; the sequences of ovine CPT1A and CPT1B cDNAs have the accession numbers Y18387 and AJ272435 respectively and the partial adipose tissue and liver CPT1A clones have the accession numbers Y18830 and Y18829 respectively. Fatty acid and ketone body metabolism differ considerably between monogastric and ruminant species. The regulation of the key enzymes involved may differ accordingly. Carnitine palmitoyltransferase 1 (CPT 1) is the key locus for the control of long-chain fatty acid beta-oxidation and liver ketogenesis. Previously we showed that CPT 1 kinetics in sheep and rat liver mitochondria differ. We cloned cDNAs for both isoforms [liver- (L-) and muscle- (M-)] of ovine CPT 1 in order to elucidate the structural features of these proteins and their genes ( CPT1A and CPT1B ). Their deduced amino acid sequences show a high degree of conservation compared with orthologues from other mammalian species, with the notable exception of the N-terminus of ovine M-CPT 1. These differences were also present in bovine M-CPT 1, whose N-terminal sequence we determined. In addition, the 5'-end of the sheep CPT1B cDNA suggested a different promoter architecture when compared with previously characterized CPT1B genes. Northern blotting revealed differences in tissue distribution for both CPT1A and CPT1B transcripts compared with other species. In particular, ovine CPT1B mRNA was less tissue restricted, and the predominant transcript in the pancreas was CPT1B. Expression in yeast allowed kinetic characterization of the two native enzymes, and of a chimaera in which the distinctive N-terminal segment of ovine M-CPT 1 was replaced with that from rat M-CPT 1. The ovine N-terminal segment influences the kinetics of the enzyme for both its substrates, such that the K (m) for palmitoyl-CoA is decreased and that for carnitine is increased for the chimaera, relative to the
Directory of Open Access Journals (Sweden)
Rufei Shen
2015-09-01
Full Text Available Nucleoside diphosphate kinase (NDPK, as a house-keeping protein, involves in various molecular processes including signal transduction, energy and drug metabolism. The main objective was to investigate NDPK kinetics in human erythrocytes and to monitor the frequency distribution of NDPK activity levels in Chinese healthy subjects and transplant recipients. METHODS: NDPK activity in erythrocytes was detected by a validated ion-pair high-performance liquid chromatogram method. NDPK kinetics studies were carried out systematically. NDPK activity levels were determined in 500 healthy subjects, 250 kidney and 250 liver transplant recipients in Chinese Han population. RESULTS: Thermal and pH stability studies indicated NDPK was relatively stable at temperature 30-45ºC and pH 6.0-9.0. In substrate dependency study, the apparent Michaelis-Menten constant (Km and maximum velocity of enzymatic reaction (Vmax increased with concentration of substrates. Meanwhile, in product inhibition study, with the increasing concentration of dATP, the Vmax of dADP decreased with constant Km and Km of dGTP increased with constant Vmax. NDPK activity levels revealed a 7-fold variability and were not normally distributed in all groups. NDPK activity levels were significantly (P<0.05 higher in transplant group than those in health group. Additionally, much higher NDPK activity levels had been shown (P<0.001 in liver transplant recipients when compared to kidney transplant cases. CONCLUSIONS: NDPK kinetics studies indicated substrate dependency of NDPK and a “ping-pong” mechanism for production inhibition. Skewness distributions of NDPK activity levels were shown in the study population. The transplant recipients showed higher NDPK activity levels when compared to healthy subjects.
Enzyme Teaching by a Virtual Laboratory
Directory of Open Access Journals (Sweden)
J.K. Sugai
2010-05-01
Full Text Available Biochemistry learning demands skills to obtaining and interpreting the experimental data. In a classical model of teaching involve student’s hands-on participation. However this model is expensive, not safe and should be carried out in a short and limited time course. With utilization of educational software these disadvantages are overcome, since the virtual activity could be realized at free full access, and is a tool for individual study. The aim of the present work is to present educational software focused on a virtual for undergraduate student of biochemistry courses. The software development was performed with the help of concept maps, ISIS Draw, ADOBE Photoshop and FLASH MX Program applied on the subject salivary amylase. It was possible to present the basic methodologies for study of the kinetic of enzyme. The substrate (starch consumption was determinate by iodine reaction, while the products (reducing sugars formation was evaluated by cupper-alkaline reaction. The protocols of the virtual experiments are present verbally as well as a subtitle. A set of exercises are disposable, which allowed an auto evaluation and a review of the subject. The experimental treatment involved the presentation of this hypermedia for Nutrition and Dentistry/UFSC undergraduate students as a tool for better comprehension of the theme and promoted the understanding of the kinetic of enzyme.
McCarty, Reid M.; Krebs, Carsten; Bandarian, Vahe
2013-01-01
7-Carboxy-7-deazaguanine (CDG) synthase (QueE) catalyzes the complex heterocyclic radical-mediated conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) to CDG in the third step of the biosynthetic pathway to all 7-deazapurines. Here we present a detailed characterization of QueE from Bacillus subtilis to delineate the mechanism of conversion of CPH4 to CDG. QueE is a member of the radical S-adenosyl-L-methionine (SAM) superfamily, all of which use a bound [4Fe-4S]+ cluster to catalyze the reductive cleavage of SAM cofactor to generate methionine and a 5′-deoxyadenosyl radical (5′-dAdo•), which initiates enzymatic transformations requiring H-atom abstraction. The UV-visible, EPR, and Mössbauer spectroscopic features of the homodimeric QueE point to the presence of a single [4Fe-4S] cluster per monomer. Steady-state kinetic experiments indicate a Km of 20 ± 7 μM for CPH4 and kcat of 5.4 ± 1.2 min-1 for the overall transformation. The kinetically determined Kapp for SAM is 45 ± 1 μM. QueE is also magnesium-dependent and exhibits a Kapp for the divalent metal ion of 0.21 ± 0.03 mM. The SAM cofactor supports multiple turnovers, indicating that it is regenerated at the end of each catalytic cycle. The mechanism of rearrangement of QueE was probed with CPH4 isotopologs containing deuterium at C-6 or the two prochiral positions at C-7. These studies implicate 5′-dAdo• as initiating the ring contraction reaction catalyzed by QueE by abstraction of the H-atom from C-6 of CPH4. PMID:23194065
Ploux, O; Breyne, O; Carillon, S; Marquet, A
1999-01-01
8-Amino-7-oxopelargonate synthase catalyzes the first committed step of biotin biosynthesis in micro-organisms and plants. Because inhibitors of this pathway might lead to antibacterials or herbicides, we have undertaken an inhibition study on 8-amino-7-oxopelargonate synthase using six different compounds. d-Alanine, the enantiomer of the substrate of this pyridoxal-5'-phosphate-dependent enzyme was found to be a competitive inhibitor with respect to l-alanine with a Ki of 0.59 mm. The fact that this inhibition constant was four times lower than the Km for l-alanine was interpreted as the consequence of the inversion-retention stereochemistry of the catalyzed reaction. Schiff base formation between l or d-alanine and pyridoxal-5'-phosphate, in the active site of the enzyme, was studied using ultraviolet/visible spectroscopy. It was found that l and d-alanine form an external aldimine with equilibrium constants K = 4.1 mm and K = 37.8 mm, respectively. However, the equilibrium constant for d-alanine aldimine formation dramatically decreased to 1.3 mm in the presence of saturating concentration of pimeloyl-CoA, the second substrate. This result strongly suggests that the binding of pimeloyl-CoA induces a conformational change in the active site, and we propose that this new topology is complementary to d-alanine and to the putative reaction intermediate since they both have the same configuration. (+/-)-8-Amino-7-oxo-8-phosphonononaoic acid (1), the phosphonate derivative of the intermediate formed during the reaction, was our most potent inhibitor with a Ki of 7 microm. This compound behaved as a reversible slow-binding inhibitor, competitive with respect to l-alanine. Kinetic investigation showed that this slow process was best described by a one-step mechanism (mechanism A) with the following rate constants: k1 = 0.27 x 103 m-1.s-1, k2 = 1.8 s-1 and half-life for dissociation t1/2 = 6.3 min. The binding of compound 1 to the enzyme was also studied using
L.P.F. Winkel (Léon)
2004-01-01
textabstractPompe’s disease is an inherited metabolic illness, caused by an inherited deficiency of an enzyme, called acid a-glucosidase. Acid a-glucosidase is a protein that breaks down glycogen (a chain of glucose molecules) into glucose (a single molecule), in a specific compartment of the cel
What classicality? Decoherence and Bohr's classical concepts
Schlosshauer, Maximilian
2010-01-01
Niels Bohr famously insisted on the indispensability of what he termed "classical concepts." In the context of the decoherence program, on the other hand, it has become fashionable to talk about the "dynamical emergence of classicality" from the quantum formalism alone. Does this mean that decoherence challenges Bohr's dictum and signifies a break with the Copenhagen interpretation-for example, that classical concepts do not need to be assumed but can be derived? In this paper we'll try to shine some light down the murky waters where formalism and philosophy cohabitate. To begin, we'll clarify the notion of classicality in the decoherence description. We'll then discuss Bohr's and Heisenberg's take on the quantum-classical problem and reflect on different meanings of the terms "classicality" and "classical concepts" in the writings of Bohr and his followers. This analysis will allow us to put forward some tentative suggestions for how we may better understand the relation between decoherence-induced classical...
Czifrák, Katalin; Páhi, András; Deák, Szabina; Kiss-Szikszai, Attila; Kövér, Katalin E; Docsa, Tibor; Gergely, Pál; Alexacou, Kyra-Melinda; Papakonstantinou, Maria; Leonidas, Demetres D; Zographos, Spyros E; Chrysina, Evangelia D; Somsák, László
2014-08-01
The reaction of thiourea with O-perbenzoylated C-(1-bromo-1-deoxy-β-D-glucopyranosyl)formamide gave the new anomeric spirocycle 1R-1,5-anhydro-D-glucitol-spiro-[1,5]-2-imino-1,3-thiazolidin-4-one. Acylation and sulfonylation with the corresponding acyl chlorides (RCOCl or RSO₂Cl where R=tBu, Ph, 4-Me-C₆H₄, 1- and 2-naphthyl) produced the corresponding 2-acylimino- and 2-sulfonylimino-thiazolidinones, respectively. Alkylation by MeI, allyl-bromide and BnBr produced mixtures of the respective N-alkylimino- and N,N'-dialkyl-imino-thiazolidinones, while reactions with 1,2-dibromoethane and 1,3-dibromopropane furnished spirocyclic 5,6-dihydro-imidazo[2,1-b]thiazolidin-3-one and 6,7-dihydro-5H-thiazolidino[3,2-a]pyrimidin-3-one, respectively. Removal of the O-benzoyl protecting groups by the Zemplén protocol led to test compounds most of which proved micromolar inhibitors of rabbit muscle glycogen phosphorylase b (RMGPb). Best inhibitors were the 2-benzoylimino- (Ki=9μM) and the 2-naphthoylimino-thiazolidinones (Ki=10 μM). Crystallographic studies of the unsubstituted spiro-thiazolidinone and the above most efficient inhibitors in complex with RMGPb confirmed the preference and inhibitory effect that aromatic (and especially 2-naphthyl) derivatives show for the catalytic site promoting the inactive conformation of the enzyme. PMID:25009003
DEFF Research Database (Denmark)
Bols, Mikael; Bjerre, Jeannette; Marinescu, Lavinia
2007-01-01
Enzymer har en enestående evne til at accelerere kemiske processer. Der forskes målrettet i at optimere enzymer baseret på cyclodextrin.......Enzymer har en enestående evne til at accelerere kemiske processer. Der forskes målrettet i at optimere enzymer baseret på cyclodextrin....
Classical dynamical description of heavy ion sequential fission
International Nuclear Information System (INIS)
Sequential fission processes are investigated in a classical fragmentation model. Dissipative forces are included. In the fissioning process the recoupling of excitational degrees of freedom to kinetic degrees of freedom is found important. 6 figures
Supplementary kinetic constants of charged particles
Ribaric, Marijan; Sustersic, Luka
2006-01-01
We put forward: (A) An improved description of classical, kinetic properties of a charged pointlike physical particle that consists, in addition to its mass and charge, also of the Eliezer and Bhabha kinetic constants; and (B) a proposal to evaluate these kinetic constants by considering the trajectories of charged particles in an acccelerator.
ENZYME KINETICS OF APLYSIN METABOLISM IN RAT LIVER MICROSOMES%海兔素在大鼠肝微粒体中的酶促反应动力学研究
Institute of Scientific and Technical Information of China (English)
丰暖; 梁惠; 马爱国; 张辉珍
2015-01-01
Objective To establish a HPLC method for the determination of aplysin in rat liver microsome, and study the enzyme kinetics of aplysin metabolism in rat liver microsome, as well as the effect of CYP3A inhibitor ketoconazole. Methods A HPLC method was developed for the determination of aplysin. Aplysin was incubated in rat liver microsome for 30 min. The effects of different incubation times and liver microsomal protein concentrations on alysin metabolism were observed. Lineweave-Burk graphic method was used to calculate the enzyme kinetic parameters. Ketoconazole (0.5, 2, 5, 10, 20, 40 mg/L) was used to inhibit the metabolism of aplysin in vitro. Results The linear range of aplysia standard curve was 0.5-100 mg/L. The intra- and inter-day RSDs were less than 3.18%. The recovery rate was 96.19%-97.83%, and a good stability at room temperature for 24 h or at -200C for a week was confirmed. The best incubation conditions for aplysin metabolism in rat liver microsome were 30 min for incubation time and 1 mg/mL for protein concentration. The enzyme kinetic parameters were as follows: Km 19.72 mg/L, Vmax 0.35 mg/min/g protein, CLint 17.75 ml/(min·g) protein. Ketoconazole was inhibitory to the metabolism of aplysin in vitro. Conclusion The established HPLC method is fast, simple, specific and sensitive and applicable in the study of the enzyme kinetics of aplysin metabolism in rat liver microsome. CYP3A may be involved in the metabolism of aplysin.%目的建立测定大鼠肝微粒体孵育液中海兔素含量的高效液相色谱法（HPLC），研究海兔素在大鼠肝微粒体中代谢的酶动力学以及CYP3A特异性抑制剂酮康唑对其代谢反应的影响。方法考察不同孵育时间、肝微粒体蛋白浓度、海兔素浓度对代谢反应的影响，并采用双倒数作图法计算海兔素的酶促反应动力学参数；观察不同浓度酮康唑（0.5，2，5，10，20，40 mg/L）对海兔素体外代谢的影响。结果海兔素的
14. Enzymes as Biocatalysts for Lipid-based Bioproducts Processing
DEFF Research Database (Denmark)
Cheong, Ling-Zhi; Guo, Zheng; Fedosov, Sergey;
2012-01-01
enzymes kinetics. Understanding of enzyme kinetics is important especially in designing efficient reaction set-ups including type of bioreactors, reaction conditions and reusability of biocatalysts to ensure efficient running cost. A brief review of state-of-the-art in industrial applications of enzymes...
Institute of Scientific and Technical Information of China (English)
柳晓泉; 任亚丽; 钱之玉; 王广基
2000-01-01
AIM:To study the enzyme kinetics of nimodipine (NDP) metabolism and the effects of selective cytochrome P-450 (CYP-450) inhibitors on the metabolism of NDP in human liver microsomes in vitro. METHODS: Microsomes from six individual human liver specimens were used to perform enzyme kinetic studies and the kinetic parameters were estimated by Eadie-Hofstee equation. Various selective CYP-450 inhibitors were used to investigate their effects on the metabolism of NDP and the principal CYP-450 isoform involved in dehydrogenation of dihydropyridine ring of NDP in human liver microsomes. RESULTS: There was an important intersubject variability in NDP metabolism in human liver microsomes. For NDP dehydrogeuase activity, the Km value was (36 + 11 ) μmol and the Vm value was ( 17 + 7) μmol · g- 1· min- 1. The dehydrogenation of dihydropyridine ring of NDP was competitively inhibited by ketoconazole (Ket) and troleandomycin (TAO), and the Ki values for Ket and TAO were 0.59 and 122.2 μmol, respectively.Phenacetin ( Pnt ), quinidine ( Qui ), diethyldithiocarbamate (DDC), sulfaphenazole (Sul), and tranylcypromine (Tta) had a little or no inhibitory effects on the dehydrogenation of NDP. CONCLUSION: The intersubject variability of NDP pharmacokinetics was attributed to the metabolic polymorphism of NDP in liver.Cytochrome P-4503A (CYP3A) is involved in the dehydrogenation of dihydropyridine ring of NDP.%目的：在体外研究人肝微粒体中尼莫地平代谢的酶动力学及选择性的细胞色素P-450(CYP450)酶抑制剂对尼莫地平代谢的影响．方法：采用人肝微粒体研究尼莫地平脱氢酶的代谢动力学，运用Eadie-Hof-stee方程估算其动力学参数．在体外运用CYP450酶的选择性抑制剂探讨其对尼莫地平代谢的影响及人肝微粒体中参与尼莫地平二氢吡啶环脱氢代谢的CYP450酶．结果：尼莫地平在人肝微粒体中的代谢存在较大的个体差异，尼莫地平脱氢酶的Km为(36±11)
Directory of Open Access Journals (Sweden)
Claudia L. GARCÍA W.
2006-01-01
, texture, activity of water, humidity and Brix degrees; then its enzyme kinetics were studied by measuring the formation of brown colour with an UV-visible spectrophotometer at 420nm. The amount of total protein (enzyme was also quantified by the Bradford method (reading at 595 nm. Once the kinetics of each maturation stage were identified, a comparison was made among each of the groups by means of Repeated Measures Analysis of Variance, showing a marked and statistically significant difference among banana of young and old maturation stages in a decreasing manner, finding the minimum point of activity of the enzyme in the most advanced maturation stages.
Energy Technology Data Exchange (ETDEWEB)
Miyakawa, H. [Sasebo College of Technology, Nagasaki (Japan); Shiraishi, F. [Kyushu Institute of Technology, Fukuoka (Japan)
1998-05-10
The effect of nonuniform activity distribution in a porous support on the apparent kinetic parameters, Vm{sup app} and Km{sup app}, of a packed-bed immobilized enzyme reactor has been theoretically investigated. Vm{sup app} and Km{sup app} increase with the increase of external diffusional resistance, regardless of the type of nonuniform activity distribution. As the external diffusional resistance becomes significant, the apparent kinetic parameters became less dependent on the substrate concentration at the reactor inlet. Like the case of diffusional resistance or electrostatic field, the nonuniform activity distribution had a significant effect on Km{sup app}. 7 refs., 3 figs.
Directory of Open Access Journals (Sweden)
Nathália Ottoboni Galdino
2008-09-01
Full Text Available A análise da presença de enzimas oxidativas como a peroxidase (POD e a polifenoloxidase (PPO e o controle da atividade destas enzimas são importantes na preservação e no processamento de alimentos. Este trabalho teve por objetivo determinar a atividade enzimática da polifenoloxidase (PPO e da peroxidase (POD do palmito de pupunha, bem como avaliar o comportamento destas enzimas frente ao tratamento térmico e assim calcular a cinética de inativação térmica das mesmas para suas porções termorresistente e termolábil. Para a extração de peroxidase (POD e polifenoloxidase (PPO de palmito, utilizou-se solução tampão fosfato de sódio 100 mM com diferentes pHs (5,5; 6,0; 6,5 e 7,0. O melhor pH de extração da POD foi 5,5 e da PPO, 6,5. Estes extratos foram tratados em diferentes temperaturas (65, 70, 75 e 80 °C por períodos de 1 a 10 minutos. A POD e a PPO sofreram um decréscimo de 70 e 80%, respectivamente, em relação às suas atividades iniciais. As energias de ativação, nas temperaturas estudadas, para a porção termolábil e termorresistente da peroxidase foram 154,0 e 153,0 kJ.mol-1, respectivamente, enquanto que para a polifenoloxidase foram 26,3 e 27,0 kJ.mol-1, respectivamente. Resultados apresentaram valores que estão dentro da faixa de energia de ativação reportada para o processo de inativação térmica de enzimas.Analysis of oxidative enzymes such as peroxidase (POD and polyphenoloxidase (PPO and the control of the activity of these enzymes are important in food preservation and also in food processing. The aim of this work was to determine polyphenoloxidase (PPO and peroxidase (POD enzymatic activity in heart of palm, as well as to evaluate enzyme behavior during thermal treatment, determining the kinetics of thermal inactivation of the heat resistant and heat labile portions. For the extraction of peroxidase (POD and polyphenoloxidase (PPO from the heart of palm solution, 100 mM sodium phosphate buffer with
Bidirectional coherent classical communication
Harrow, Aram W.; Leung, Debbie W.
2005-01-01
A unitary interaction coupling two parties enables quantum or classical communication in both the forward and backward directions. Each communication capacity can be thought of as a tradeoff between the achievable rates of specific types of forward and backward communication. Our first result shows that for any bipartite unitary gate, bidirectional coherent classical communication is no more difficult than bidirectional classical communication — they have the same achievable rate regions. ...
Entanglement in Classical Optics
Ghose, Partha; Mukherjee, Anirban
2013-01-01
The emerging field of entanglement or nonseparability in classical optics is reviewed, and its similarities with and differences from quantum entanglement clearly pointed out through a recapitulation of Hilbert spaces in general, the special restrictions on Hilbert spaces imposed in quantum mechanics and the role of Hilbert spaces in classical polarization optics. The production of Bell-like states in classical polarization optics is discussed, and new theorems are proved to discriminate betw...
Classical, Semi-classical and Quantum Noise
Poor, H; Scully, Marlan
2012-01-01
David Middleton was a towering figure of 20th Century engineering and science and one of the founders of statistical communication theory. During the second World War, the young David Middleton, working with Van Fleck, devised the notion of the matched filter, which is the most basic method used for detecting signals in noise. Over the intervening six decades, the contributions of Middleton have become classics. This collection of essays by leading scientists, engineers and colleagues of David are in his honor and reflect the wide influence that he has had on many fields. Also included is the introduction by Middleton to his forthcoming book, which gives a wonderful view of the field of communication, its history and his own views on the field that he developed over the past 60 years. Focusing on classical noise modeling and applications, Classical, Semi-Classical and Quantum Noise includes coverage of statistical communication theory, non-stationary noise, molecular footprints, noise suppression, Quantum e...
Teleportation via classical entanglement
Rafsanjani, Seyed Mohammad Hashemi; Magaña-Loaiza, Omar S; Boyd, Robert W
2015-01-01
We present a classical counterpart to quantum teleportation that uses classical entanglement instead of quantum entanglement. In our implementation we take advantage of classical entanglement among three parties: orbital angular momentum (OAM), polarization, and the radial degrees of freedom of a beam of light. We demonstrate the teleportation of arbitrary OAM states, in the subspace spanned by any two OAM states, to the polarization of the same beam. Our letter presents the first classical demonstration of a commonly-perceived--quantum phenomenon that requires entanglement among more than two parties.
Controlled enzyme catalyzed heteropolysaccharide degradation
DEFF Research Database (Denmark)
Rasmussen, Louise Enggaard
The work presented in this PhD thesis has provided a better understanding of the enzyme kinetics and quantitative phenomena of the hydrolysis of xylan substrates by selected pure enzyme preparations. Furthermore, the options for producing specific substituted xylooligosaccharides from selected...... substrates by specific xylanase treatment have been examined. The kinetics of the enzymatic degradation of water-extractable wheat arabinoxylan (WE-AX) during designed treatments with selected monocomponent enzymes was investigated by monitoring the release of xylose and arabinose. The results of different...... effects between -xylosidase and the α-L-arabinofuranosidases on the xylose release were low as compared to the effect of xylanase addition with β-xylosidase, which increased the xylose release by ~25 times in 30 minutes. At equimolar addition levels of the four enzymes, the xylanase activity was thus rate...
DEFF Research Database (Denmark)
Villadsen, John
2015-01-01
his chapter predicts the specific rates of reaction by means of a mathematical expression, the kinetics of the reaction. This expression can be derived through a mechanistic interpretation of an enzymatically catalyzed reaction, but it is essentially of empirical nature for cell reactions. The...... models can be used in mass balances for design of processes under process conditions not yet studied experimentally. The value of the predictive kinetic model depends on the quality of the experimental data on which the model is based, and well-founded kinetic models for enzyme reactions have a...... considerable predictive power. This is also true for cell reaction models, when the model is used in its proper context. The chapter first discusses the kinetics for enzymatically catalyzed reactions (“enzyme reactions”). The kinetics can be derived from a mechanistic model. Then, the chapter derives empirical...
Purification and characterization of two fully deuterated enzymes
Crespi, H. L.; Katz, J. J.; Parmerter, S.; Rokop, S.
1969-01-01
Comparative data reveal little difference between kinetic and thermal stabilities of pure preparations of two ordinary enzymes and their fully deuterated counterparts. The effects of temperature on the enzymes proved to be consistent with earlier results.
Tang, J. Y.
2015-09-01
The Michaelis-Menten kinetics and the reverse Michaelis-Menten kinetics are two popular mathematical formulations used in many land biogeochemical models to describe how microbes and plants would respond to changes in substrate abundance. However, the criteria of when to use which of the two are often ambiguous. Here I show that these two kinetics are special approximations to the Equilibrium Chemistry Approximation kinetics, which is the first order approximation to the quadratic kinetics that solves the equation of enzyme-substrate complex exactly for a single enzyme single substrate biogeochemical reaction with the law of mass action and the assumption of quasi-steady-state for the enzyme-substrate complex and that the product genesis from enzyme-substrate complex is much slower than the equilibration between enzyme-substrate complexes, substrates and enzymes. In particular, I showed that the derivation of the Michaelis-Menten kinetics does not consider the mass balance constraint of the substrate, and the reverse Michaelis-Menten kinetics does not consider the mass balance constraint of the enzyme, whereas both of these constraints are taken into account in the Equilibrium Chemistry Approximation kinetics. By benchmarking against predictions from the quadratic kinetics for a wide range of substrate and enzyme concentrations, the Michaelis-Menten kinetics was found to persistently under-predict the normalized sensitivity ∂ ln v / ∂ ln k2+ of the reaction velocity v with respect to the maximum product genesis rate k2+, persistently over-predict the normalized sensitivity ∂ ln v / ∂ ln k1+ of v with respect to the intrinsic substrate affinity k1+, persistently over-predict the normalized sensitivity ∂ ln v / ∂ ln [ E ]T of v with respect the total enzyme concentration [ E ]T and persistently under-predict the normalized sensitivity ∂ ln v / ∂ ln [ S ]T of v with respect to the total substrate concentration [ S ]T. Meanwhile, the reverse Michaelis
Directory of Open Access Journals (Sweden)
J. Y. Tang
2015-09-01
Full Text Available The Michaelis–Menten kinetics and the reverse Michaelis–Menten kinetics are two popular mathematical formulations used in many land biogeochemical models to describe how microbes and plants would respond to changes in substrate abundance. However, the criteria of when to use which of the two are often ambiguous. Here I show that these two kinetics are special approximations to the Equilibrium Chemistry Approximation kinetics, which is the first order approximation to the quadratic kinetics that solves the equation of enzyme-substrate complex exactly for a single enzyme single substrate biogeochemical reaction with the law of mass action and the assumption of quasi-steady-state for the enzyme-substrate complex and that the product genesis from enzyme-substrate complex is much slower than the equilibration between enzyme-substrate complexes, substrates and enzymes. In particular, I showed that the derivation of the Michaelis–Menten kinetics does not consider the mass balance constraint of the substrate, and the reverse Michaelis–Menten kinetics does not consider the mass balance constraint of the enzyme, whereas both of these constraints are taken into account in the Equilibrium Chemistry Approximation kinetics. By benchmarking against predictions from the quadratic kinetics for a wide range of substrate and enzyme concentrations, the Michaelis–Menten kinetics was found to persistently under-predict the normalized sensitivity ∂ ln v / ∂ ln k2+ of the reaction velocity v with respect to the maximum product genesis rate k2+, persistently over-predict the normalized sensitivity ∂ ln v / ∂ ln k1+ of v with respect to the intrinsic substrate affinity k1+, persistently over-predict the normalized sensitivity ∂ ln v / ∂ ln [ E ]T of v with respect the total enzyme concentration [ E ]T and persistently under-predict the normalized sensitivity ∂ ln v / ∂ ln [ S ]T of v with respect to the total substrate concentration [ S ]T
Lectures on Classical Integrability
Torrielli, Alessandro
2016-01-01
We review some essential aspects of classically integrable systems. The detailed outline of the lectures consists of: 1. Introduction and motivation, with historical remarks; 2. Liouville theorem and action-angle variables, with examples (harmonic oscillator, Kepler problem); 3. Algebraic tools: Lax pairs, monodromy and transfer matrices, classical r-matrices and exchange relations, non-ultralocal Poisson brackets, with examples (non-linear Schroedinger model, principal chiral field); 4. Features of classical r-matrices: Belavin-Drinfeld theorems, analyticity properties, and lift of the classical structures to quantum groups; 5. Classical inverse scattering method to solve integrable differential equations: soliton solutions, spectral properties and the Gel'fand-Levitan-Marchenko equation, with examples (KdV equation, Sine-Gordon model). Prepared for the Durham Young Researchers Integrability School, organised by the GATIS network. This is part of a collection of lecture notes.
Institute of Scientific and Technical Information of China (English)
王宗瑞; 赵广荣
2012-01-01
4-Hydroxyphenylglycine aminotransferase which can synthesize D-phenylglycine transaminase is produced by Pseudomonas. The hpgt gene was synthesized through the codon optimization technology. The recombinant prokaryotic plasmid pCDF-hpgt was obtained. The plasmid was transformed into the competent cell E. coli BL21 (DE3). The recombinant His-HpgT protein was obtained after the optimized expression and purified by nickel chelate affinity chromatography method. The enzyme activity of the forward and reverse reactions was measured and the activity of the forward reaction reached 749mU/mg which was lower than the reverse, 2 257mU/mg. Also the optimized temperature and pH were measured, with the result of 35癚.anA 8.0. Other kinetic parameters and the mechanism analysis of enzyme characteristics were explained. The enzyme affinity to phenylglycine was higher than the glutamate which obtained by the Michaelis-Menten equation; and the reaction was inhibited by the lower concentration of phenylglyoxylic acid.%苯甘氨酸氨基转移酶(4-Hydroxyphenylglycine aminotransferase)是假单胞菌所产生的一种能够合成D-苯甘氨酸的重要转氨酶.利用密码子优化技术,合成苯甘氨酸转移酶基因.构建原核重组质粒pCDF-hpgt,转入感受态细胞E.coli BL21 (DE3),优化表达His-HpgT蛋白.利用Ni-NTA柱纯化技术获得高纯度的His-HpgT融合蛋白.分别测定融合蛋白在正反向反应中的酶活力单位及最佳的反应温度、pH值及其他动力学参数,并对该酶特性作相关的机理分析.测定结果表明,正向反应和反向反应的酶比活力分别为749mU/mg、2 257mU/mg,此酶分解苯甘氨酸的能力要强于合成苯甘氨酸；正向反应的最适温度与pH分别是35℃和8.0；由米氏方程得出该酶对苯甘氨酸的亲和力远大于谷氨酸；较低浓度的苯乙醛酸即可抑制反应的进行.
Introducing Michaelis-Menten Kinetics through Simulation
Halkides, Christopher J.; Herman, Russell
2007-01-01
We describe a computer tutorial that introduces the concept of the steady state in enzyme kinetics. The tutorial allows students to produce graphs of the concentrations of free enzyme, enzyme-substrate complex, and product versus time in order to learn about the approach to steady state. By using a range of substrate concentrations and rate…
21 CFR 862.2500 - Enzyme analyzer for clinical use.
2010-04-01
... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Enzyme analyzer for clinical use. 862.2500 Section... Instruments § 862.2500 Enzyme analyzer for clinical use. (a) Identification. An enzyme analyzer for clinical use is a device intended to measure enzymes in plasma or serum by nonkinetic or kinetic measurement...
Institute of Scientific and Technical Information of China (English)
阳海鹰; 钟玉环; 陈琳; 李桦; 庄笑梅
2015-01-01
目的：研究中药有效成分补骨脂素和异补骨脂素的细胞色素P450（CYP）酶促动力学特征，比较其结构和种属差异，为体内药代动力学特征的预测提供科学依据。方法建立补骨脂素和异补骨脂素的液相色谱串联质谱（LC-MS/MS）检测方法，在优化人和大鼠肝微粒体孵育体系和评价体外代谢稳定性的基础上，进行了代谢稳定性和酶促动力学研究，应用非线性回归法计算最大反应速率（Vmax）和米氏常数（Km）。结果应用建立的LC-MS/MS检测方法，补骨脂素、异补骨脂素在肝微粒体孵育液中定量范围为0.1~50.0μmol·L-1，线性关系良好，精密度和准确度等满足检测要求。体外代谢稳定性研究显示，当底物浓度为1μmol·L-1，蛋白浓度为0.5 g·L-1，孵育40 min内，补骨脂素和异补骨脂素在大鼠和人肝微粒体呈线性消除，体外半衰期分别为74.5，95.0，74.5和173.3 min。补骨脂素在大鼠和人肝微粒体中的Vmax分别为：（1.140±0.080）μmol·min-1·g-1蛋白，（0.620±0.060）μmol·min-1·g-1蛋白；Km分别为（12.9±0.3）μmol·L-1和（7.4±1.3）μmol·L-1。异补骨脂素在大鼠和人肝微粒体中的Vmax分别为（0.251±0.012）μmol·min-1·g-1蛋白和（0.103±0.014）μmol·min-1·g-1蛋白；Km分别为：（3.0±0.4）μmol·L-1和（3.4±0.7）μmol·L-1。结论补骨脂素和异补骨脂素的CYP酶促动力学特征及代谢稳定性具有一定的种属和结构差异，在大鼠两者基于CYP酶的代谢清除过程可能相似。而在人体，异补骨脂素的CYP代谢清除可能慢于补骨脂素，导致药代动力学特征的差异。%OBJECTIVE To investigate and compare the enzyme kinetic characters of psoralen (PRN)and isopsoralen(IPRN)in rat and human liver microsomes. METHODS PRN and IPRN in liver microsomes incubates were determined using LC-MS/MS. The enzyme kinetic and metabolic stability of PRN and IPRN were
Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory.
Gao, J
2016-01-01
Path-integral free energy perturbation (PI-FEP) theory is presented to directly determine the ratio of quantum mechanical partition functions of different isotopologs in a single simulation. Furthermore, a double averaging strategy is used to carry out the practical simulation, separating the quantum mechanical path integral exactly into two separate calculations, one corresponding to a classical molecular dynamics simulation of the centroid coordinates, and another involving free-particle path-integral sampling over the classical, centroid positions. An integrated centroid path-integral free energy perturbation and umbrella sampling (PI-FEP/UM, or simply, PI-FEP) method along with bisection sampling was summarized, which provides an accurate and fast convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. The PI-FEP method is illustrated by a number of applications, to highlight the computational precision and accuracy, the rule of geometrical mean in kinetic isotope effects, enhanced nuclear quantum effects in enzyme catalysis, and protein dynamics on temperature dependence of kinetic isotope effects. PMID:27498645
Grassmannians of classical buildings
Pankov, Mark
2010-01-01
Buildings are combinatorial constructions successfully exploited to study groups of various types. The vertex set of a building can be naturally decomposed into subsets called Grassmannians. The book contains both classical and more recent results on Grassmannians of buildings of classical types. It gives a modern interpretation of some classical results from the geometry of linear groups. The presented methods are applied to some geometric constructions non-related to buildings - Grassmannians of infinite-dimensional vector spaces and the sets of conjugate linear involutions. The book is self
Davidson and classical pragmatism
Directory of Open Access Journals (Sweden)
Paula Rossi
2007-06-01
Full Text Available In this paper I wish to trace some connections between Donald Davidson's work (1917-2003 and two major representatives of the classical pragmatist movement: Charles S. Peirce (1839-1914 and William James (1842-1910. I will start with a basic characterization of classical pragmatism; then, I shall examine certain conceptions in Peirce's and James' pragmatism, in order to establish affinities with Davidson´s thought. Finally, and bearing in mind the previous con-nections, I will reflect briefly on the relevance –often unrecognized- of classical pragmatist ideas in the context of contemporary philosophi-cal discussions.
Controlled enzyme catalyzed heteropolysaccharide degradation:Xylans
Rasmussen, Louise Enggaard; Meyer, Anne S.
2011-01-01
The work presented in this PhD thesis has provided a better understanding of the enzyme kinetics and quantitative phenomena of the hydrolysis of xylan substrates by selected pure enzyme preparations. Furthermore, the options for producing specific substituted xylooligosaccharides from selected substrates by specific xylanase treatment have been examined. The kinetics of the enzymatic degradation of water-extractable wheat arabinoxylan (WE-AX) during designed treatments with selected monocompo...
Physics of classical electromagnetism
Fujimoto, Minoru
2007-01-01
The classical electromagnetism described by the Maxwell equations constitutes a fundamental law in contemporary physics. Even with the advent of sophisticated new materials, the principles of classical electromagnetism are still active in various applied areas in today’s advanced communication techniques. Physics of Classical Electromagnetism, by Minoru Fujimoto, is written with concise introductory arguments emphasizing the original field concept, with an aim at understanding objectives in modern information technology. Following basic discussions of electromagnetism with a modernized approach, this book will provide readers with an overview of current problems in high-frequency physics. To further the reader’s understanding of the concepts and applications discussed, each illustration within the book shows the location of all active charges, and the author has provided many worked-out examples throughout the book. Physics of Classical Electromagnetism is intended for students in physics and engineering ...
Quirk, R
1984-11-01
The specialised medical knowledge about dancers' injuries is negligible compared with that which surrounds sports medicine. The author discusses his experience in the management of more than 2000 injuries sustained by dancers of classical ballet. PMID:6151832
Classical and Quantum Intertwine
Blanchard, Ph.; Jadczyk, A.
1993-01-01
Model interactions between classical and quantum systems are briefly discussed. These include: general measurement-like couplings, Stern-Gerlach experiment, model of a counter, quantum Zeno effect, SQUID-tank model.
Kinetic theory of nonideal gases and nonideal plasmas
Klimontovich, Yu L
2013-01-01
Kinetic Theory of Nonideal Gases and Nonideal Plasmas presents the fundamental aspects of the kinetic theory of gases and plasmas. The book consists of three parts, which attempts to present some of the ideas, methods and applications in the study of the kinetic processes in nonideal gases and plasmas. The first part focuses on the classical kinetic theory of nonideal gases. The second part discusses the classical kinetic theory of fully ionized plasmas. The last part is devoted to the quantum kinetic theory of nonideal gases and plasmas. A concluding chapter is included, which presents a shor
Horzela, Andrzej; Kapuscik, Edward
1993-01-01
An alternative picture of classical many body mechanics is proposed. In this picture particles possess individual kinematics but are deprived from individual dynamics. Dynamics exists only for the many particle system as a whole. The theory is complete and allows to determine the trajectories of each particle. It is proposed to use our picture as a classical prototype for a realistic theory of confined particles.
Davidson and classical pragmatism
Paula Rossi
2007-01-01
In this paper I wish to trace some connections between Donald Davidson's work (1917-2003) and two major representatives of the classical pragmatist movement: Charles S. Peirce (1839-1914) and William James (1842-1910). I will start with a basic characterization of classical pragmatism; then, I shall examine certain conceptions in Peirce's and James' pragmatism, in order to establish affinities with Davidson´s thought. Finally, and bearing in mind the previous con-nections, I will reflect brie...
Institute of Scientific and Technical Information of China (English)
刘莹; 王国丽
2011-01-01
To compare the differences of enzyme kinetics of puerarin and its crude extract metabolism via rat liver microsomes, a HPLC method was established for quantitative analysis of puerarin in liver microsomes incubation system with p-hydroxy benzoic acid as internal standard. An optimum incubation system was found and the parameters of kinetics were analyzed and calculated with the software of CraphPad Prism 5.0. In the metabolic system,the optimum incubated time was 20 min.and the optimum protein concentration of rat liver microsomes was 1.0 mg/mL. The Km, Vmax and Clint ( Vmax/Km) of monomeric puerarin were (0. 93 ±0. 17) μmol/L,(93.59 ±2. 82) nmol/min'mg and (97.49 ±1.07) mL/min'mg, respectively. Those of puerarin in crude extract were (1.02 ±0.09) u,mol/L, (22.48 ± 1. 53) nmol/min-mg and (22. 04 ± 1. 72) mL/min'mg, respectively. The Km values of two kinds of puerarin were similar,but their Vmax and Clint had significant differences. The Vmax values varied by 4.16 folds and the Clint values differed by 4.42 fold. The results showed that the metabolism of puerarin was faster than that of puerarin in crude extract via rat liver microsomes. Other components in Chinese herbs may influence the metabolism of the active ones.%为了研究葛根素单体和葛根提取物中的葛根素在大鼠肝微粒体中的代谢是否存在差异,建立微粒体孵育体系.采用高效液相色谱法测定葛根素在肝微粒体代谢系统中的含量,并应用GraphPad Prism 5.0软件分析数据,计算酶促反应动力学参数.在体外代谢系统中,葛根素单体的酶促反应动力学参数Km为(0.93±0.17)μmol/L,Vmax为(93.59±2.82) nmol/min·mg,CLint(Vmax／Km)为(100.6±1.07) mL/min·mg；葛根提取物中葛根素的相应的动力学参数分别为(1.02±0.09)μmol/L,(22.48±1.53) nmol/min· mg和(22.04±1.72) mL/min·mg.葛根素单体和葛根提取物中的葛根素在大鼠肝微粒体的代谢存在明显的差异,葛根素单体的代谢速度快于
DEFF Research Database (Denmark)
van Leeuwen, Theo; Djonov, Emilia
After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images.......After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images....
Energy Technology Data Exchange (ETDEWEB)
Motwani, Hitesh V., E-mail: hitesh.motwani@mmk.su.se; Törnqvist, Margareta
2014-12-15
1,3-Butadiene (BD) is a rodent and human carcinogen. In the cancer tests, mice have been much more susceptible than rats with regard to BD-induced carcinogenicity. The species-differences are dependent on metabolic formation/disappearance of the genotoxic BD epoxy-metabolites that lead to variations in the respective in vivo doses, i.e. “area under the concentration-time curve” (AUC). Differences in AUC of the most gentoxic BD epoxy-metabolite, diepoxybutane (DEB), are considered important with regard to cancer susceptibility. The present work describes: the application of cob(I)alamin for accurate measurements of in vitro enzyme kinetic parameters associated with BD epoxy-metabolites in human, mouse and rat; the use of published data on hemoglobin (Hb) adduct levels of BD epoxides from BD exposure studies on the three species to calculate the corresponding AUCs in blood; and a parallelogram approach for extrapolation of AUC of DEB based on the in vitro metabolism studies and adduct data from in vivo measurements. The predicted value of AUC of DEB for humans from the parallelogram approach was 0.078 nM · h for 1 ppm · h of BD exposure compared to 0.023 nM · h/ppm · h as calculated from Hb adduct levels observed in occupational exposure. The corresponding values in nM · h/ppm · h were for mice 41 vs. 38 and for rats 1.26 vs. 1.37 from the parallelogram approach vs. experimental exposures, respectively, showing a good agreement. This quantitative inter-species extrapolation approach will be further explored for the clarification of metabolic rates/pharmacokinetics and the AUC of other genotoxic electrophilic compounds/metabolites, and has a potential to reduce and refine animal experiments. - Highlights: • In vitro metabolism to in vivo dose extrapolation of butadiene metabolites was proposed. • A parallelogram approach was introduced to estimate dose (AUC) in humans and rodents. • AUC of diepoxybutane predicted in humans was 0.078 nM h/ppm h
International Nuclear Information System (INIS)
1,3-Butadiene (BD) is a rodent and human carcinogen. In the cancer tests, mice have been much more susceptible than rats with regard to BD-induced carcinogenicity. The species-differences are dependent on metabolic formation/disappearance of the genotoxic BD epoxy-metabolites that lead to variations in the respective in vivo doses, i.e. “area under the concentration-time curve” (AUC). Differences in AUC of the most gentoxic BD epoxy-metabolite, diepoxybutane (DEB), are considered important with regard to cancer susceptibility. The present work describes: the application of cob(I)alamin for accurate measurements of in vitro enzyme kinetic parameters associated with BD epoxy-metabolites in human, mouse and rat; the use of published data on hemoglobin (Hb) adduct levels of BD epoxides from BD exposure studies on the three species to calculate the corresponding AUCs in blood; and a parallelogram approach for extrapolation of AUC of DEB based on the in vitro metabolism studies and adduct data from in vivo measurements. The predicted value of AUC of DEB for humans from the parallelogram approach was 0.078 nM · h for 1 ppm · h of BD exposure compared to 0.023 nM · h/ppm · h as calculated from Hb adduct levels observed in occupational exposure. The corresponding values in nM · h/ppm · h were for mice 41 vs. 38 and for rats 1.26 vs. 1.37 from the parallelogram approach vs. experimental exposures, respectively, showing a good agreement. This quantitative inter-species extrapolation approach will be further explored for the clarification of metabolic rates/pharmacokinetics and the AUC of other genotoxic electrophilic compounds/metabolites, and has a potential to reduce and refine animal experiments. - Highlights: • In vitro metabolism to in vivo dose extrapolation of butadiene metabolites was proposed. • A parallelogram approach was introduced to estimate dose (AUC) in humans and rodents. • AUC of diepoxybutane predicted in humans was 0.078 nM h/ppm h
Illustrating Enzyme Inhibition Using Gibbs Energy Profiles
Bearne, Stephen L.
2012-01-01
Gibbs energy profiles have great utility as teaching and learning tools because they present students with a visual representation of the energy changes that occur during enzyme catalysis. Unfortunately, most textbooks divorce discussions of traditional kinetic topics, such as enzyme inhibition, from discussions of these same topics in terms of…
Enzyme Catalysis and the Gibbs Energy
Ault, Addison
2009-01-01
Gibbs-energy profiles are often introduced during the first semester of organic chemistry, but are less often presented in connection with enzyme-catalyzed reactions. In this article I show how the Gibbs-energy profile corresponds to the characteristic kinetics of a simple enzyme-catalyzed reaction. (Contains 1 figure and 1 note.)
Kosmidis, Kosmas; Karalis, Vangelis; Argyrakis, Panos; Macheras, Panos
2004-01-01
Two different approaches were used to study the kinetics of the enzymatic reaction under heterogeneous conditions to interpret the unusual nonlinear pharmacokinetics of mibefradil. Firstly, a detailed model based on the kinetic differential equations is proposed to study the enzymatic reaction under spatial constraints and in vivo conditions. Secondly, Monte Carlo simulations of the enzyme reaction in a two-dimensional square lattice, placing special emphasis on the input and output of the substrate were applied to mimic in vivo conditions. Both the mathematical model and the Monte Carlo simulations for the enzymatic reaction reproduced the classical Michaelis-Menten (MM) kinetics in homogeneous media and unusual kinetics in fractal media. Based on these findings, a time-dependent version of the classic MM equation was developed for the rate of change of the substrate concentration in disordered media and was successfully used to describe the experimental plasma concentration-time data of mibefradil and derive estimates for the model parameters. The unusual nonlinear pharmacokinetics of mibefradil originates from the heterogeneous conditions in the reaction space of the enzymatic reaction. The modified MM equation can describe the pharmacokinetics of mibefradil as it is able to capture the heterogeneity of the enzymatic reaction in disordered media. PMID:15345531
Classically-Controlled Quantum Computation
Perdrix, Simon; Jorrand, Philippe
2004-01-01
Quantum computations usually take place under the control of the classical world. We introduce a Classically-controlled Quantum Turing Machine (CQTM) which is a Turing Machine (TM) with a quantum tape for acting on quantum data, and a classical transition function for a formalized classical control. In CQTM, unitary transformations and measurements are allowed. We show that any classical TM is simulated by a CQTM without loss of efficiency. The gap between classical and quantum computations, ...
Learning Classical Music Club
2010-01-01
There is a new CERN Club called “Learning Classical Music at CERN”. We are aiming to give classical music lessons for different instruments (see link) for students from 5 to 100 years old. We are now ready to start our activities in the CERN barracks. We are now in the enrollment phase and hope to start lessons very soon ! Club info can be found in the list of CERN Club: http://user.web.cern.ch/user/Communication/SocialLifeActivities/Clubs/Clubs.html Salvatore Buontempo Club President
Dzhunushaliev, V D
1997-01-01
The spherically symmetric solution in classical SU(3) Yang - Mills theory is found. It is supposed that such solution describes a classical quark. It is regular in origin and hence the interaction between two quarks is small on the small distance. The obtained solution has the singularity on infinity. It is possible that is the reason why the free quark cannot exist. Evidently, nonlocality of this object leads to the fact that in quantum chromodynamic the difficulties arise connected with investigation of quarks interaction on large distance.
Brehm, Enrico M
2016-01-01
In this work, we introduce classical holographic codes. These can be understood as concatenated probabilistic codes and can be represented as networks uniformly covering hyperbolic space. In particular, classical holographic codes can be interpreted as maps from bulk degrees of freedom to boundary degrees of freedom. Interestingly, they are shown to exhibit features similar to those expected from the AdS/CFT correspondence. Among these are a version of the Ryu-Takayanagi formula and intriguing properties regarding bulk reconstruction and boundary representations of bulk operations. We discuss the relation of our findings with expectations from AdS/CFT and, in particular, with recent results from quantum error correction.
Classical mechanics with Maxima
Timberlake, Todd Keene
2016-01-01
This book guides undergraduate students in the use of Maxima—a computer algebra system—in solving problems in classical mechanics. It functions well as a supplement to a typical classical mechanics textbook. When it comes to problems that are too difficult to solve by hand, computer algebra systems that can perform symbolic mathematical manipulations are a valuable tool. Maxima is particularly attractive in that it is open-source, multiple-platform software that students can download and install free of charge. Lessons learned and capabilities developed using Maxima are easily transferred to other, proprietary software.
Elementary classical hydrodynamics
Chirgwin, B H; Langford, W J; Maxwell, E A; Plumpton, C
1967-01-01
Elementary Classical Hydrodynamics deals with the fundamental principles of elementary classical hydrodynamics, with emphasis on the mechanics of inviscid fluids. Topics covered by this book include direct use of the equations of hydrodynamics, potential flows, two-dimensional fluid motion, waves in liquids, and compressible flows. Some general theorems such as Bernoulli's equation are also considered. This book is comprised of six chapters and begins by introducing the reader to the fundamental principles of fluid hydrodynamics, with emphasis on ways of studying the motion of a fluid. Basic c
Classic Problems of Probability
Gorroochurn, Prakash
2012-01-01
"A great book, one that I will certainly add to my personal library."—Paul J. Nahin, Professor Emeritus of Electrical Engineering, University of New Hampshire Classic Problems of Probability presents a lively account of the most intriguing aspects of statistics. The book features a large collection of more than thirty classic probability problems which have been carefully selected for their interesting history, the way they have shaped the field, and their counterintuitive nature. From Cardano's 1564 Games of Chance to Jacob Bernoulli's 1713 Golden Theorem to Parrondo's 1996 Perplexin
International Nuclear Information System (INIS)
The classical nova outburst occurs on the white dwarf component in a close binary system. Nova systems are members of the general class of cataclysmic variables and other members of the class are the Dwarf Novae, AM Her variables, Intermediate Polars, Recurrent Novae, and some of the Symbiotic variables. Although multiwavelength observations have already provided important information about all of these systems, in this review I will concentrate on the outbursts of the classical and recurrent novae and refer to other members of the class only when necessary. 140 refs., 1 tab
Frank, Irmgard
2016-01-01
The notion from ab-initio molecular dynamics simulations that nuclear motion is best described by classical Newton dynamics instead of the time-dependent Schr{\\"o}dinger equation is substantiated. In principle a single experiment should bring clarity. Caution is however necessary, as temperature dependent effects must be eliminated when trying to determine the existence of a zero-point energy.
Strong Coupling and Classicalization
Dvali, Gia
2016-01-01
Classicalization is a phenomenon in which a theory prevents itself from entering into a strong-coupling regime, by redistributing the energy among many weakly-interacting soft quanta. In this way, the scattering process of some initial hard quanta splits into a large number of soft elementary processes. In short, the theory trades the strong coupling for a high-multiplicity of quanta. At very high energies, the outcome of such a scattering experiment is a production of soft states of high occupation number that are approximately classical. It is evident that black hole creation in particle collision at super-Planckian energies is a result of classicalization, but there is no a priory reason why this phenomenon must be limited to gravity. If the hierarchy problem is solved by classicalization, the LHC has a chance of detecting a tower of new resonances. The lowest-lying resonances must appear right at the strong coupling scale in form of short-lived elementary particles. The heavier members of the tower must b...
Czech Academy of Sciences Publication Activity Database
Axelsson, Owe
1. Berlin, Heidelberg: Springer-Verlag, 2013 - (Björm, E.), s. 205-224 ISBN 978-3-540-70528-4 Institutional support: RVO:68145535 Keywords : classical iterative methods * applied computational mathematics * encyclopedia Subject RIV: BA - General Mathematics http://www.springerreference.com/docs/ navigation .do?m=Encyclopedia+of+Applied+and+Computational+Mathematics+%28Mathematics+and+Statistics%29-book224
Classical and quantum satisfiability
de Araújo, Anderson; 10.4204/EPTCS.81.6
2012-01-01
We present the linear algebraic definition of QSAT and propose a direct logical characterization of such a definition. We then prove that this logical version of QSAT is not an extension of classical satisfiability problem (SAT). This shows that QSAT does not allow a direct comparison between the complexity classes NP and QMA, for which SAT and QSAT are respectively complete.
Why Study Classical Languages?
Lieberman, Samuel
This speech emphasizes the significance of living literatures and living cultures which owe a direct debt to the Romans and the Greeks from whom they can trace their origins. After commenting on typical rejoinders to the question "Why study classical languages?" and poking fun at those who advance jaded, esoteric responses, the author dispels the…
Camic, Charles
2008-01-01
They seem the perfect bookends for the social psychologist's collection of "classics" of the field. Two volumes, nearly identical in shape and weight and exactly a century old in 2008--each professing to usher "social psychology" into the world as they both place the hybrid expression square in their titles but then proceed to stake out the field…
Mecanica Clasica (Classical Mechanics)
Rosu, H. C.
1999-01-01
First Internet graduate course on Classical Mechanics in Spanish (Castellano). This is about 80% of the material I covered during the January-June 1999 semester at IFUG in the Mexican city of Leon. English and Romanian versions are in (slow) progress and hopefully will be arXived. For a similar course on Quantum Mechanics, see physics/9808031
Classical Mythology. Fourth Edition.
Morford, Mark P. O.; Lenardon, Robert J.
Designed for students with little or no background in classical literature, this book introduces the Greek and Roman myths of creation, myths of the gods, Greek sagas and local legends, and presents contemporary theories about the myths. Drawing on Homer, Hesiod, Pindar, Vergil, and others, the book provides many translations and paraphrases of…
Huddleston, Gregory H.
1993-01-01
Describes one teacher's methods for introducing to secondary English students the concepts of Classicism and Romanticism in relation to pictures of gardens, architecture, music, and literary works. Outlines how the unit leads to a writing assignment based on collected responses over time. (HB)
Mecanica Clasica (Classical Mechanics)
Rosu, H C
1999-01-01
First Internet undergraduate course on Classical Mechanics in Spanish (Castellano). This is about 80% of the material I covered during the January-June 1999 semester at IFUG in the Mexican city of Leon. English and Romanian versions are in (slow) progress and hopefully will be arXived. For a similar course on Quantum Mechanics, see physics/9808031
Classical electromagnetic radiation
Heald, Mark A
2012-01-01
Newly corrected, this highly acclaimed text is suitable for advanced physics courses. The author presents a very accessible macroscopic view of classical electromagnetics that emphasizes integrating electromagnetic theory with physical optics. The survey follows the historical development of physics, culminating in the use of four-vector relativity to fully integrate electricity with magnetism.
Nelson, Norman N.; Fisch, Forest N.
1973-01-01
Discussed are techniques of presentation and solution of the Classical Cake Problem. A frosted cake with a square base is to be cut into n pieces with the volume of cake and frosting the same for each piece. Needed are minimal geometric concepts and the formula for the volume of a prism. (JP)
DEFF Research Database (Denmark)
Feldt-Rasmussen, B; Dinesen, B; Deckert, M
1985-01-01
An enzyme linked immunoadsorbent assay for urinary albumin using commercially available reagents is described. The assay range is 2.5-120 micrograms/l. When samples are analysed in two standard dilutions, the assayable albumin concentration range is 2.5-240 mg/l, covering the clinical range from...
McBroom, Rachel; Oliver-Hoyo, Maria T.
2007-01-01
Many students view biology and chemistry as two unrelated, separate sciences; how these courses are generally taught in high schools may do little to change that impression. The study of enzymes provide a great opportunity for both biology and chemistry teachers to share with students the interdisciplinary nature of science. This article describes…
Analogies between classical statistical mechanics and quantum mechanics
International Nuclear Information System (INIS)
Some analogies between nonequilibrium classical statistical mechanics and quantum mechanics, at the level of the Liouville equation and at the kinetic level, are commented on. A theorem, related to the Vlasov equation applied to a plasma, is proved. The theorem presents an analogy with Ehrenfest's theorem of quantum mechanics. An analogy between the plasma kinetic theory and Bohm's quantum theory with 'hidden variables' is also shown. (Author)
Shape-Dependent Biomimetic Inhibition of Enzyme by Nanoparticles and Their Antibacterial Activity.
Cha, Sang-Ho; Hong, Jin; McGuffie, Matt; Yeom, Bongjun; VanEpps, J Scott; Kotov, Nicholas A
2015-09-22
Enzyme inhibitors are ubiquitous in all living systems, and their biological inhibitory activity is strongly dependent on their molecular shape. Here, we show that small zinc oxide nanoparticles (ZnO NPs)-pyramids, plates, and spheres-possess the ability to inhibit activity of a typical enzyme β-galactosidase (GAL) in a biomimetic fashion. Enzyme inhibition by ZnO NPs is reversible and follows classical Michaelis-Menten kinetics with parameters strongly dependent on their geometry. Diverse spectroscopic, biochemical, and computational experimental data indicate that association of GAL with specific ZnO NP geometries interferes with conformational reorganization of the enzyme necessary for its catalytic activity. The strongest inhibition was observed for ZnO nanopyramids and compares favorably to that of the best natural GAL inhibitors while being resistant to proteases. Besides the fundamental significance of this biomimetic function of anisotropic NPs, their capacity to serve as degradation-resistant enzyme inhibitors is technologically attractive and is substantiated by strong shape-specific antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA), endemic for most hospitals in the world. PMID:26325486
Marklof, Jens
2009-01-01
One of the central challenges in kinetic theory is the derivation of macroscopic evolution equations--describing, for example, the dynamics of an electron gas--from the underlying fundamental microscopic laws of classical or quantum mechanics. An iconic mathematical model in this research area is the Lorentz gas, which describes an ensemble of non-interacting point particles in an infinite array of spherical scatterers. In the case of a disordered scatterer configuration, the classical results by Gallavotti, Spohn and Boldrighini-Bunimovich-Sinai show that the time evolution of a macroscopic particle cloud is governed, in the limit of small scatterer density (Boltzmann-Grad limit), by the linear Boltzmann equation. In this lecture I will discuss the recent discovery that for a periodic configuration of scatterers the linear Boltzmann equation fails, and the random flight process that emerges in the Boltzmann-Grad limit is substantially more complicated. The key ingredient in the description of the limiting st...
Directory of Open Access Journals (Sweden)
Roberval Soares Lima
2007-02-01
Full Text Available Initially, all major factors that affect the rate of the AldH-catalyzed reaction (enzyme concentration, substrate concentration, temperature and pH were investigated. Optimal activity was observed between pH values of 7.5 and 9.5 in the temperature range of 25 to 50 ºC. Kinetic parameters, such as Km (2.92 µmol L-1 and Vmax (1.33 10-2 µmol min-1 demonstrate a strong enzyme-substrate affinity. The sensors were based on screen-printed electrodes modified with the Meldola Blue-Reinecke salt (MBRS combination. Operational conditions (NAD+ and substrate contents, enzyme loading and response time were optimized. Also, two enzyme immobilization procedures were tested: entrapment in poly(vinyl alcohol bearing styrylpyridinium groups (PVA-SbQ and crosslinking with glutaraldehyde. Chronoamperometry was employed to observe the biosensor responses during enzymatic hydrolysis of propionaldehyde and also to construct inhibition curves with maneb and zineb fungicides. Best results were found with the following conditions: [NAD+] = 0.25 mmol L-1; [propionaldehyde] = 80 µmol L-1; enzyme loading = 0.8 U per electrode; response time = 10 min, and inhibition time = 10 min. Current intensities around 103 ± 13 nA with the sensors and good stability was obtained for both immobilization procedures. Detection limits, calculated using 10% inhibition were 31.5 µg L-1 and 35 µg L-1 for maneb and zineb, respectively. Results obtained with other MBRS-modified electrodes consisting of mono and bi-enzymic sensors were compared. The ability to catalyze NADH oxidation by MB was also highlighted.
Quantum emulation of classical dynamics
Margolus, Norman
2011-01-01
In statistical mechanics, it is well known that finite-state classical lattice models can be recast as quantum models, with distinct classical configurations identified with orthogonal basis states. This mapping makes classical statistical mechanics on a lattice a special case of quantum statistical mechanics, and classical combinatorial entropy a special case of quantum entropy. In a similar manner, finite-state classical dynamics can be recast as finite-energy quantum dynamics. This mapping...
Innovative Therapy for Classic Galactosemia - Tale of Two HTS
Tang, M; Odejinmi, SI; Vankayalapati, H; Wierenga, K; Lai, K.
2011-01-01
Classic Galactosemia is an autosomal recessive disorder caused by the deficiency of galactose-1-phosphate uridylyltransferase (GALT), one of the key enzymes in the Leloir pathway of galactose metabolism. While the neonatal morbidity and mortality of the disease are now mostly prevented by newborn screening and galactose restriction, long-term outcome for older children and adults with this disorder remains unsatisfactory. The pathophysiology of Classic Galactosemia is complex, but there is co...
International Nuclear Information System (INIS)
The author has studied the kinetics of heparin and heparin fractions after intravenous administration in humans and in this thesis the results of this study are reported. Basic knowledge about the physico-chemical properties of heparin and its interactions with proteins resulting in anticoagulant and lipolytic effects are discussed in a review (chapter II), which also comprises some clinical aspects of heparin therapy. In chapter III the kinetics of the anticoagulant effect are described after intravenous administration of five commercial heparin preparations. A mathematical model is presented that fits best to these kinetics. The kinetics of the anticoagulant and lipolytic effects after intravenous injection of various 35S-radiolabelled heparin fractions and their relationship with the disappearance of the radiolabel are described in chapter IV. Chapter V gives a description of the kinetics of two radiolabels after injection of in vitro formed complexes consisting of purified, 125I-radiolabelled antithrombin III and various 35S-radiolabelled heparin fractions. (Auth.)
Randomness: quantum versus classical
Khrennikov, Andrei
2015-01-01
Recent tremendous development of quantum information theory led to a number of quantum technological projects, e.g., quantum random generators. This development stimulates a new wave of interest in quantum foundations. One of the most intriguing problems of quantum foundations is elaboration of a consistent and commonly accepted interpretation of quantum state. Closely related problem is clarification of the notion of quantum randomness and its interrelation with classical randomness. In this short review we shall discuss basics of classical theory of randomness (which by itself is very complex and characterized by diversity of approaches) and compare it with irreducible quantum randomness. The second part of this review is devoted to the information interpretation of quantum mechanics (QM) in the spirit of Zeilinger and Brukner (and QBism of Fuchs et al.) and physics in general (e.g., Wheeler's "it from bit") as well as digital philosophy of Chaitin (with historical coupling to ideas of Leibnitz). Finally, w...
Classical and statistical thermodynamics
Rizk, Hanna A
2016-01-01
This is a text book of thermodynamics for the student who seeks thorough training in science or engineering. Systematic and thorough treatment of the fundamental principles rather than presenting the large mass of facts has been stressed. The book includes some of the historical and humanistic background of thermodynamics, but without affecting the continuity of the analytical treatment. For a clearer and more profound understanding of thermodynamics this book is highly recommended. In this respect, the author believes that a sound grounding in classical thermodynamics is an essential prerequisite for the understanding of statistical thermodynamics. Such a book comprising the two wide branches of thermodynamics is in fact unprecedented. Being a written work dealing systematically with the two main branches of thermodynamics, namely classical thermodynamics and statistical thermodynamics, together with some important indexes under only one cover, this treatise is so eminently useful.
Computation in Classical Mechanics
Timberlake, Todd
2007-01-01
There is a growing consensus that physics majors need to learn computational skills, but many departments are still devoid of computation in their physics curriculum. Some departments may lack the resources or commitment to create a dedicated course or program in computational physics. One way around this difficulty is to include computation in a standard upper-level physics course. An intermediate classical mechanics course is particularly well suited for including computation. We discuss the ways we have used computation in our classical mechanics courses, focusing on how computational work can improve students' understanding of physics as well as their computational skills. We present examples of computational problems that serve these two purposes. In addition, we provide information about resources for instructors who would like to include computation in their courses.
International Nuclear Information System (INIS)
Exchange of data and algorithms among accelerator physics programs is difficult because of unnecessary differences in input formats and internal data structures. To alleviate these problems a C++ class library called CLASSIC (Class Library for Accelerator System Simulation and Control) is being developed with the goal to provide standard building blocks for computer programs used in accelerator design. It includes modules for building accelerator lattice structures in computer memory using a standard input language, a graphical user interface, or a programmed algorithm. It also provides simulation algorithms. These can easily be replaced by modules which communicate with the control system of the accelerator. Exchange of both data and algorithm between different programs using the CLASSIC library should present no difficulty
Directory of Open Access Journals (Sweden)
Adriana Coutinho de Azevedo Guimarães
2008-06-01
Full Text Available This study aimed to elucidate what injuries are most likely to occur due to classical ballet practice. The research used national and international bibliography. The bibliography analysis indicated that technical and esthetical demands lead to a practice of non-anatomical movements, causing the ballet dancer to suffer from a number of associated lesions. Most of the injuries are caused by technical mistakes and wrong training. Troubles in children are usually due to trying to force external rotation at hip level and to undue use of point ballet slippers. The commonest lesions are in feet and ankles, followed by knees and hips. The rarest ones are in the upper limbs. These injuries are caused by exercise excess, by repetitions always in the same side and by wrong and early use of point slippers. The study reached the conclusion that incorrect application of classical ballet technique predisposes the dancers to characteristic injuries.
Classical Diophantine equations
1993-01-01
The author had initiated a revision and translation of "Classical Diophantine Equations" prior to his death. Given the rapid advances in transcendence theory and diophantine approximation over recent years, one might fear that the present work, originally published in Russian in 1982, is mostly superseded. That is not so. A certain amount of updating had been prepared by the author himself before his untimely death. Some further revision was prepared by close colleagues. The first seven chapters provide a detailed, virtually exhaustive, discussion of the theory of lower bounds for linear forms in the logarithms of algebraic numbers and its applications to obtaining upper bounds for solutions to the eponymous classical diophantine equations. The detail may seem stark--- the author fears that the reader may react much as does the tourist on first seeing the centre Pompidou; notwithstanding that, Sprind zuk maintainsa pleasant and chatty approach, full of wise and interesting remarks. His emphases well warrant, ...
Dutton, P. Leslie; Moser, Christopher C.
2011-01-01
Fundamental research into bioinorganic catalysis of the kind presented at this Faraday Discussion has the potential to turn inspiration drawn from impressive natural energy and chemical transformations into artificial catalyst constructions useful to mankind. Creating bio-inspired artificial constructions requires a level of understanding well beyond simple description of structures and mechanisms of natural enzymes. To be useful, such description must be augmented by a practical sense of str...
Are superparamagnetic spins classical?
Garanin, D. A.
2008-01-01
Effective giant spins of magnetic nanoparticles are considered classically in the conventional theory of superparamagnetism based on the Landau-Lifshitz-Langevin equation. However, microscopic calculations for a large spin with uniaxial anisotropy, coupled to the lattice via the simplest generic mechanism, show that the results of the conventional theory are not reproduced in the limit S ->\\infty. In particular, the prefactor Gamma_0 in the Arrhenius escape rate over the barrier Gamma =Gamma_...
Adriana Coutinho de Azevedo Guimarães; Joseani Paulini Neves Simas
2008-01-01
This study aimed to elucidate what injuries are most likely to occur due to classical ballet practice. The research used national and international bibliography. The bibliography analysis indicated that technical and esthetical demands lead to a practice of non-anatomical movements, causing the ballet dancer to suffer from a number of associated lesions. Most of the injuries are caused by technical mistakes and wrong training. Troubles in children are usually due to trying to force external ...
Institute of Scientific and Technical Information of China (English)
WANG HAIRONG
2010-01-01
@@ North Korea's Phibada Opera Troupe arrived in Beijing on May3,bringing with it a Korean opera adapted from China's classic novel A Dream of Red Mansions written by Cao Xueqin(around 1715-63),a great novelist of the Qing Dynasty(1644-1911).The troupe,invited by the Chinese Ministry of Culture,is one of the largest performing groups having visited China in recent years.
Computation in Classical Mechanics
Timberlake, Todd; Hasbun, Javier E.
2007-01-01
There is a growing consensus that physics majors need to learn computational skills, but many departments are still devoid of computation in their physics curriculum. Some departments may lack the resources or commitment to create a dedicated course or program in computational physics. One way around this difficulty is to include computation in a standard upper-level physics course. An intermediate classical mechanics course is particularly well suited for including computation. We discuss th...
Sociology and Classical Liberalism
KLEIN, Daniel; Stern, Lotta
2005-01-01
We advocate the development of a classical-liberal character within professional sociology. The American Sociological Association (ASA) is taken as representative of professional sociology in the United States. We review the ASA’s activities and organizational statements, to show the association’s leftist character. Internal criticism is often very uneasy about leftist domination of the field. We present survey results establishing that, in voting and in policy views, the ASA membership is mo...
Rogers, Ibram
2008-01-01
As a 26-year-old English teacher in 1958, Chinua Achebe had no idea that the book he was writing would become a literary classic, not only in Africa but also throughout the world. He could only try to articulate the feelings he had for his countrymen and women. Achebe had a burning desire to tell the true story of Africa and African humanity. The…
Strong, John
2004-01-01
An intermediate course in optics, this volume explores both experimental and theoretical concepts, offering practical knowledge of geometrical optics that will enhance students' comprehension of any relevant applied science. Its exposition of the concepts of classical optics is presented with a minimum of mathematical detail but presumes some knowledge of calculus, vectors, and complex numbers.Subjects include light as wave motion; superposition of wave motions; electromagnetic waves; interaction of light and matter; velocities and scattering of light; polarized light and dielectric boundarie
Diffusion of Classical Solitons
Dziarmaga, J.; Zakrzewski, W.
1998-01-01
We study the diffusion and deformation of classical solitons coupled to thermal noise. The diffusion coefficient for kinks in the $\\phi^4$ theory is predicted up to the second order in $kT$. The prediction is verified by numerical simulations. Multiskyrmions in the vector O(3) sigma model are studied within the same formalism. Thermal noise results in a diffusion on the multisoliton collective coordinate space (moduli space). There are entropic forces which tend, for example, to bind pairs of...
Waters, C Kenneth
2004-12-01
I present an account of classical genetics to challenge theory-biased approaches in the philosophy of science. Philosophers typically assume that scientific knowledge is ultimately structured by explanatory reasoning and that research programs in well-established sciences are organized around efforts to fill out a central theory and extend its explanatory range. In the case of classical genetics, philosophers assume that the knowledge was structured by T. H. Morgan's theory of transmission and that research throughout the later 1920s, 30s, and 40s was organized around efforts to further validate, develop, and extend this theory, I show that classical genetics was structured by an integration of explanatory reasoning (associated with the transmission theory) and investigative strategies (such as the 'genetic approach'). The investigative strategies, which have been overlooked in historical and philosophical accounts, were as important as the so-called laws of Mendelian genetics. By the later 1920s, geneticists of the Morgan school were no longer organizing research around the goal of explaining inheritance patterns; rather, they were using genetics to investigate a range of biological phenomena that extended well beyond the explanatory domain of transmission theories. Theory-biased approaches in history and philosophy of science fail to reveal the overall structure of scientific knowledge and obscure the way it functions. PMID:15682554
On the Galilean covariance of classical mechanics
International Nuclear Information System (INIS)
A Galilean covariant approach to classical mechanics of a single interacting particle is described. In this scheme constitutive relations defining forces are rejected and acting forces are determined by some fundamental differential equations. It is shown that total energy of the interacting particle transforms under Galilean transformations differently from the kinetic energy. The statement is illustrated on the exactly solvable examples of the harmonic oscillator and the case of constant forces and also, in the suitable version of the perturbation theory, for the anharmonic oscillator. (author)
Schoonen, Lise; Nolte, Roeland J M; van Hest, Jan C M
2016-08-14
The study of enzyme behavior in small nanocompartments is crucial for the understanding of biocatalytic processes in the cellular environment. We have developed an enzymatic conjugation strategy to attach a model enzyme to the interior of a cowpea chlorotic mottle virus capsid. It is shown that with this methodology high encapsulation efficiencies can be achieved. Additionally, we demonstrate that the encapsulation does not affect the enzyme performance in terms of a decreased activity or a hampered substrate diffusion. Finally, it is shown that the encapsulated enzymes are protected against proteases. We believe that our strategy can be used to study enzyme kinetics in an environment that approaches physiological conditions. PMID:27407020
THERMODYNAMICAL LAWS AND KINETICS OF THERMAL-INACTIVATION
Directory of Open Access Journals (Sweden)
Sheelendra Kumar Yadav
2016-02-01
Full Text Available This paper presented the analysis of the fourth law of thermodynamics, the nature of the dark energy and potential to generate such an energy. This interpretation is based on geometric modeling of space as a phase fluid and the momentum generated by the time. Based on this analysis and by the properties of the classical thermo dynamics, the fourth law of thermodynamics is proposed to account for the dominating energy in the universe. Such a law is very important to account for the dominating component of the universe, the 70 % dark energy that is behind the accelerated expansion of the universe. The effect of heat treatment on the activities of quality related.Enzymes: peroxides (POD, polyphoneoxides(PPOetc.studied over a temperature range of 50 to 800C using mathematical analysis of the kinetic and thermodynamic parameters for the thermo inactivation of the enzymes .For peroxides in the first phase of inactivation indicates that a high amount of energy was required to initiate its de maturation, and supports why it is used as a marker for inactivation of quality-related enzymes. Analysis of the fourth law of thermodynamics and dark energy is proposed. Such a law presents an explanation of the expansion of the universe by the negative pressure generated by the momentum associated with as a mechanical variable.
Directory of Open Access Journals (Sweden)
Laurent Chusseau
2013-02-01
Full Text Available We show that the thermodynamics of ideal gases may be derived solely from the Democritean concept of corpuscles moving in vacuum plus a principle of simplicity, namely that these laws are independent of the laws of motion, aside from the law of energy conservation. Only a single corpuscle in contact with a heat bath submitted to a z and t-invariant force is considered. Most of the end results are known but the method appears to be novel. The mathematics being elementary, the present paper should facilitate the understanding of the ideal gas law and of classical thermodynamics even though not-usually-taught concepts are being introduced.
Mechanics classical and quantum
Taylor, T T
2015-01-01
Mechanics: Classical and Quantum explains the principles of quantum mechanics via the medium of analytical mechanics. The book describes Schrodinger's formulation, the Hamilton-Jacobi equation, and the Lagrangian formulation. The author discusses the Harmonic Oscillator, the generalized coordinates, velocities, as well as the application of the Lagrangian formulation to systems that are partially or entirely electromagnetic in character under certain conditions. The book examines waves on a string under tension, the isothermal cavity radiation, and the Rayleigh-Jeans result pertaining to the e
Institute of Scientific and Technical Information of China (English)
2002-01-01
FIVE years ago, an ancient Chinese air was beamed to outer space as a PR exercise. To humankind, music is a universal language, so the tune seemed an ideal medium for communication with extraterrestrial intelligence. So far there has been no response, but it is believed that the tune will play for a billion years, and eventually be heard and understood. The melody is called High Mountain and Flowing Stream, and it is played on the guqin, a seven-stringed classical musical instrument similar to the zither.
Institute of Scientific and Technical Information of China (English)
C.S. Chang
2007-01-01
@@ The ITER relevant edge plasmas in the present day experiments are in the kinetic regime,with the pedestalions in the long-mean-free-path banans collisionality regime and the pedestal electrons in the banana-plateau regime.
Enzyme immobilization by means of ultrafiltration techniques.
Scardi, V; Cantarella, M; Gianfreda, L; Palescandolo, R; Alfani, F; Greco, G
1980-01-01
Unstirred, plane membrane, ultrafiltration cells have been used as enzymatic reactor units. Because of the concentration polarization phenomena which take place in the system, at steady-state the enzyme is confined (dynamically immobilized) within an extremely narrow region upstream the ultrafiltration membrane. Correspondingly its concentration attains fairly high values. Kinetic studies have been therefore performed under quite unusual experimental conditions in order to better approximate local enzyme concentration levels in immobilized enzyme systems. Studies have been also carried out on the kinetics of enzyme deactivation in the continuous presence of substrate and reaction products. Once the enzyme concentration profile is completely developed, further injection into the system of suitable amounts of an inert proteic macromolecule (albumin polymers) gives rise to the formation of a gel layer onto the ultrafiltration membrane within which the enzyme is entrapped (statically immobilized). The effect of this immobilization technique has been studied as far as the kinetics of the main reaction, the substrate mass transfer resistances and the enzyme stability are concerned. The rejective properties of such gel layers towards enzymatic molecules have been exploited in producing multilayer, multi-enzymatic reactors. PMID:7417597
DEFF Research Database (Denmark)
2009-01-01
A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises.......A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises....
International Nuclear Information System (INIS)
This book gives descriptions of chemical kinetics. It starts summary of chemical kinetics and reaction mechanism, and explains basic velocity law, experiment method for determination of reaction velocity, temperature dependence of reaction velocity, theory of reaction velocity, theory on reaction of unimolecular, process of atom and free radical, reaction in solution, catalysis, photochemical reaction, such as experiment and photochemical law and rapid reaction like flame, beam of molecule and shock tube.
Numerical calculation of classical and non-classical electrostatic potentials
Christensen, D; Neyenhuis, B; Christensen, Dan; Durfee, Dallin S.; Neyenhuis, Brian
2006-01-01
We present a numerical exercise in which classical and non-classical electrostatic potentials were calculated. The non-classical fields take into account effects due to a possible non-zero photon rest mass. We show that in the limit of small photon rest mass, both the classical and non-classical potential can be found by solving Poisson's equation twice, using the first calculation as a source term in the second calculation. Our results support the assumptions in a recent proposal to use ion interferometry to search for a non-zero photon rest mass.
Kinetic mean field theories: Results of energy constraint in maximizing entropy
Stell, G.; Karkheck, J.; Beijeren, H. van
1983-01-01
Structure of liquids and solids; crystallography Classical, semiclassical, and quantum theories of liquid structure Statistical theories of liquid structure - Kinetic and transport theory of fluids; physical properties of gases Kinetic and transport theory
Cosmological dynamics of scalar field with non-minimal kinetic term
Kröger, H; Melkonyan, G.; Rubin, S. G.
2003-01-01
We investigate dynamics of scalar field with non-minimal kinetic term. Nontrivial behavior of the field in the vicinity of singular points of kinetic term is observed. In particular, the singular points could serve as attractor for classical solutions.
Fano Interference in Classical Oscillators
Satpathy, S.; Roy, A.; Mohapatra, A.
2012-01-01
We seek to illustrate Fano interference in a classical coupled oscillator by using classical analogues of the atom-laser interaction. We present an analogy between the dressed state picture of coherent atom-laser interaction and a classical coupled oscillator. The Autler-Townes splitting due to the atom-laser interaction is analogous to the…
Enzymes: The possibility of production and applications
Petronijević Živomir B.
2003-01-01
Enzymes are biological catalysts with increasing application in the food pharmaceutical, cosmetic, textile and chemical industry. They are also important as reagents in chemical analysis, leather fabrications and as targets for the design of new drugs. Keeping in mind the growing need to replace classical chemical processes by alternative ones, because of ever growing environmental pollution, it is important that enzyme and other biotechnological processes are economical. Therefore, price dec...
Optimization of collective enzyme activity via spatial localization
Buchner, Alexander; Tostevin, Filipe; Hinzpeter, Florian; Gerland, Ulrich
2013-01-01
The spatial organization of enzymes often plays a crucial role in the functionality and efficiency of enzymatic pathways. To fully understand the design and operation of enzymatic pathways, it is therefore crucial to understand how the relative arrangement of enzymes affects pathway function. Here we investigate the effect of enzyme localization on the flux of a minimal two-enzyme pathway within a reaction-diffusion model. We consider different reaction kinetics, spatial dimensions, and loss ...
Enzyme technology: Key to selective biorefining
DEFF Research Database (Denmark)
Meyer, Anne S.
2014-01-01
Development of selective biomass upgrading processes is a crucial prerequisite for unfolding the potential of biomass in biorefinery processes. The biorefinery concept designates that different value-added compounds are produced from the same crop or biomass stream. Selectivity with respect to the...... reaction is a unique trait of enzyme catalysis. Since enzyme selectivity means that a specific reaction is catalysed between particular species to produce definite products, enzymes are particularly fit for converting specific compounds in mixed biomass streams. Since enzymes are protein molecules their...... rational use in biorefinery processes requires an understanding of the basic features of enzymes and reaction traits with respect to specificity, kinetics, reaction optima, stability and structure-function relations – we are now at a stage where it is possible to use nature’s enzyme structures as starting...
Supramolecular Tectonics for Enzyme-like Reagents
Institute of Scientific and Technical Information of China (English)
MAO; LuYuan
2001-01-01
The enzyme-likes and bioactive species were closely related with the life phenomena and served as the reagent of bioassy1,2. In present works, the flow cytometry (FCM) and rapid-scanning stopped-flow (RSSF) spectroscopy combine with the stopped-flow difference UV/Vis spectra, FT-IR and other methods of assay, being used to study the biomimetic reaction and enzyme mimic. Based on catalytic kinetics of enzyme reaction3,4, the reaction mechanisms of the enzyme-likes had been studied and some new methods of kinetic determination were proposed. The study and methods not only provided the basic theoretical models for the life science, but also widened the application fields of biomimetic and analytical chemistry. The main contents of our works and the supramolecular models can be described as follows: ……
Mechanical Systems, Classical Models
Teodorescu, Petre P
2009-01-01
This third volume completes the Work Mechanical Systems, Classical Models. The first two volumes dealt with particle dynamics and with discrete and continuous mechanical systems. The present volume studies analytical mechanics. Topics like Lagrangian and Hamiltonian mechanics, the Hamilton-Jacobi method, and a study of systems with separate variables are thoroughly discussed. Also included are variational principles and canonical transformations, integral invariants and exterior differential calculus, and particular attention is given to non-holonomic mechanical systems. The author explains in detail all important aspects of the science of mechanics, regarded as a natural science, and shows how they are useful in understanding important natural phenomena and solving problems of interest in applied and engineering sciences. Professor Teodorescu has spent more than fifty years as a Professor of Mechanics at the University of Bucharest and this book relies on the extensive literature on the subject as well as th...
Grassmannization of classical models
Pollet, Lode; Prokof'ev, Nikolay V; Svistunov, Boris V
2016-01-01
Applying Feynman diagrammatics to non-fermionic strongly correlated models with local constraints might seem generically impossible for two separate reasons: (i) the necessity to have a Gaussian (non-interacting) limit on top of which the perturbative diagrammatic expansion is generated by Wick's theorem, and (ii) the Dyson's collapse argument implying that the expansion in powers of coupling constant is divergent. We show that for arbitrary classical lattice models both problems can be solved/circumvented by reformulating the high-temperature expansion (more generally, any discrete representation of the model) in terms of Grassmann integrals. Discrete variables residing on either links, plaquettes, or sites of the lattice are associated with the Grassmann variables in such a way that the partition function (and correlations) of the original system and its Grassmann-field counterpart are identical. The expansion of the latter around its Gaussian point generates Feynman diagrams. A proof-of-principle implement...
Directory of Open Access Journals (Sweden)
Maryann Wilson
2013-01-01
Full Text Available BACKGROUND: The impact of a scientific article is proportional to the citations it has received. In this study, we set out to identify the most cited works in epileptology in order to evaluate research trends in this field. METHODS: According to the Web of Science database, articles with more than 400 citations qualify as "citation classics". We conducted a literature search on the ISI Web of Science bibliometric database for scientific articles relevant to epilepsy. RESULTS: We retrieved 67 highly cited articles (400 or more citations, which were published in 31 journals: 17 clinical studies, 42 laboratory studies, 5 reviews and 3 classification articles. Clinical studies consisted of epidemiological analyses (n=3, studies on the clinical phenomenology of epilepsy (n=5 – including behavioral and prognostic aspects – and articles focusing on pharmacological (n=6 and non-pharmacological (n=3 treatment. The laboratory studies dealt with genetics (n=6, animal models (n=27, and neurobiology (n=9 – including both neurophysiology and neuropathology studies. The majority (61% of citation classics on epilepsy were published after 1986, possibly reflecting the expansion of research interest in laboratory studies driven by the development of new methodologies, specifically in the fields of genetics and animal models. Consequently, clinical studies were highly cited both before and after the mid 80s, whilst laboratory researches became widely cited after 1990. CONCLUSIONS: Our study indicates that the main drivers of scientific impact in the field of epileptology have increasingly become genetic and neurobiological studies, along with research on animal models of epilepsy. These articles are able to gain the highest numbers of citations in the time span of a few years and suggest potential directions for future research.
Tang, J. Y.
2015-12-01
The Michaelis-Menten kinetics and the reverse Michaelis-Menten kinetics are two popular mathematical formulations used in many land biogeochemical models to describe how microbes and plants would respond to changes in substrate abundance. However, the criteria of when to use either of the two are often ambiguous. Here I show that these two kinetics are special approximations to the equilibrium chemistry approximation (ECA) kinetics, which is the first-order approximation to the quadratic kinetics that solves the equation of an enzyme-substrate complex exactly for a single-enzyme and single-substrate biogeochemical reaction with the law of mass action and the assumption of a quasi-steady state for the enzyme-substrate complex and that the product genesis from enzyme-substrate complex is much slower than the equilibration between enzyme-substrate complexes, substrates, and enzymes. In particular, I show that the derivation of the Michaelis-Menten kinetics does not consider the mass balance constraint of the substrate, and the reverse Michaelis-Menten kinetics does not consider the mass balance constraint of the enzyme, whereas both of these constraints are taken into account in deriving the equilibrium chemistry approximation kinetics. By benchmarking against predictions from the quadratic kinetics for a wide range of substrate and enzyme concentrations, the Michaelis-Menten kinetics was found to persistently underpredict the normalized sensitivity ∂ ln v / ∂ ln k2+ of the reaction velocity v with respect to the maximum product genesis rate k2+, persistently overpredict the normalized sensitivity ∂ ln v / ∂ ln k1+ of v with respect to the intrinsic substrate affinity k1+, persistently overpredict the normalized sensitivity ∂ ln v / ∂ ln [E]T of v with respect the total enzyme concentration [E]T, and persistently underpredict the normalized sensitivity ∂ ln v / ∂ ln [S]T of v with respect to the total substrate concentration [S]T. Meanwhile, the
Protein engineering of enzymes for process applications
DEFF Research Database (Denmark)
Woodley, John M
2013-01-01
Scientific progress in the field of enzyme modification today enables the opportunity to tune a given biocatalyst for a specific industrial application. Much work has been focused on extending the substrate repertoire and altering selectivity. Nevertheless, it is clear that many new forthcoming...... opportunities will be targeted on modification to enable process application. This article discusses the challenges involved in enzyme modification focused on process requirements, such as the need to fulfill reaction thermodynamics, specific activity under the required conditions, kinetics at required...
Schoonen, Lise; Nolte, Roeland J. M.; van Hest, Jan C. M.
2016-07-01
The study of enzyme behavior in small nanocompartments is crucial for the understanding of biocatalytic processes in the cellular environment. We have developed an enzymatic conjugation strategy to attach a model enzyme to the interior of a cowpea chlorotic mottle virus capsid. It is shown that with this methodology high encapsulation efficiencies can be achieved. Additionally, we demonstrate that the encapsulation does not affect the enzyme performance in terms of a decreased activity or a hampered substrate diffusion. Finally, it is shown that the encapsulated enzymes are protected against proteases. We believe that our strategy can be used to study enzyme kinetics in an environment that approaches physiological conditions.The study of enzyme behavior in small nanocompartments is crucial for the understanding of biocatalytic processes in the cellular environment. We have developed an enzymatic conjugation strategy to attach a model enzyme to the interior of a cowpea chlorotic mottle virus capsid. It is shown that with this methodology high encapsulation efficiencies can be achieved. Additionally, we demonstrate that the encapsulation does not affect the enzyme performance in terms of a decreased activity or a hampered substrate diffusion. Finally, it is shown that the encapsulated enzymes are protected against proteases. We believe that our strategy can be used to study enzyme kinetics in an environment that approaches physiological conditions. Electronic supplementary information (ESI) available: Experimental procedures for the cloning, expression, and purification of all proteins, as well as supplementary figures and calculations. See DOI: 10.1039/c6nr04181g
Directory of Open Access Journals (Sweden)
Rolando Mendoza
2012-01-01
Full Text Available El objetivo de este trabajo fue determinar la cinética de inactivación de la enzima peroxidasa y la cinética del color y textura en tubérculos de papa criolla (Solanum tuberosum grupo phureja sometidos a escaldado mediante agua a 80°C, 90°C y vapor saturado a 93°C. Los coeficientes de transferencia de calor para el escaldado en agua oscilaron entre 214 y 230 W °C-1 m-2 mientras que para vapor saturado fueron en promedio 84.5 W °C-1 m-2. A diferentes tiempos de precocción el tubérculo de papa criolla presentó una zona en donde ocurrió pardeamiento enzimático, hecho que fue modelado según la cinética de Michaelis-Menten y otra zona en donde el cambio de color disminuyó debido a la inactivación enzimática que correspondió a una cinética de primer orden, de manera similar al comportamiento de la textura. La inactivación de la enzima peroxidasa obedeció al mecanismo de Lumry-Eyring.The objective of this work was to determine the inactivation kinetics of peroxidase enzyme and the change in color and texture in golden potato tubers (Solanum tuberosum phureja group exposed to blanching with water at 80°C, 90°C and to saturated steam at 93°C. The heat transfer coefficients for the blanch water ranged between 214 and 230 W °C-1 m-2 while for saturated steam they showed an average of 84.5 W °C-1 m-2. At different pre-cooking times the golden potato tuber showed an area that developed enzymatic browning, which was fitted to the Michaelis-Menten kinetic model and another area where the color change decreased due to enzyme inactivation, which corresponded to first order kinetics, in a similar way as the texture behavior. The inactivation of peroxidase enzyme followed the Lumry-Eyring mechanism.
Classicalization of quantum variables and quantum–classical hybrids
International Nuclear Information System (INIS)
The extraction of classical degrees of freedom in quantum mechanics is studied in the stochastic variational method. By using this classicalization, a hybrid model constructed from quantum and classical variables (quantum–classical hybrids) is derived. In this procedure, conservation laws such as energy are maintained, and Ehrenfest's theorem is still satisfied with modification. The criterion for the applicability of quantum–classical hybrids is also discussed. - Highlights: • The new derivation of a quantum–classical hybrid (QCH) model is discussed based on a variational principle. • Any conserved quantities are automatically defined as the invariant transforms of a stochastic action. • The quantitative criterion to determine the validity of QCH is proposed. • Ehrenfest's theorem is satisfied in a modified way
Tuning the kinetics of cadherin adhesion
Sivasankar, Sanjeevi
2013-01-01
Cadherins are Ca2+ dependent cell-cell adhesion proteins that maintain the structural integrity of the epidermis; their principle function is to resist mechanical force. This review summarizes the biophysical mechanisms by which classical cadherins tune adhesion and withstand mechanical stress. We first relate the structure of classical cadherins to their equilibrium binding properties. We then review the role of mechanical perturbations in tuning the kinetics of cadherin adhesion. In particu...
Generalization of the Activated Complex Theory of Reaction Rates. II. Classical Mechanical Treatment
Marcus, R. A.
1964-01-01
In its usual classical form activated complex theory assumes a particular expression for the kinetic energy of the reacting system -- one associated with a rectilinear motion along the reaction coordinate. The derivation of the rate expression given in the present paper is based on the general kinetic energy expression.
Lipid metabolizing enzyme activities modulated by phospholipid substrate lateral distribution.
Salinas, Dino G; Reyes, Juan G; De la Fuente, Milton
2011-09-01
Biological membranes contain many domains enriched in phospholipid lipids and there is not yet clear explanation about how these domains can control the activity of phospholipid metabolizing enzymes. Here we used the surface dilution kinetic theory to derive general equations describing how complex substrate distributions affect the activity of enzymes following either the phospholipid binding kinetic model (which assumes that the enzyme molecules directly bind the phospholipid substrate molecules), or the surface-binding kinetic model (which assumes that the enzyme molecules bind to the membrane before binding the phospholipid substrate). Our results strongly suggest that, if the enzyme follows the phospholipid binding kinetic model, any substrate redistribution would increase the enzyme activity over than observed for a homogeneous distribution of substrate. Besides, enzymes following the surface-binding model would be independent of the substrate distribution. Given that the distribution of substrate in a population of micelles (each of them a lipid domain) should follow a Poisson law, we demonstrate that the general equations give an excellent fit to experimental data of lipases acting on micelles, providing reasonable values for kinetic parameters--without invoking special effects such as cooperative phenomena. Our theory will allow a better understanding of the cellular-metabolism control in membranes, as well as a more simple analysis of the mechanisms of membrane acting enzymes. PMID:21108012
Wan Ahmad Tajuddin Wan Abdullah; Sidiq Mohamad Khidzir
2007-01-01
We study a minimalist kinetic model for economies. A system of agents with local trading rules display emergent demand behaviour. We examine the resulting wealth distribution to look for non-thermal behaviour. We compare and contrast this model with other similar models.
Crowder, Martin J
2001-01-01
If something can fail, it can often fail in one of several ways and sometimes in more than one way at a time. There is always some cause of failure, and almost always, more than one possible cause. In one sense, then, survival analysis is a lost cause. The methods of Competing Risks have often been neglected in the survival analysis literature. Written by a leading statistician, Classical Competing Risks thoroughly examines the probability framework and statistical analysis of data of Competing Risks. The author explores both the theory of the subject and the practicalities of fitting the models to data. In a coherent, self-contained, and sequential account, the treatment moves from the bare bones of the Competing Risks setup and the associated likelihood functions through survival analysis using hazard functions. It examines discrete failure times and the difficulties of identifiability, and concludes with an introduction to the counting-process approach and the associated martingale theory.With a dearth of ...
Grafakos, Loukas
2014-01-01
The main goal of this text is to present the theoretical foundation of the field of Fourier analysis on Euclidean spaces. It covers classical topics such as interpolation, Fourier series, the Fourier transform, maximal functions, singular integrals, and Littlewood–Paley theory. The primary readership is intended to be graduate students in mathematics with the prerequisite including satisfactory completion of courses in real and complex variables. The coverage of topics and exposition style are designed to leave no gaps in understanding and stimulate further study. This third edition includes new Sections 3.5, 4.4, 4.5 as well as a new chapter on “Weighted Inequalities,” which has been moved from GTM 250, 2nd Edition. Appendices I and B.9 are also new to this edition. Countless corrections and improvements have been made to the material from the second edition. Additions and improvements include: more examples and applications, new and more relevant hints for the existing exercises, new exercises, and...
Sullivan, Woodruff Turner
1982-01-01
Radio techniques were the nrst to lead astronomy away from the quiescent and limited Universe revealed by traditional observations at optical wave lengths. In the earliest days of radio astronomy, a handful of radio physicists and engineers made one startling discovery after another as they opened up the radio sky. With this collection of classic papers and the extensive intro ductory material, the reader can experience these exciting discoveries, as well as understand the developing techniques and follow the motivations which prompted the various lines of inquiry. For instance he or she will follow in detail the several attempts to detect radio waves from the sun at the turn of the century; the unravelling by Jansky of a "steady hiss type static"; the incredible story of Reber who built a 9 meter dish in his backyard in 1937 and then mapped the Milky Way; the vital discoveries by Hey and colleagues of radio bursts from the Sun and of a discrete source in the constellation of Cygnus; the development of re...
Hypocoercivity in metastable settings and kinetic simulated annealing
Monmarché, Pierre
2015-01-01
Classical analysis of the simulated annealing algorithm is combined with the more recent hypocoercive method of distorted entropy to prove the convergence for large time of the kinetic Langevin annealing with logarithmic cooling schedule.
Classical and quantum effective theories
Polonyi, Janos
2014-01-01
A generalization of the action principle of classical mechanics, motivated by the Closed Time Path (CTP) scheme of quantum field theory, is presented to deal with initial condition problems and dissipative forces. The similarities of the classical and the quantum cases are underlined. In particular, effective interactions which describe classical dissipative forces represent the system-environment entanglement. The relation between the traditional effective theories and their CTP extension is briefly discussed and few qualitative examples are mentioned.
Population in the classic economics
Adnan Doğruyol
2013-01-01
Growth subject in economics is an important factor of development. Classic economics ecole indicates the population as main variable which tender of growth. On the other hand T. R. Malthus is known as economist who regards population as a problem and brings up it among the classical economists. However, Adam Smith is an intellectual who discussed population problem earlier on the classic economics theory. According to Adam Smith one of the main factors that realise the growth is labour. In ad...
Coherent Communication of Classical Messages
Harrow, Aram W.
2003-01-01
We define "coherent communication" in terms of a simple primitive, show it is equivalent to the ability to send a classical message with a unitary or isometric operation, and use it to relate other resources in quantum information theory. Using coherent communication, we are able to generalize super-dense coding to prepare arbitrary quantum states instead of only classical messages. We also derive single-letter formulae for the classical and quantum capacities of a bipartite unitary gate assi...
The classic: Bone morphogenetic protein.
Urist, Marshall R; Strates, Basil S
2009-12-01
This Classic Article is a reprint of the original work by Marshall R. Urist and Basil S. Strates, Bone Morphogenetic Protein. An accompanying biographical sketch of Marshall R. Urist, MD is available at DOI 10.1007/s11999-009-1067-4; a second Classic Article is available at DOI 10.1007/s11999-009-1069-2; and a third Classic Article is available at DOI 10.1007/s11999-009-1070-9. The Classic Article is copyright 1971 by Sage Publications Inc. Journals and is reprinted with permission from Urist MR, Strates BS. Bone morphogenetic protein. J Dent Res. 1971;50:1392-1406. PMID:19727989
2007-01-01
M51, whose name comes from being the 51st entry in Charles Messier's catalog, is considered to be one of the classic examples of a spiral galaxy. At a distance of about 30 million light-years from Earth, it is also one of the brightest spirals in the night sky. A composite image of M51, also known as the Whirlpool Galaxy, shows the majesty of its structure in a dramatic new way through several of NASA's orbiting observatories. X-ray data from NASA's Chandra X-ray Observatory reveals point-like sources (purple) that are black holes and neutron stars in binary star systems. Chandra also detects a diffuse glow of hot gas that permeates the space between the stars. Optical data from the Hubble Space Telescope (green) and infrared emission from the Spitzer Space Telescope (red) both highlight long lanes in the spiral arms that consist of stars and gas laced with dust. A view of M51 with the Galaxy Evolution Explorer telescope shows hot, young stars that produce lots of ultraviolet energy (blue). The textbook spiral structure is thought be the result of an interaction M51 is experiencing with its close galactic neighbor, NGC 5195, which is seen just above. Some simulations suggest M51's sharp spiral shape was partially caused when NGC 5195 passed through its main disk about 500 million years ago. This gravitational tug of war may also have triggered an increased level of star formation in M51. The companion galaxy's pull would be inducing extra starbirth by compressing gas, jump-starting the process by which stars form.
Enzyme detection by microfluidics
DEFF Research Database (Denmark)
2013-01-01
Microfluidic-implemented methods of detecting an enzyme, in particular a DNA-modifying enzyme, are provided, as well as methods for detecting a cell, or a microorganism expressing said enzyme. The enzyme is detected by providing a nucleic acid substrate, which is specifically targeted by that...... enzyme...
Kinetics of transformation on ZIF-67 crystals
Feng, Xuhui; Carreon, Moises A.
2015-05-01
Herein we report the structural evolution of ZIF-67 as a function of time at room temperature. We have identified the different stages of ZIF-67 formation (nucleation, crystallization, growth, and steady state periods) and elucidated its kinetics of transformation. It was found that the nucleation and growth of ZIF-67 crystals followed the classic Avrami's kinetics. Fundamental studies on the kinetics of formation of porous crystals demonstrated here should facilitate the preparation of MOF phases with controlled crystal size and extent of crystallinity.
Kreuzer, Hans Jürgen
1986-01-01
This monograph deals with the kinetics of adsorption and desorption of molecules physisorbed on solid surfaces. Although frequent and detailed reference is made to experiment, it is mainly concerned with the theory of the subject. In this, we have attempted to present a unified picture based on the master equation approach. Physisorption kinetics is by no means a closed and mature subject; rather, in writing this monograph we intended to survey a field very much in flux, to assess its achievements so far, and to give a reasonable basis from which further developments can take off. For this reason we have included many papers in the bibliography that are not referred to in the text but are of relevance to physisorption. To keep this monograph to a reasonable size, and also to allow for some unity in the presentation of the material, we had to omit a number of topics related to physisorption kinetics. We have not covered to any extent the equilibrium properties of physisorbed layers such as structures, phase tr...
Institute of Scientific and Technical Information of China (English)
2002-01-01
The heyday of Beijing’s classical music beganin 1993, when top-quality sound equipment andrecords were imported. Also in that year, BeijingMusic Radio presented a classical music programtitled "Fan’s Club" and founded the "Music and
Dynamical Symmetries in Classical Mechanics
Boozer, A. D.
2012-01-01
We show how symmetries of a classical dynamical system can be described in terms of operators that act on the state space for the system. We illustrate our results by considering a number of possible symmetries that a classical dynamical system might have, and for each symmetry we give examples of dynamical systems that do and do not possess that…
A New Perspective on Classical Ideal Gases
Directory of Open Access Journals (Sweden)
Fabrice Philippe
2013-08-01
Full Text Available The ideal-gas barometric and pressure laws are derived from the Democritian concept of independent corpuscles moving in vacuum, plus a principle of simplicity, namely that these laws are independent of the kinetic part of the Hamiltonian. A single corpuscle in contact with a heat bath in a cylinder and submitted to a constant force (weight is considered. The paper importantly supplements a previously published paper: First, the stability of ideal gases is established. Second, we show that when walls separate the cylinder into parts and are later removed, the entropy is unaffected. We obtain full agreement with Landsberg’s and others’ (1994 classical thermodynamic result for the entropy of a column of gas submitted to gravity.
Classical dynamics a modern perspective
Sudarshan, Ennackal Chandy George
2016-01-01
Classical dynamics is traditionally treated as an early stage in the development of physics, a stage that has long been superseded by more ambitious theories. Here, in this book, classical dynamics is treated as a subject on its own as well as a research frontier. Incorporating insights gained over the past several decades, the essential principles of classical dynamics are presented, while demonstrating that a number of key results originally considered only in the context of quantum theory and particle physics, have their foundations in classical dynamics.Graduate students in physics and practicing physicists will welcome the present approach to classical dynamics that encompasses systems of particles, free and interacting fields, and coupled systems. Lie groups and Lie algebras are incorporated at a basic level and are used in describing space-time symmetry groups. There is an extensive discussion on constrained systems, Dirac brackets and their geometrical interpretation. The Lie-algebraic description of ...
Kinetic coefficients for quark-antiquark plasma with quantum treatment of color
International Nuclear Information System (INIS)
We discuss the near-equilibrium state of the q-q-bar plasma treated as a system of classical particles with quantized color charges. The matrix of the kinetic coefficients is calculated (in the relaxation approximation of the transport equation) and compared with its classical version: The color Ohm law is recovered but the structure of the kinetic matrix is different
Enzyme immobilization: an update
Homaei, Ahmad Abolpour; Sariri, Reyhaneh; Vianello, Fabio; Stevanato, Roberto
2013-01-01
Compared to free enzymes in solution, immobilized enzymes are more robust and more resistant to environmental changes. More importantly, the heterogeneity of the immo-bilized enzyme systems allows an easy recovery of both enzymes and products, multiple re-use of enzymes, continuous operation of enzymatic processes, rapid termination of reactions, and greater variety of bioreactor designs. This paper is a review of the recent literatures on enzyme immobilization by various techniques, the need...
Onida, Giovanni; Andreoni, Wanda
1995-09-01
A classical trajectory mapping method was developed to study chemical reactions in solution and in enzymes. In this method, the trajectories were calculated on a classical potential surface and the free energy profile was obtained by mapping the classical surface to the quantum mechanical surface obtained by the semiempirical AM1 method. There is no need to perform expensive quantum mechanical calculations at each iteration step. This method was applied to proton transfer reactions both in aqueous solution and in papain. The results are encouraging, indicating the applicability of this hybrid method to chemical reactions both in solution and in enzymes.
Non-equilibrium thermodynamics and physical kinetics
Bikkin, Halid
2014-01-01
This graduate textbook covers contemporary directions of non-equilibrium statistical mechanics as well as classical methods of kinetics. With one of the main propositions being to avoid terms such as "obviously" and "it is easy to show", this treatise is an easy-to-read introduction into this traditional, yet vibrant field.
Oxide glasses free of classical network formers
International Nuclear Information System (INIS)
The kinetic theory of glass formation (Uhlmann 1972, Uhlmann ampersand Yinnon 1983) relegates the classical network theory to just one specific, though large and important, region of potential glass compositions. Accordingly, a large number of interesting oxide systems free of the network forming oxides of SiO2, GeO2, P2O5, B2O3, can be found and exploited for particular applications, e.g. attractive compromises between optical performance and stability. Identification and characterizations of glasses in such systems are briefly reviewed in what follows, stressing most recent developments, as well as less accessible reports. Cations of lower field strength not favoring oxide network formation will typically have absorption edges at desirable e.g. lower ir frequencies (higher wavelengths) in fibers guiding conventional laser frequencies. When higher linear and nonlinear refractivity is called for, optimization depends on a compromise between the positive effect of a high atomic number and low polarizability of oxygen with the negative effect of higher valency causing dilution with oxygen. Moreover, some systems free of classical network formers exhibit low scattering
Akibue, Seiseki; Owari, Masaki; Kato, Go; Murao, Mio
2016-01-01
Phenomena induced by the existence of entanglement, such as nonlocal correlations, exhibit characteristic properties of quantum mechanics distinguishing from classical theories. When entanglement is accompanied by classical communication, it enhances the power of quantum operations jointly performed by two spatially separated parties. Such a power has been analyzed by the gap between the performances of joint quantum operations implementable by local operations at each party connected by clas...
Quantum localization of Classical Mechanics
Batalin, Igor A
2016-01-01
Quantum localization of classical mechanics within the BRST-BFV and BV (or field-antifield) quantization methods are studied. It is shown that a special choice of gauge fixing functions (or BRST-BFV charge) together with the unitary limit leads to Hamiltonian localization in the path integral of the BRST-BFV formalism. In turn, we find that a special choice of gauge fixing functions being proportional to extremals of an initial non-degenerate classical action together with a very special solution of the classical master equation result in Lagrangian localization in the partition function of the BV formalism.
Quantum localization of classical mechanics
Batalin, Igor A.; Lavrov, Peter M.
2016-07-01
Quantum localization of classical mechanics within the BRST-BFV and BV (or field-antifield) quantization methods are studied. It is shown that a special choice of gauge fixing functions (or BRST-BFV charge) together with the unitary limit leads to Hamiltonian localization in the path integral of the BRST-BFV formalism. In turn, we find that a special choice of gauge fixing functions being proportional to extremals of an initial non-degenerate classical action together with a very special solution of the classical master equation result in Lagrangian localization in the partition function of the BV formalism.
The Wigner representation of classical mechanics, quantization and classical limit
International Nuclear Information System (INIS)
Starting from the Liouvillian formulation of classical physics it is possible by means of a Fourier transform to introduce the Wigner representation and to derive an operator structure to classical mechanisms. The importance of this new representation lies on the fact that it turns out to be suitable route to establish a general method of quantization directly from the equations of motion without alluding to the existence of Hamiltonian and Lagrangian functions. Following this approach we quantize only the motion of a Browian particle with non-linear friction in the Markovian approximation - the thermal bath may be quantum or classical -, thus when the bath is classically described we obtain a master equation which reduces to Caldeira-Legget equation for the linear friction case, and when the reservoir is quantum we get an equation reducing to the one found by Caldeira et al. By neglecting the environmental influence we show that the system can be approximately described by equations of motion in terms of wave function, such as the Schrodinger-Langevin equation and equations of the Caldirola-Kanai type. Finally to make the present study self-consistent we evaluate the classical limit of these dynamical equations employing a new classical limiting method h/2π → 0. (author)
Space-time reactor kinetics for heterogeneous reactor structure
International Nuclear Information System (INIS)
An attempt is made to formulate time dependent diffusion equation based on Feinberg-Galanin theory in the from analogue to the classical reactor kinetic equation. Parameters of these equations could be calculated using the existing codes for static reactor calculation based on the heterogeneous reactor theory. The obtained kinetic equation could be analogues in form to the nodal kinetic equation. Space-time distribution of neutron flux in the reactor can be obtained by solving these equations using standard methods
Simulation of non-classical diffusion in polymers
Wilmers, Jana; Bargmann, Swantje
2014-05-01
The present contribution is concerned with the computational modelling of non-classical diffusion in amorphous polymers. Special attention is paid to the limiting case of Case II diffusion. Application of the dual-phase-lag concept to Fick's first law leads to a description of Case II behaviour. The change in material properties during the glass transition is explicitly accounted for by a concentration dependent formulation of the material parameters. The proposed model is well suited for modelling the sharp diffusion front and linear uptake kinetics associated with Case II diffusion. Application of a concentration dependent diffusion coefficient reduces the concentration gradient behind the front to a minimum. For the solution procedure, a finite element scheme in space and a finite difference method in time are applied. Three-dimensional numerical results are presented for classical Fickian and non-classical Case II diffusion. This paper adds to the basic understanding of the computational modelling of the Case II diffusion phenomenon.
Revision of the classical nucleation theory for supersaturated solutions
Borisenko, Alexander
2015-01-01
During the processes of nucleation and growth of a precipitate cluster from a supersaturated solution, the diffusion flux between the cluster and the solution changes the solute concentration near the cluster-solution interface from its average bulk value. This feature affects the rates of attachment and detachment of solute atoms at the interface and, therefore, alters the entire nucleation kinetics. Unless quite obvious, this effect has been ignored in the classical nucleation theory. To illustrate the results of this new approach, for the case of homogeneous nucleation, we calculate the total solubility (including the contribution from heterophase fluctuations) and the nucleation rate as functions of two parameters of the model and compare these results to the classical ones. One can conclude that discrepancies with the classical nucleation theory are great in the diffusion-limited regime, when the bulk diffusion mobility of solute atoms is small compared to the interfacial one, while in the opposite inter...
eduction for Michaelis-Menten-Henri kinetics in the presence of diffusion
Directory of Open Access Journals (Sweden)
Leonid V. Kalachev
2007-05-01
Full Text Available The Michaelis-Menten-Henri (MMH mechanism is one of the paradigm reaction mechanisms in biology and chemistry. In its simplest form, it involves a substrate that reacts (reversibly with an enzyme, forming a complex which is transformed (irreversibly into a product and the enzyme. Given these basic kinetics, a dimension reduction has traditionally been achieved in two steps, by using conservation relations to reduce the number of species and by exploiting the inherent fast-slow structure of the resulting equations. In the present article, we investigate how the dynamics change if the species are additionally allowed to diffuse. We study the two extreme regimes of large diffusivities and of small diffusivities, as well as an intermediate regime in which the time scale of diffusion is comparable to that of the fast reaction kinetics. We show that reduction is possible in each of these regimes, with the nature of the reduction being regime dependent. Our analysis relies on the classical method of matched asymptotic expansions to derive approximations for the solutions that are uniformly valid in space and time.
Classical and stochastic Laplacian growth
Gustafsson, Björn; Vasil’ev, Alexander
2014-01-01
This monograph covers a multitude of concepts, results, and research topics originating from a classical moving-boundary problem in two dimensions (idealized Hele-Shaw flows, or classical Laplacian growth), which has strong connections to many exciting modern developments in mathematics and theoretical physics. Of particular interest are the relations between Laplacian growth and the infinite-size limit of ensembles of random matrices with complex eigenvalues; integrable hierarchies of differential equations and their spectral curves; classical and stochastic Löwner evolution and critical phenomena in two-dimensional statistical models; weak solutions of hyperbolic partial differential equations of singular-perturbation type; and resolution of singularities for compact Riemann surfaces with anti-holomorphic involution. The book also provides an abundance of exact classical solutions, many explicit examples of dynamics by conformal mapping as well as a solid foundation of potential theory. An extensive biblio...
New perspectives on classical electromagnetism
Cote, Paul J.
2009-01-01
The fallacies associated with the gauge concept in electromagnetism are illustrated. A clearer and more valid formulation of the basics of classical electromagnetism is provided by recognizing existing physical constraints as well as the physical reality of the vector potential.
Classical Mechanics and Symplectic Integration
DEFF Research Database (Denmark)
Nordkvist, Nikolaj; Hjorth, Poul G.
2005-01-01
Content: Classical mechanics: Calculus of variations, Lagrange’s equations, Symmetries and Noether’s theorem, Hamilton’s equations, cannonical transformations, integrable systems, pertubation theory. Symplectic integration: Numerical integrators, symplectic integrators, main theorem on symplectic...
Fano interference in classical oscillators
International Nuclear Information System (INIS)
We seek to illustrate Fano interference in a classical coupled oscillator by using classical analogues of the atom-laser interaction. We present an analogy between the dressed state picture of coherent atom-laser interaction and a classical coupled oscillator. The Autler-Townes splitting due to the atom-laser interaction is analogous to the splitting of normal-mode frequencies of a coupled oscillator. Using this analogy, we simulate and experimentally demonstrate Fano interference and the associated phenomena in three-level atoms in a coupled electrical resonator circuit. This work aims to highlight analogies between classical and quantum systems for students at the postgraduate and graduate levels. Also, the reported technique can be easily realized in undergraduate laboratories. (paper)
Elementary charges in classical electrodynamics
KAPU'{S}CIK, Edward
1999-01-01
In the framework of classical electrodynamics elementary particles are treated as capacitors. The electrostatic potentials satisfy equations of the Schrödinger type. An interesting "quantization condition" for elementary charges is derived.
Probabilities for classically forbidden transitions using classical and classical path methods
International Nuclear Information System (INIS)
Limits are established for the applicability of purely classical methods for calculating nonreactive, inelastic transition probabilities in collinear collisions of a structureless atom and a harmonic oscillator. These limits, obtained by comparison with previous exact quantum mechanical results, indicate that such methods are inappropriate not only for ''classically forbidden'' but for many ''classically allowed'' transitions (in spite of the fact that they are widely used to calculate probabilities for such processes). A classical path method in the context of infinite-order time-dependent perturbation theory is described which yields extremely accurate transition probabilities even for the most classically forbidden transitions in the collinear atom--harmonic oscillator system. The essential features of this method are: (1) the use of the expectation value of the total interaction potential in determining the atom--oscillator (central force) trajectory, and (2) the use of the arithmetic mean of the initial and final velocities of relative motion in the (elastic) central force trajectory. This choice of interaction potential allows the relative motion to be coupled to changes in the internal state of the oscillator. The present classical method is further applied to three-dimensional atom-breathing sphere collisions, and exact quantum mechanical calculations are also carried out. Comparison of the classical path and exact quantum results shows excellent agreement both in the specific inelastic cross section and in the individual partial-wave contributions
Lee, Charles K; Monk, Colin R; Daniel, Roy M
2013-01-01
Of the two independent processes by which enzymes lose activity with increasing temperature, irreversible thermal inactivation and rapid reversible equilibration with an inactive form, the latter is only describable by the Equilibrium Model. Any investigation of the effect of temperature upon enzymes, a mandatory step in rational enzyme engineering and study of enzyme temperature adaptation, thus requires determining the enzymes' thermodynamic parameters as defined by the Equilibrium Model. The necessary data for this procedure can be collected by carrying out multiple isothermal enzyme assays at 3-5°C intervals over a suitable temperature range. If the collected data meet requirements for V max determination (i.e., if the enzyme kinetics are "ideal"), then the enzyme's Equilibrium Model parameters (ΔH eq, T eq, ΔG (‡) cat, and ΔG (‡) inact) can be determined using a freely available iterative model-fitting software package designed for this purpose.Although "ideal" enzyme reactions are required for determination of all four Equilibrium Model parameters, ΔH eq, T eq, and ΔG (‡) cat can be determined from initial (zero-time) rates for most nonideal enzyme reactions, with substrate saturation being the only requirement. PMID:23504427
Gyrocenter-gauge kinetic theory
Energy Technology Data Exchange (ETDEWEB)
H. Qin; W. M. Tang; W. W. Lee
2000-08-07
Gyrocenter-gauge kinetic theory is developed as an extension of the existing gyrokinetic theories. In essence, the formalism introduced here is a kinetic description of magnetized plasmas in the gyrocenter coordinates which is fully equivalent to the Vlasov-Maxwell system in the particle coordinates. In particular, provided the gyroradius is smaller than the scale-length of the magnetic field, it can treat high frequency range as well as the usual low frequency range normally associated with gyrokinetic approaches. A significant advantage of this formalism is that it enables the direct particle-in-cell simulations of compressional Alfven waves for MHD applications and of RF waves relevant to plasma heating in space and laboratory plasmas. The gyrocenter-gauge kinetic susceptibility for arbitrary wavelength and arbitrary frequency electromagnetic perturbations in a homogeneous magnetized plasma is shown to recover exactly the classical result obtained by integrating the Vlasov-Maxwell system in the particle coordinates. This demonstrates that all the waves supported by the Vlasov-Maxwell system can be studied using the gyrocenter-gauge kinetic model in the gyrocenter coordinates. This theoretical approach is so named to distinguish it from the existing gyrokinetic theory, which has been successfully developed and applied to many important low-frequency and long parallel wavelength problems, where the conventional meaning of gyrokinetic has been standardized. Besides the usual gyrokinetic distribution function, the gyrocenter-gauge kinetic theory emphasizes as well the gyrocenter-gauge distribution function, which sometimes contains all the physics of the problems being studied, and whose importance has not been realized previously. The gyrocenter-gauge distribution function enters Maxwell's equations through the pull-back transformation of the gyrocenter transformation, which depends on the perturbed fields. The efficacy of the gyrocenter-gauge kinetic approach
Enzymes: The possibility of production and applications
Directory of Open Access Journals (Sweden)
Petronijević Živomir B.
2003-01-01
Full Text Available Enzymes are biological catalysts with increasing application in the food pharmaceutical, cosmetic, textile and chemical industry. They are also important as reagents in chemical analysis, leather fabrications and as targets for the design of new drugs. Keeping in mind the growing need to replace classical chemical processes by alternative ones, because of ever growing environmental pollution, it is important that enzyme and other biotechnological processes are economical. Therefore, price decrease and stability and enzyme preparation efficiency increase are required more and more. This paper presents a short review of methods for yield increase and the improvement of the quality of enzyme products as commercial products, as well as a review of the possibilities of their application.
Anderson localization from classical trajectories
Brouwer, Piet W.; Altland, Alexander
2008-01-01
We show that Anderson localization in quasi-one dimensional conductors with ballistic electron dynamics, such as an array of ballistic chaotic cavities connected via ballistic contacts, can be understood in terms of classical electron trajectories only. At large length scales, an exponential proliferation of trajectories of nearly identical classical action generates an abundance of interference terms, which eventually leads to a suppression of transport coefficients. We quantitatively descri...
Gaussian Dynamics is Classical Dynamics
Habib, Salman
2004-01-01
A direct comparison of quantum and classical dynamical systems can be accomplished through the use of distribution functions. This is useful for both fundamental investigations such as the nature of the quantum-classical transition as well as for applications such as quantum feedback control. By affording a clear separation between kinematical and dynamical quantum effects, the Wigner distribution is particularly valuable in this regard. Here we discuss some consequences of the fact that when...
Quantum systems as classical systems
Cassa, Antonio
2001-01-01
A characteristical property of a classical physical theory is that the observables are real functions taking an exact outcome on every (pure) state; in a quantum theory, at the contrary, a given observable on a given state can take several values with only a predictable probability. However, even in the classical case, when an observer is intrinsically unable to distinguish between some distinct states he can convince himself that the measure of its ''observables'' can have several values in ...
Quantum money with classical verification
International Nuclear Information System (INIS)
We propose and construct a quantum money scheme that allows verification through classical communication with a bank. This is the first demonstration that a secure quantum money scheme exists that does not require quantum communication for coin verification. Our scheme is secure against adaptive adversaries - this property is not directly related to the possibility of classical verification, nevertheless none of the earlier quantum money constructions is known to possess it
Classical theory of radiating strings
Copeland, Edmund J.; Haws, D.; Hindmarsh, M.
1990-01-01
The divergent part of the self force of a radiating string coupled to gravity, an antisymmetric tensor and a dilaton in four dimensions are calculated to first order in classical perturbation theory. While this divergence can be absorbed into a renormalization of the string tension, demanding that both it and the divergence in the energy momentum tensor vanish forces the string to have the couplings of compactified N = 1 D = 10 supergravity. In effect, supersymmetry cures the classical infinities.
Quantum money with classical verification
Energy Technology Data Exchange (ETDEWEB)
Gavinsky, Dmitry [NEC Laboratories America, Princeton, NJ (United States)
2014-12-04
We propose and construct a quantum money scheme that allows verification through classical communication with a bank. This is the first demonstration that a secure quantum money scheme exists that does not require quantum communication for coin verification. Our scheme is secure against adaptive adversaries - this property is not directly related to the possibility of classical verification, nevertheless none of the earlier quantum money constructions is known to possess it.
Neutron inverse kinetics via Gaussian Processes
International Nuclear Information System (INIS)
Highlights: ► A novel technique for the interpretation of experiments in ADS is presented. ► The technique is based on Bayesian regression, implemented via Gaussian Processes. ► GPs overcome the limits of classical methods, based on PK approximation. ► Results compares GPs and ANN performance, underlining similarities and differences. - Abstract: The paper introduces the application of Gaussian Processes (GPs) to determine the subcriticality level in accelerator-driven systems (ADSs) through the interpretation of pulsed experiment data. ADSs have peculiar kinetic properties due to their special core design. For this reason, classical – inversion techniques based on point kinetic (PK) generally fail to generate an accurate estimate of reactor subcriticality. Similarly to Artificial Neural Networks (ANNs), Gaussian Processes can be successfully trained to learn the underlying inverse neutron kinetic model and, as such, they are not limited to the model choice. Importantly, GPs are strongly rooted into the Bayes’ theorem which makes them a powerful tool for statistical inference. Here, GPs have been designed and trained on a set of kinetics models (e.g. point kinetics and multi-point kinetics) for homogeneous and heterogeneous settings. The results presented in the paper show that GPs are very efficient and accurate in predicting the reactivity for ADS-like systems. The variance computed via GPs may provide an indication on how to generate additional data as function of the desired accuracy.
International Nuclear Information System (INIS)
Recently, the in vivo processes of platelet function and the reaction and interaction of platelets with components of the blood vessel wall and artificial surfaces have received increasing attention. In this article the focus is placed on two aspects of platelet function and kinetics as revealed by 111In-labelled platelets. First the interaction of platelets with foreign prosthetic surfaces is discussed and some interesting facets of platelet functions that have come to light, are pointed out. Secondly, experiences with the development and refinement of an improved technique, namely the dual-isotope subtraction method, which increases the sensitivity of platelet imaging and allows the detection of relatively small areas of platelet deposition with accuracy, are described
Rethinking hydrogen-bond kinetics
Prada-Gracia, Diego
2013-01-01
At the fundamental level, our understanding of water hydrogen-bond dynamics has been largely built on the detailed analysis of classical molecular simulations. The latter served to develop a plethora of hydrogen bond definitions based on different properties, including geometrical distances, topology and energetics. Notwithstanding, no real consensus emerged from these approaches, making the development of a consistent and reliable definition elusive. In this contribution, a framework to study hydrogen bonds in liquid water based purely on kinetics is presented. This approach makes use of the analysis of commitment probabilities without relying on arbitrarily chosen order parameters and cutoffs. Our results provide evidence for a self-consistent description, resulting in a clear multi-exponential behavior of the kinetics.
Kinetic theory of tearing instability
International Nuclear Information System (INIS)
The guiding-center kinetic equation with Fokker-Planck collision term is used to study, in cylindrical geometry, a class of dissipative instabilities of which the classical tearing mode is an archetype. Variational solution of the kinetic equation obviates the use of an approximate Ohm's law or adiabatic assumption, as used in previous studies, and it provides a dispersive relation which is uniformly valid for any ratio of wave frequency to collision frequency. One result of using the rigorous collision operator is the prediction of a new instability. This instability, driven by the electron temperature gradient, is predicted to occur under the long mean-free path conditions of present tokamak experiments, and has significant features in common with the kink-like oscillations observed in such experiments
Does classical liberalism imply democracy?
Directory of Open Access Journals (Sweden)
David Ellerman
2015-12-01
Full Text Available There is a fault line running through classical liberalism as to whether or not democratic self-governance is a necessary part of a liberal social order. The democratic and non-democratic strains of classical liberalism are both present today—particularly in the United States. Many contemporary libertarians and neo-Austrian economists represent the non-democratic strain in their promotion of non-democratic sovereign city-states (start-up cities or charter cities. We will take the late James M. Buchanan as a representative of the democratic strain of classical liberalism. Since the fundamental norm of classical liberalism is consent, we must start with the intellectual history of the voluntary slavery contract, the coverture marriage contract, and the voluntary non-democratic constitution (or pactum subjectionis. Next we recover the theory of inalienable rights that descends from the Reformation doctrine of the inalienability of conscience through the Enlightenment (e.g. Spinoza and Hutcheson in the abolitionist and democratic movements. Consent-based governments divide into those based on the subjects’ alienation of power to a sovereign and those based on the citizens’ delegation of power to representatives. Inalienable rights theory rules out that alienation in favor of delegation, so the citizens remain the ultimate principals and the form of government is democratic. Thus the argument concludes in agreement with Buchanan that the classical liberal endorsement of sovereign individuals acting in the marketplace generalizes to the joint action of individuals as the principals in their own organizations.
No Return to Classical Reality
Jennings, David
2015-01-01
At a fundamental level, the classical picture of the world is dead, and has been dead now for almost a century. Pinning down exactly which quantum phenomena are responsible for this has proved to be a tricky and controversial question, but a lot of progress has been made in the past few decades. We now have a range of precise statements showing that whatever the ultimate laws of Nature are, they cannot be classical. In this article, we review results on the fundamental phenomena of quantum theory that cannot be understood in classical terms. We proceed by first granting quite a broad notion of classicality, describe a range of quantum phenomena (such as randomness, discreteness, the indistinguishability of states, measurement-uncertainty, measurement-disturbance, complementarity, noncommutativity, interference, the no-cloning theorem, and the collapse of the wave-packet) that do fall under its liberal scope, and then finally describe some aspects of quantum physics that can never admit a classical understandi...
Bairoch, A
1994-01-01
The ENZYME data bank is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it contains the following data for each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided: EC number Recommended name Alternative names (if any) Catalytic activity Cofactors (if any) Pointers to the SWISS-PROT protein sequence entrie(s) that correspond to the enzyme (if any) Pointers to human disease(s) associated with a deficiency of the enzyme (if any). PMID:7937072
Classical isodual theory of antimatter
Santilli, R M
1997-01-01
An inspection of the contemporary physics literature reveals that, while matter is treated at all levels of study, from Newtonian mechanics to quantum field theory, antimatter is solely treated at the level of second quantization. For the purpose of initiating the restoration of full equivalence in the treatments of matter and antimatter in due time, in this paper we present a classical representation of antimatter which begins at the primitive Newtonian level with expected images at all subsequent levels. By recalling that charge conjugation of particles into antiparticles is anti-automorphic, the proposed theory of antimatter is based on a new map, called isoduality, which is also anti-automorphic, yet it is applicable beginning at the classical level and then persists at the quantum level. As part of our study, we present novel anti-isomorphic isodual images of the Galilean, special and general relativities and show the compatibility of their representation of antimatter with all available classical experi...
Casimir Effect The Classical Limit
Feinberg, J; Revzen, M
2001-01-01
We analyze the high temperature limit of the Casimir effect. A simple physical argument suggests that the Casimir energy (as opposed to the Casimir free energy) should vanish in the classical limit. We check the validity of this argument for massless scalar field confined in a cavity with boundaries of arbitrary shape, using path integral formalism. We are able to verify this suggestion only when the boundaries consist of disjoint pieces. Moreover, we find in these cases that the contribution to the Casimir entropy by field modes that depend on that separation, tends, in the classical limit, to a finite asymptotic value which depends only on the geometry of the cavity. Thus the Casimir force between disjoint pieces of the boundary in the classical limit is entropy driven and is governed by a dimensionless number characterizing the arbitrary geometry of the cavity. Contributions to the Casimir thermodynamical quantities due to each individual connected component of the boundary exhibit logarithmic deviations i...
Population in the classic economics
Directory of Open Access Journals (Sweden)
Adnan Doğruyol
2013-02-01
Full Text Available Growth subject in economics is an important factor of development. Classic economics ecole indicates the population as main variable which tender of growth. On the other hand T. R. Malthus is known as economist who regards population as a problem and brings up it among the classical economists. However, Adam Smith is an intellectual who discussed population problem earlier on the classic economics theory. According to Adam Smith one of the main factors that realise the growth is labour. In addition to population made it established. The aim of this study is analyzing the mental relationship between Malthus whose name has been identified with relation between population-growth and Smith who discussed this subject first time but put it off on process of theorisation.
Extracting kinetic information from literature with KineticRE.
Freitas, Ana Alão; Costa, Hugo; Rocha, Miguel; Rocha, Isabel
2015-01-01
To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents. PMID:26673933
Biocatalytic synthesis of pyruvate from DL-lactate with enzymes in Pseudomonas sp
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
A novel method of preparing pyruvate from DL-lactate catalyzed by enzymes from a bacterial strain of Pseudomonas sp. SM-6 was proposed. Catalytic processes of cell-free extract enzymes and immobilized enzymes were evaluated. The kinetic data were studied, too.
Comparing classical and quantum equilibration
Malabarba, Artur S L; Short, Anthony J
2016-01-01
By using a physically-relevant and theory independent definition of measurement-based equilibration, we show quantitatively that equilibration is easier for quantum systems than for classical systems, in the situation where the initial state of the system is completely known (pure state). This shows that quantum equilibration is a fundamental, nigh unavoidable, aspect of physical systems, while classical equilibration relies on experimental ignorance. When the state is not completely known, a mixed state, this framework also shows quantum equilibration requires weaker conditions.
Classical planning and causal implicatures
DEFF Research Database (Denmark)
Blackburn, Patrick Rowan; Benotti, Luciana
In this paper we motivate and describe a dialogue manager (called Frolog) which uses classical planning to infer causal implicatures. A causal implicature is a type of Gricean relation implicature, a highly context dependent form of inference. As we shall see, causal implicatures are important for...... generate clarification requests"; as a result we can model task-oriented dialogue as an interactive process locally structured by negotiation of the underlying task. We give several examples of Frolog-human dialog, discuss the limitations imposed by the classical planning paradigm, and indicate the...
Classical analogy of Fano resonances
International Nuclear Information System (INIS)
We present an analogy of Fano resonances in quantum interference to classical resonances in the harmonic oscillator system. It has a manifestation as a coupled behaviour of two effective oscillators associated with propagating and evanescent waves. We illustrate this point by considering a classical system of two coupled oscillators and interfering electron waves in a quasi-one-dimensional narrow constriction with a quantum dot. Our approach provides a novel insight into Fano resonance physics and provides a helpful view in teaching Fano resonances
Principal bundles the classical case
Sontz, Stephen Bruce
2015-01-01
This introductory graduate level text provides a relatively quick path to a special topic in classical differential geometry: principal bundles. While the topic of principal bundles in differential geometry has become classic, even standard, material in the modern graduate mathematics curriculum, the unique approach taken in this text presents the material in a way that is intuitive for both students of mathematics and of physics. The goal of this book is to present important, modern geometric ideas in a form readily accessible to students and researchers in both the physics and mathematics communities, providing each with an understanding and appreciation of the language and ideas of the other.
Enzyme Therapy: Current Perspectives.
UmaMaheswari, Thiyagamoorthy; Hemalatha, Thiagarajan; Sankaranarayanan, Palavesam; Puvanakrishnan, Rengarajulu
2016-01-01
Enzymes control all metabolic processes in human system from simple digestion of food to highly complex immune response. Physiological reactions occuring in healthy individuals are disturbed when enzymes are deficient or absent. Enzymes are administered for normalizing biological function in certain pathologies. Initially, crude proteolytic enzymes were used for the treatment of gastrointestinal disorders. Recent advances have enabled enzyme therapy as a promising tool in the treatment of cardiovascular, oncological and hereditary diseases. Now, a spectrum of other diseases are also covered under enzyme therapy. But, the available information on the use of enzymes as therapeutic agents for different diseases is scanty. This review details the enzymes which have been used to treat various diseases/disorders. PMID:26891548
Non-existence of Physical Classical Solutions to Euler's Equations of Rigid Body Dynamics
Wilkinson, Mark
2015-01-01
We prove that one cannot construct, for arbitrary initial data, global-in-time physical classical solutions to Euler's equations of continuum rigid body mechanics when the constituent rigid bodies are not perfect spheres. By 'physical' solutions, we mean those that conserve the total linear momentum, angular momentum and kinetic energy of any given initial datum. The reason for absence of classical solutions is due to the non-existence of velocity scattering maps which resolve a collision bet...
CLASSIC APPROACH TO BUSINESS COACHING
Żukowska, Joanna
2011-01-01
The purpose of this paper is to present business coaching in a classical way. An overview of coaching definitions will be provided. Attention will be drawn to coaching components and varieties. Moreover, a brief description of coach competences and tools supporting their work will be offered. Joanna Żukowska
Identity from classical invariant theory
International Nuclear Information System (INIS)
A simple derivation is given of a well-known relation involving the so-called Cayley Operator of classical invariant theory. The proof is induction-free and independent of Capelli's identity; it makes use only of a known-theorem in the theory of determinants and some elementary combinatorics
On classical and quantum liftings
Accardi, L.; Chruściński, Dariusz; Kossakowski, Andrzej; Matsuoka, T.; Ohya, Masanori
2011-01-01
We analyze the procedure of lifting in classical stochastic and quantum systems. It enables one to `lift' a state of a system into a state of `system+reservoir'. This procedure is important both in quantum information theory and the theory of open systems. We illustrate the general theory of liftings by a particular class related to so called circulant states.
Classical Virasoro irregular conformal block
Rim, Chaiho
2015-01-01
Virasoro irregular conformal block with arbitrary rank is obtained for the classical limit or equivalently Nekrasov-Shatashvili limit using the beta-deformed irregular matrix model (Penner-type matrix model for the irregular conformal block). The same result is derived using the generalized Mathieu equation which is equivalent to the loop equation of the irregular matrix model.
Teaching Classical Mechanics Using Smartphones
Chevrier, Joel; Madani, Laya; Ledenmat, Simon; Bsiesy, Ahmad
2013-01-01
A number of articles published in this column have dealt with topics in classical mechanics. This note describes some additional examples employing a smartphone and the new software iMecaProf. Steve Jobs presented the iPhone as "perfect for gaming." Thanks to its microsensors connected in real time to the numerical world, physics…
Classical Music as Enforced Utopia
Leech-Wilkinson, Daniel
2016-01-01
In classical music composition, whatever thematic or harmonic conflicts may be engineered along the way, everything always turns out for the best. Similar utopian thinking underlies performance: performers see their job as faithfully carrying out their master's (the composer's) wishes. The more perfectly they represent them, the happier the…
Measurement-Based Classical Computation
Hoban, Matty J.; Wallman, Joel J.; Anwar, Hussain; Usher, Naïri; Raussendorf, Robert; Browne, Dan E.
2014-04-01
Measurement-based quantum computation (MBQC) is a model of quantum computation, in which computation proceeds via adaptive single qubit measurements on a multiqubit quantum state. It is computationally equivalent to the circuit model. Unlike the circuit model, however, its classical analog is little studied. Here we present a classical analog of MBQC whose computational complexity presents a rich structure. To do so, we identify uniform families of quantum computations [refining the circuits introduced by Bremner et al. Proc. R. Soc. A 467, 459 (2010)] whose output is likely hard to exactly simulate (sample) classically. We demonstrate that these circuit families can be efficiently implemented in the MBQC model without adaptive measurement and, thus, can be achieved in a classical analog of MBQC whose resource state is a probability distribution which has been created quantum mechanically. Such states (by definition) violate no Bell inequality, but, if widely held beliefs about computational complexity are true, they, nevertheless, exhibit nonclassicality when used as a computational resource—an imprint of their quantum origin.
Invariants in Supersymmetric Classical Mechanics
Alonso Izquierdo, Alberto; González León, Miguel Ángel; Mateos Guilarte, Juan
2000-01-01
[EN] The bosonic second invariant of SuperLiouville models in supersymmetric classical mechanics is described. [ES] El segundo campo cuántico de bosones invariante del modelo SuperLiouville es descrito en la mecanica clasica supersimétrica.
Quantum Proofs for Classical Theorems
Drucker, A.; Wolf,
2009-01-01
Alongside the development of quantum algorithms and quantum complexity theory in recent years, quantum techniques have also proved instrumental in obtaining results in classical (non-quantum) areas. In this paper we survey these results and the quantum toolbox they use.
Functional Techniques in Classical Mechanics
Gozzi, E
2001-01-01
In 1931 Koopman and von Neumann extended previous work of Liouville and provided an operatorial version of Classical Mechanics (CM). In this talk we will review a path-integral formulation of this operatorial version of CM. In particular we will study the geometrical nature of the many auxiliary variables present and of the unexpected universal symmetries generated by the functional technique.
Agglomeration Economies in Classical Music
DEFF Research Database (Denmark)
Borowiecki, Karol Jan
2015-01-01
This study investigates agglomeration effects for classical music production in a wide range of cities for a global sample of composers born between 1750 and 1899. Theory suggests a trade-off between agglomeration economies (peer effects) and diseconomies (peer crowding). I test this hypothesis...
Neo-classical impurity transport
International Nuclear Information System (INIS)
The neo-classical theory for impurity transport in a toroidal plasma is outlined, and the results discussed. A general account is given of the impurity behaviour and its dependence on collisionality. The underlying physics is described with special attention to the role of the poloidal rotation
On Classical and Quantum Cryptography
I. V. Volovich; Volovich, Ya. I.
2001-01-01
Lectures on classical and quantum cryptography. Contents: Private key cryptosystems. Elements of number theory. Public key cryptography and RSA cryptosystem. Shannon`s entropy and mutual information. Entropic uncertainty relations. The no cloning theorem. The BB84 quantum cryptographic protocol. Security proofs. Bell`s theorem. The EPRBE quantum cryptographic protocol.
Supersymmetric classical mechanics: free case
International Nuclear Information System (INIS)
We present a review work on Supersymmetric Classical Mechanics in the context of a Lagrangian formalism, with N = 1-supersymmetry. We show that the N = 1 supersymmetry does not allow the introduction of a potencial energy term depending on a single commuting supercoordinate, φ(t;Θ). (author)
Enzyme inhibition by iminosugars
DEFF Research Database (Denmark)
López, Óscar; Qing, Feng-Ling; Pedersen, Christian Marcus;
2013-01-01
Imino- and azasugar glycosidase inhibitors display pH dependant inhibition reflecting that both the inhibitor and the enzyme active site have groups that change protonation state with pH. With the enzyme having two acidic groups and the inhibitor one basic group, enzyme-inhibitor complexes with...
A note on the reverse Michaelis-Menten kinetics
Energy Technology Data Exchange (ETDEWEB)
Wang, Gangsheng [ORNL; Post, Wilfred M [ORNL
2013-01-01
We theoretically derive a general equation describing the enzyme kinetics that can be further simplified to the typical Michaelis-Menten (M-M) kinetics and the reverse M-M equation (RM-M) proposed by Schimel and Weintraub (2003). We discuss the conditions under which the RM-M is valid with this theoretical derivation. These conditions are contrary to the assumptions of Schimel and Weintraub (2003) and limit the applicability of the model in field soil environments. Nonetheless, Schimel and Weintraub s RM-M model is useful and has the ability to produce a non-linear response of SOM decomposition to enzyme concentration consistent with observations. Regardless of the theoretical basis, if we assume that the M-M and the RM-M could be equivalent, our sensitivity analysis indicates that enzyme plays a more sensitive role in the M-M kinetics compared with in the RM-M kinetics.
Analysis of slow-binding enzyme inhibitors at elevated enzyme concentrations.
Perdicakis, Basil; Montgomery, Heather J; Guillemette, J Guy; Jervis, Eric
2005-02-15
The improvement in the characterization of slow-binding inhibitors achieved by performing experiments at elevated enzyme concentrations is presented. In particular, the characterization of slow-binding inhibitors conforming to a two-step mode of inhibition with a steady-state dissociation constant that is much lower than the initial dissociation constant with enzyme is discussed. For these systems, inhibition is rapid and low steady-state product concentrations are produced at saturating inhibitor concentrations. By working at elevated enzyme concentrations, improved signal-to-noise ratios are achieved and data may be collected at saturating inhibitor levels. Numerical simulations confirmed that improved parameter estimates are obtained and useful data to discern the mechanism of slow-binding inhibition are produced by working at elevated enzyme concentrations. The saturation kinetics that were unobservable in two previous studies of an enzyme inhibitor system were measured by performing experiments at an elevated enzyme concentration. These results indicate that consideration of the quality of the data acquired using a particular assay is an important factor when selecting the enzyme concentration at which to perform experiments used to characterize the class of enzyme inhibitors examined herein. PMID:15691501
Nanoparticles for Use in Enzyme Assays.
Kim, Young-Pil; Kim, Hak-Sung
2016-02-01
Nanoparticles (NPs) have created new ways to enhance the performance of classical biosensors in analytical sciences. NPs with unprecedented physiochemical properties can serve both as excellent carriers of bioreceptors and as signal enhancers, leading to improved assay platforms with high sensitivity and selectivity. Because enzymes play central roles in many cellular functions, specific and precise assays of their functions are of great significance in medical science and biotechnology. Here we review recent advances in NP-based biosensors and their use in enzyme assays. With fast and specific responses to enzyme-mediated reactions, NPs transduce and amplify the initial responses into various types of signals, such as electrochemical, optical and magnetic ones. Translation of their potential should lead to functionalized NPs finding wide applications in diagnostics, drug development and biotechnology. PMID:26662229
Classical trajectory Monte Carlo investigation for Lorentz ionization of H (1s)
Institute of Scientific and Technical Information of China (English)
He Bin; Wang Jian-Guo; Liu Chun-Lei
2013-01-01
Lorentz ionization of H(1s) is investigated by classical trajectory Monte Carlo (CTMC) simulation.The effect of the transverse magnetic field on the considered process is analyzed in terms of the time evolution of interactions in the system,total electron energy,and electron trajectories.A classical mechanism for the ionization is found,where the variation of the kinetic energy of the nuclei is found to be important in the process.Compared with the results of tunneling ionization,the classical mechanism becomes more and more important with the increase of the velocity of the H-atom or the strength of the magnetic field.
Enzyme activity in the crowded milieu.
Directory of Open Access Journals (Sweden)
Tobias Vöpel
Full Text Available The cytosol of a cell is a concentrated milieu of a variety of different molecules, including small molecules (salts and metabolites and macromolecules such as nucleic acids, polysaccharides, proteins and large macromolecular complexes. Macromolecular crowding in the cytosolic environment is proposed to influence various properties of proteins, including substrate binding affinity and enzymatic activity. Here we chose to use the synthetic crowding agent Ficoll, which is commonly used to mimic cytosolic crowding conditions to study the crowding effect on the catalytic properties of glycolytic enzymes, namely phosphoglycerate kinase, glyceraldehyde 3-phosphate dehydrogenase, and acylphosphatase. We determined the kinetic parameters of these enzymes in the absence and in the presence of the crowding agent. We found that the Michaelis constant, K(m, and the catalytic turnover number, k(cat, of these enzymes are not perturbed by the presence of the crowding agent Ficoll. Our results support earlier findings which suggested that the Michaelis constant of certain enzymes evolved in consonance with the substrate concentration in the cell to allow effective enzyme function in bidirectional pathways. This conclusion is further supported by the analysis of nine other enzymes for which the K(m values in the presence and absence of crowding agents have been measured.
A De Novo Variant in Galactose-1-P Uridylyltransferase (GALT) Leading to Classic Galactosemia
Tran, Thanh-Thanh (Claire) V.; Liu, Ying; Michael E Zwick; Ramachandran, Dhanya; Cutler, David J.; Huang, Xiaoping; Gerard T. Berry; Fridovich-Keil, Judith L.
2015-01-01
Classic galactosemia (CG) is a potentially lethal genetic disease that results from profound impairment of galactose-1-P uridylyltransferase (GALT), the middle enzyme in the Leloir pathway of galactose metabolism. Patients with CG carry pathogenic loss-of-function mutations in both of their GALT alleles; the parents of patients are considered obligate carriers. We report here a first exception to that rule – a de novoGALT variant in a patient with classic galactosemia. The new variant, c.563A...
Functional and structural impact of the most prevalent missense mutations in classic galactosemia
Coelho, Ana I; Trabuco, Matilde; Ramos, Ruben; Silva, Maria João; Tavares de Almeida, Isabel; Leandro, Paula; Rivera, Isabel; Vicente, João B
2014-01-01
Galactose-1-phosphate uridylyltransferase (GALT) is a key enzyme in galactose metabolism, particularly important in the neonatal period due to ingestion of galactose-containing milk. GALT deficiency results in the genetic disorder classic galactosemia, whose pathophysiology is still not fully elucidated. Whereas classic galactosemia has been hypothesized to result from GALT misfolding, a thorough functional–structural characterization of GALT most prevalent variants was still lacking, hamperi...
Comparison of Three Different Methods for Measuring Classical Pathway Complement Activity
Jaskowski, Troy D; Martins, Thomas B; Litwin, Christine M.; Hill, Harry R.
1999-01-01
The complement system plays an important role in host defense against infection and in most inflammatory processes. The standard 50% hemolytic complement (CH50) assay is the most commonly used method of screening patient sera for functional activity of the classical complement pathway. Our objective in this study was to compare two newer methods (the enzyme immunoassay and the liposome immunoassay) to a commercial CH50 assay for measuring total classical complement activity. We conclude that ...
Paredes Julio Cesar Muñoz; Oliveira Liliane Guimarães; Braga Alexandre de Carvalho; Trevisol Iara Maria; Roehe Paulo Michel
1999-01-01
An indirect enzyme linked immunoassay (ELISA-I) was developed and standardized for the serological diagnosis of classical swine fever (CSF). For the comparison, nine hundred and thirty-seven swine serum samples were tested by serum neutralization followed by immunoperoxidase staining (NPLA), considered as the standard. Of these, 223 were positive and 714 negative for neutralizing antibodies to classical swine fever virus (CSFV). In relation to the NPLA, the ELISA-I presented a 98.2% sensitivi...
Teaching Classical Mechanics using Smartphones
Chevrier, Joel; Ledenmat, Simon; Bsiesy, Ahmad
2012-01-01
Using a personal computer and a smartphone, iMecaProf is a software that provides a complete teaching environment for practicals associated to a Classical Mechanics course. iMecaProf proposes a visual, real time and interactive representation of data transmitted by a smartphone using the formalism of Classical Mechanics. Using smartphones is more than using a set of sensors. iMecaProf shows students that important concepts of physics they here learn, are necessary to control daily life smartphone operations. This is practical introduction to mechanical microsensors that are nowadays a key technology in advanced trajectory control. First version of iMecaProf can be freely downloaded. It will be tested this academic year in Universit\\'e Joseph Fourier (Grenoble, France)
Classical databases and knowledge organization
DEFF Research Database (Denmark)
Hjørland, Birger
2015-01-01
) in the design and use of classical databases. An underlying issue is the kind of retrieval system for which one should aim. Warner’s (2010) differentiation between the computer science traditions and an older library-oriented tradition seems important; the former aim to transform queries......This paper considers classical bibliographic databases based on the Boolean retrieval model (such as MEDLINE and PsycInfo). This model is challenged by modern search engines and information retrieval (IR) researchers, who often consider Boolean retrieval a less efficient approach. The paper...... examines this claim and argues for the continued value of Boolean systems, which suggests two further considerations: (1) the important role of human expertise in searching (expert searchers and “information literate” users) and (2) the role of library and information science and knowledge organization (KO...
Classical Concepts in Quantum Programming
Oemer, B
2002-01-01
The rapid progress of computer technology has been accompanied by a corresponding evolution of software development, from hardwired components and binary machine code to high level programming languages, which allowed to master the increasing hardware complexity and fully exploit its potential. This paper investigates, how classical concepts like hardware abstraction, hierarchical programs, data types, memory management, flow of control and structured programming can be used in quantum computing. The experimental language QCL will be introduced as an example, how elements like irreversible functions, local variables and conditional branching, which have no direct quantum counterparts, can be implemented, and how non-classical features like the reversibility of unitary transformation or the non-observability of quantum states can be accounted for within the framework of a procedural programming language.
Classical theory of algebraic numbers
Ribenboim, Paulo
2001-01-01
Gauss created the theory of binary quadratic forms in "Disquisitiones Arithmeticae" and Kummer invented ideals and the theory of cyclotomic fields in his attempt to prove Fermat's Last Theorem These were the starting points for the theory of algebraic numbers, developed in the classical papers of Dedekind, Dirichlet, Eisenstein, Hermite and many others This theory, enriched with more recent contributions, is of basic importance in the study of diophantine equations and arithmetic algebraic geometry, including methods in cryptography This book has a clear and thorough exposition of the classical theory of algebraic numbers, and contains a large number of exercises as well as worked out numerical examples The Introduction is a recapitulation of results about principal ideal domains, unique factorization domains and commutative fields Part One is devoted to residue classes and quadratic residues In Part Two one finds the study of algebraic integers, ideals, units, class numbers, the theory of decomposition, iner...
Classical Probability and Quantum Outcomes
Directory of Open Access Journals (Sweden)
James D. Malley
2014-05-01
Full Text Available There is a contact problem between classical probability and quantum outcomes. Thus, a standard result from classical probability on the existence of joint distributions ultimately implies that all quantum observables must commute. An essential task here is a closer identification of this conflict based on deriving commutativity from the weakest possible assumptions, and showing that stronger assumptions in some of the existing no-go proofs are unnecessary. An example of an unnecessary assumption in such proofs is an entangled system involving nonlocal observables. Another example involves the Kochen-Specker hidden variable model, features of which are also not needed to derive commutativity. A diagram is provided by which user-selected projectors can be easily assembled into many new, graphical no-go proofs.
From classical to quantum physics
Stehle, Philip
2017-01-01
Suitable for lay readers as well as students, this absorbing survey explores the twentieth-century transition from classical to quantum physics. Author Philip Stehle traces the shift in the scientific worldview from the work of Galileo, Newton, and Darwin to the modern-day achievements of Max Planck, Albert Einstein, Ernest Rutherford, Niels Bohr, and others of their generation. His insightful overview examines not only the history of quantum physics but also the ways that progress in the discipline changed our understanding of the physical world and forces of nature. This chronicle of the second revolution in the physical sciences conveys the excitement and suspense that new developments produced in the scientific community. The narrative ranges from the classical physics of the seventeenth-century to the emergence of quantum mechanics with the entrance of the electron, the rise of relativity theory, the development of atomic theory, and the recognition of wave-particle duality. Relevant mathematical details...
On refinement of certain laws of classical electrodynamics
Mende, F F
2004-01-01
The problems considered refer to the material equations of electric- and magnetoelectric induction. Some contradictions found in fundamental studies on classical electrodynamics have been explained. The notion magnetoelectric induction has been introduced, which permits symmetrical writing of the induction laws. It is shown that the results of the special theory of relativity can be obtained from these laws through the Galilean transformations. The permittivity and permeability of materials media are shown to be independent of frequency. The notions magnetoelectrokinetic and electromagnetopotential waves and kinetic capacity have been introduced. It is shown that along with the longitudinal Langmuir resonance, the transverse resonance is possible in nonmagnetized plasma, and both the resonances are degenerate. A new notion scalar-vector potential is introduced, which permits solution of all present-day problems of classical electrodynamics. The use of the scalar-vector potential makes the magnetic field notio...
Classical Models of Subatomic Particles
Mann, R. B.; Morris, M. S.
1993-01-01
We look at the program of modelling a subatomic particle---one having mass, charge, and angular momentum---as an interior solution joined to a classical general-relativistic Kerr-Newman exterior spacetime. We find that the assumption of stationarity upon which the validity of the Kerr-Newman exterior solution depends is in fact violated quantum mechanically for all known subatomic particles. We conclude that the appropriate stationary spacetime matched to any known subatomic particle is flat ...
Classical models of subatomic particles
International Nuclear Information System (INIS)
We look at the program of modelling a subatomic particle - one having mass, charge, and angular momentum - as an interior solution joined to a classical general-relativistic Kerr-Newman exterior spacetime. We find that the assumption of stationarity upon which the validity of the Kerr-Newman exterior solution depends is in fact violated quantum mechanically for all known subatomic particles. We conclude that the appropriate stationary spacetime matched to any known subatomic particle is flat space. (orig.)
Semi-classical signal analysis
Laleg-Kirati, Taous-Meriem; Sorine, Michel
2010-01-01
This study introduces a new signal analysis method called SCSA, based on a semi-classical approach. The main idea in the SCSA is to interpret a pulse-shaped signal as a potential of a Schr\\"odinger operator and then to use the discrete spectrum of this operator for the analysis of the signal. We present some numerical examples and the first results obtained with this method on the analysis of arterial blood pressure waveforms.
Classic ballet dancers postural patterns
Joseani Paulini Neves Simas; Sebastião Iberes Lopes Melo
2008-01-01
The aim of this study was to evaluate classic ballet practice and its influence on postural patterns and (a) identify the most frequent postural changes; (b) determine the postural pattern; (c) verify the existence of association of practice time and postural changes. The investigation was carried out in two stages: one, description in which 106 dancers participated; the other, causal comparative in which 50 dancers participated; and (a) questionnaire; (b) a checkerboard; (c) postural chart; ...
Classical Concepts in Quantum Programming
Oemer, Bernhard
2002-01-01
The rapid progress of computer technology has been accompanied by a corresponding evolution of software development, from hardwired components and binary machine code to high level programming languages, which allowed to master the increasing hardware complexity and fully exploit its potential. This paper investigates, how classical concepts like hardware abstraction, hierarchical programs, data types, memory management, flow of control and structured programming can be used in quantum comput...
Semi-classical signal analysis
Laleg-Kirati, Taous-Meriem
2012-09-30
This study introduces a new signal analysis method, based on a semi-classical approach. The main idea in this method is to interpret a pulse-shaped signal as a potential of a Schrödinger operator and then to use the discrete spectrum of this operator for the analysis of the signal. We present some numerical examples and the first results obtained with this method on the analysis of arterial blood pressure waveforms. © 2012 Springer-Verlag London Limited.
Gauge Invariance in Classical Electrodynamics
Engelhardt, W
2005-01-01
The concept of gauge invariance in classical electrodynamics assumes tacitly that Maxwell's equations have unique solutions. By calculating the electromagnetic field of a moving particle both in Lorenz and in Coulomb gauge and directly from the field equations we obtain, however, contradicting solutions. We conclude that the tacit assumption of uniqueness is not justified. The reason for this failure is traced back to the inhomogeneous wave equations which connect the propagating fields and their sources at the same time.
To Foundations of Classical Electrodynamics
Bessonov, E. G.
1997-01-01
In the present work foundations of the law of the energy conservation and the introduction of particles in the classical electrodynamics are discussed. We pay attention to a logic error which takes place at an interpretation of the Poynting's theorem as the law of conservation of energy. It was shown that the laws of conservation of energy and momentum of the system of electromagnetic fields and charged particles does not follow from the equations of electrodynamics and the violation of these...
Applications of classical detonation theory
Energy Technology Data Exchange (ETDEWEB)
Davis, W.C.
1994-09-01
Classical detonation theory is the basis for almost all calculations of explosive systems. One common type of calculation is of the detailed behavior of inert parts driven by explosive, predicting pressures, velocities, positions, densities, energies, etc as functions of time. Another common application of the theory is predicting the detonation state and expansion isentrope of a new explosive or mixtures, perhaps an explosive that has not yet been made. Both types of calculations are discussed.
A Sensitive Cyclic Nucleotide Phosphodiesterase Assay for Transient Enzyme Kinetics
Lookeren Campagne, Michiel M. van; Haastert, Peter J.M. van
1983-01-01
A new assay for cyclic nucleotide phosphodiesterase has been developed by using reverse-phase column chromatography for the separation of product and substrate of the enzymatic reaction. The polar 5'-nucleotides are not retarded by the column, while the more lipophilic cyclic nucleotides bind to the
Multiscale Simulations: From Enzyme Kinetics to Fluctuating Hydrodynamics
Shang, Barry Zhongqi
2013-01-01
The development of multiscale methods for computational simulation of biophysical systems represents a significant challenge. Effective computational models that bridge physical insights obtained from atomistic simulations and experimental findings are lacking. An accurate passing of information between these scales would enable: (1) an improved physical understanding of structure-function relationships, and (2) enhanced rational strategies for molecular engineering and materials design. Two ...
Effective use of enzyme microreactors : thermal, kinetic and ethical guidelines
Swarts, J.W.
2009-01-01
Microreactor technology is reported to have many benefits over regular chemical methods. Due to the small dimensions over which temperature and concentration gradients can exist, mass and heat transfer can be very quick. This could minimize the time needed for heating and mixing, due to a reduction
Kinetics of Enzyme Biodegradation of New Synthesized Copolymers
Directory of Open Access Journals (Sweden)
Rosa Mateva
2005-04-01
Full Text Available Block copolymers of the poly-(hexanlactam-co-block-poly-(?-valerolactone from ABA-type were synthesized via anionic polymerization of hexanlactam (HL with the sodium salt of hexanlactam (Na-HL as an initiator and polymeric activator (PAC. PAC, on the base of poly-?-valerolactone (PVL, was used as a soft central block. Synthetic PVL is very attractive biomaterial - nontoxic, biocompatibility and biodegradable polyester[5-8]. Modification of HL with PVL, renders these system biodegradable[1]. Isolated copolymers were characterized by various spectroscopic techniques. The effect of the chemical and physical structure of the synthesized block copolymers on the biodegradation was investigated. Biodegradation of block copolyester amides was studied by means of lipase and involves the enzymatic hydrolysis of ester groups in PVL.
Kinetics of Enzyme Biodegradation of New Synthesized Copolymers
Rosa Mateva; Natalia Toncheva; Lubov Yotova
2005-01-01
Block copolymers of the poly-(hexanlactam)-co-block-poly-(?-valerolactone) from ABA-type were synthesized via anionic polymerization of hexanlactam (HL) with the sodium salt of hexanlactam (Na-HL) as an initiator and polymeric activator (PAC). PAC, on the base of poly-?-valerolactone (PVL), was used as a soft central block. Synthetic PVL is very attractive biomaterial - nontoxic, biocompatibility and biodegradable polyester[5-8]. Modification of HL with PVL, renders these system biodegradable...
Savoglidis, Georgios; da Silveira Dos Santos, Aline Xavier; Riezman, Isabelle; Angelino, Paolo; Riezman, Howard; Hatzimanikatis, Vassily
2016-09-01
We present a model-based method, designated Inverse Metabolic Control Analysis (IMCA), which can be used in conjunction with classical Metabolic Control Analysis for the analysis and design of cellular metabolism. We demonstrate the capabilities of the method by first developing a comprehensively curated kinetic model of sphingolipid biosynthesis in the yeast Saccharomyces cerevisiae. Next we apply IMCA using the model and integrating lipidomics data. The combinatorial complexity of the synthesis of sphingolipid molecules, along with the operational complexity of the participating enzymes of the pathway, presents an excellent case study for testing the capabilities of the IMCA. The exceptional agreement of the predictions of the method with genome-wide data highlights the importance and value of a comprehensive and consistent engineering approach for the development of such methods and models. Based on the analysis, we identified the class of enzymes regulating the distribution of sphingolipids among species and hydroxylation states, with the D-phospholipase SPO14 being one of the most prominent. The method and the applications presented here can be used for a broader, model-based inverse metabolic engineering approach. PMID:27113440
Rindler particles and classical radiation
International Nuclear Information System (INIS)
We describe the quantum and classical radiation emitted by a uniformly accelerating point source in terms of the elementary processes of absorption and emission of Rindler scalar photons of the Fulling-Davies-Unruh bath observed by a co-accelerating observer. To this end we compute the rate at which a DeWitt detector emits a Minkowski scalar particle with defined transverse momentum per unit of proper time of the source and we show that it corresponds to the induced absorption or spontaneous and induced emission of Rindler particles from the thermal bath. We then take what could be called the inert limit of the DeWitt detector by considering the limit of no energy gap. As suggested by DeWitt, we identify, in this limit, the detector with a classical point source and verify the consistency of our computation with the classical result. Finally, we study the behaviour of the emission rate in D spacetime dimensions in connection with the so-called apparent statistics inversion
Rindler Photons and Classical Radiation
Díaz, D E
2001-01-01
We describe the quantum and classical radiation by a uniformly accelerating point source in terms of the elementary processes of absorption and emission of Rindler scalar photons of the Fulling-Davies-Unruh bath observed by a co-accelerating observer.To this end we compute the emission rate by a DeWitt detector of a Minkowski scalar field particle with defined transverse momentum per unit of proper time of the source and we show that it corresponds to the induced absorption or spontaneous and induced emission of Rindler photons from the thermal bath. We then take what could be called the inert limit of the DeWitt detector by considering the limit of zero gap energy. As suggested by DeWitt, we identify in this limit the detector with a classical point source and verify the consistency of our computation with the classical result. Finally, we study the behavior of the emission rate in D space-time dimensions in connection with the so called apparent statistics inversion.
Quantum systems as classical systems
Cassa, A
2001-01-01
A characteristical property of a classical physical theory is that the observables are real functions taking an exact outcome on every (pure) state; in a quantum theory, at the contrary, a given observable on a given state can take several values with only a predictable probability. However, even in the classical case, when an observer is intrinsically unable to distinguish between some distinct states he can convince himself that the measure of its ''observables'' can have several values in a random way with a statistical character. What kind of statistical theory is obtainable in this way? It is possible, for example, to obtain exactly the statistical previsions of quantum mechanics? Or, in other words, can a physical system showing a classical behaviour appear to be a quantum system to a confusing observer? We show that from a mathematical viewpoint it is not difficult to produce a theory with hidden variables having this property. We don't even try to justify in physical terms the artificial construction ...
Quantum to Classical Randomness Extractors
Berta, Mario; Wehner, Stephanie
2011-01-01
Even though randomness is an essential resource for many information processing tasks, it is not easily found in nature. The goal of randomness extraction is to distill (almost) perfect randomness from a weak source of randomness. When the source yields a classical string X, many extractor constructions are known. Yet, when considering a physical randomness source, X is itself ultimately the result of a measurement on an underlying quantum system. When characterizing the power of a source to supply randomness it is hence a natural question to ask, how much classical randomness we can extract from a quantum state. To tackle this question we here take on the study of quantum-to-classical randomness extractors (QC-extractors). We provide constructions of QC-extractors based on measurements in a full set of mutually unbiased bases (MUBs), and certain single qubit measurements. As the first application, we show that any QC-extractor gives rise to entropic uncertainty relations with respect to quantum side informat...
Discrete Kinetic Models and Conservation Laws
Vinerean, Mirela Cristina
2005-01-01
Classical kinetic theory of gases is based on the Boltzmann equation (BE) which describes the evolution of a system of particles undergoing collisions preserving mass, momentum and energy. Discretization methods have been developed on the idea of replacing the original BE by a finite set of nonlinear hyperbolic PDEs corresponding to the densities linked to a suitable finite set of velocities. One open problem related to the discrete BE is the construction of normal (fulfilling only physical c...
A Simple Classroom Teaching Technique to Help Students Understand Michaelis-Menten Kinetics
Runge, Steven W.; Hill, Brent J. F.; Moran, William M.
2006-01-01
A new, simple classroom technique helps cell biology students understand principles of Michaelis-Menten enzyme kinetics. A student mimics the enzyme and the student's hand represents the enzyme's active site. The catalytic event is the transfer of marbles (substrate molecules) by hand from one plastic container to another. As predicted, increases…
Enzymes for improved biomass conversion
Energy Technology Data Exchange (ETDEWEB)
Brunecky, Roman; Himmel, Michael E.
2016-02-02
Disclosed herein are enzymes and combinations of the enzymes useful for the hydrolysis of cellulose and the conversion of biomass. Methods of degrading cellulose and biomass using enzymes and cocktails of enzymes are also disclosed.
Directory of Open Access Journals (Sweden)
M. Plebani
2011-09-01
Full Text Available Skeletal muscle disorders may result in release of muscle enzymes into the circulation and give increased serum enzyme activity. A variety of enzymes routinely determined in the clinical laboratory may be elevated, but creatine kinase is the enzyme present in the highest concentration in muscle, and in every variety of muscle disease is the serum enzyme which shows the greatest incidence and degree of elevation. Aspartate aminotransferase is the enzyme associated most significantly with inflammation. A diagnostic algorithm based on the combined measurement of creatine kinase, aspartate aminotransferase and aldolase has been found to discriminate muscular distrophies from polymyositis and other myopathies. This combination of laboratory tests has diagnostic application and thus allows the clinician to better select patients who need to have a skeletal muscle biopsy as a diagnostic procedure.
Kinetic study of sphingomyelin hydrolysis for ceramide production
DEFF Research Database (Denmark)
Zhang, Long; Hellgren, Lars; Xu, Xuebing
2008-01-01
reaction at 65 °C. The reactions for both the soluble and immobilized enzymes followed Michaelis–Menten kinetics. Km's for the soluble and immobilized enzymes were 1.07 ± 0.32 and 1.26 ± 0.19 mM, respectively. The value of Vmax was markedly decreased by the immobilization without much change in Km, as if...... cosmetic and pharmaceutical industries such as in hair and skin care products. The enzymatic hydrolysis of sphingomyelin has been proved to be a feasible method to produce ceramide. The kinetic performance of sphingomyelin hydrolysis in the optimal two-phase (water:organic solvent) reaction system was...... investigated to elucidate the possible reaction mechanism and also to further improve the hydrolysis performance. Enzyme in solution had less thermal stability than the enzyme powder and the immobilized enzyme. The thermal inactivation of phospholipase C in all the three forms did not follow the first order...
Relativistic Entropy and Related Boltzmann Kinetics
Kaniadakis, G
2009-01-01
It is well known that the particular form of the two-particle correlation function, in the collisional integral of the classical Boltzmman equation, fix univocally the entropy of the system, which turn out to be the Boltzmann-Gibbs-Shannon entropy. In the ordinary relativistic Boltzmann equation, some standard generalizations, with respect its classical version, imposed by the special relativity, are customarily performed. The only ingredient of the equation, which tacitely remains in its original classical form, is the two-particle correlation function, and this fact imposes that also the relativistic kinetics is governed by the Boltzmann-Gibbs-Shannon entropy. Indeed the ordinary relativistic Boltzmann equation admits as stationary stable distribution, the exponential Juttner distribution. Here, we show that the special relativity laws and the maximum entropy principle, suggest a relativistic generalization also of the two-particle correlation function and then of the entropy. The so obtained, fully relativ...
The Relation between Classical and Quantum Electrodynamics
Directory of Open Access Journals (Sweden)
Mario Bacelar Valente
2011-01-01
Full Text Available Quantum electrodynamics presents intrinsic limitations in the description of physical processes that make it impossible to recover from it the type of description we have in classical electrodynamics. Hence one cannot consider classical electrodynamics as reducing to quantum electrodynamics and being recovered from it by some sort of limiting procedure. Quantum electrodynamics has to be seen not as an more fundamental theory, but as an upgrade of classical electrodynamics, which permits an extension of classical theory to the description of phenomena that, while being related to the conceptual framework of the classical theory, cannot be addressed from the classical theory.
Distribution kinetics of polymer crystallization and the Avrami equation
Yang, Jiao; McCoy, Benjamin J; Madras, Giridhar
2005-01-01
Cluster distribution kinetics is adopted to explore the kinetics of polymer crystallization. Population balance equations based on crystal size distribution and concentration of amorphous polymer segments are solved numerically and the related dynamic moment equations are also solved. The model accounts for heterogeneous or homogeneous nucleation and crystal growth. Homogeneous nucleation rates follow the classical surface-energy nucleation theory. Different mass dependences of growth and dis...
Casimir effect: The classical limit
International Nuclear Information System (INIS)
We analyze the high temperature (or classical) limit of the Casimir effect. A useful quantity which arises naturally in our discussion is the 'relative Casimir energy', which we define for a configuration of disjoint conducting boundaries of arbitrary shapes, as the difference of Casimir energies between the given configuration and a configuration with the same boundaries infinitely far apart. Using path integration techniques, we show that the relative Casimir energy vanishes exponentially fast in temperature. This is consistent with a simple physical argument based on Kirchhoff's law. As a result the 'relative Casimir entropy', which we define in an obviously analogous manner, tends, in the classical limit, to a finite asymptotic value which depends only on the geometry of the boundaries. Thus the Casimir force between disjoint pieces of the boundary, in the classical limit, is entropy driven and is governed by a dimensionless number characterizing the geometry of the cavity. Contributions to the Casimir thermodynamical quantities due to each individual connected component of the boundary exhibit logarithmic deviations in temperature from the behavior just described. These logarithmic deviations seem to arise due to our difficulty to separate the Casimir energy (and the other thermodynamical quantities) from the 'electromagnetic' self-energy of each of the connected components of the boundary in a well defined manner. Our approach to the Casimir effect is not to impose sharp boundary conditions on the fluctuating field, but rather take into consideration its interaction with the plasma of 'charge carriers' in the boundary, with the plasma frequency playing the role of a physical UV cutoff. This also allows us to analyze deviations from a perfect conductor behavior
Resonance Van Hove Singularities in Wave Kinetics
Shi, Yi-Kang
2015-01-01
Wave kinetic theory has been developed to describe the statistical dynamics of weakly nonlinear, dispersive waves. However, we show that systems which are generally dispersive can have resonant sets of wave modes with identical group velocities, leading to a local breakdown of dispersivity. This shows up as a geometric singularity of the resonant manifold and possibly as an infinite phase measure in the collision integral. Such singularities occur widely for classical wave systems, including acoustical waves, Rossby waves, helical waves in rotating fluids, light waves in nonlinear optics and also in quantum transport, e.g. kinetics of electron-hole excitations (matter waves) in graphene. These singularities are the exact analogue of the critical points found by Van Hove in 1953 for phonon dispersion relations in crystals. The importance of these singularities in wave kinetics depends on the dimension of phase space $D=(N-2)d$ ($d$ physical space dimension, $N$ the number of waves in resonance) and the degree ...
Advances In Classical Field Theory
Yahalom, Asher
2011-01-01
Classical field theory is employed by physicists to describe a wide variety of physical phenomena. These include electromagnetism, fluid dynamics, gravitation and quantum mechanics. The central entity of field theory is the field which is usually a multi component function of space and time. Those multi component functions are usually grouped together as vector fields as in the case in electromagnetic theory and fluid dynamics, in other cases they are grouped as tensors as in theories of gravitation and yet in other cases they are grouped as complex functions as in the case of quantum mechanic
Superadditivity of classical capacity revisited
Energy Technology Data Exchange (ETDEWEB)
Pilyavets, Oleg V.; Karpov, Evgueni A.; Schäfer, Joachim [QuIC, Ecole Polytechnique, Université Libre de Bruxelles, CP 165, 1050 Brussels (Belgium)
2014-12-04
We introduce new type of superadditivity for classical capacity of quantum channels, which involves the properties of channels’ environment. By imposing different restrictions on the total energy contained in channels’ environment we can consider different types of superadditivity. Using lossy bosonic and additive noise quantum channels as examples, we demonstrate that their capacities can be either additive or superadditive depending on the values of channels parameters. The parameters corresponding to transition between the additive and superadditive cases are related with recently found critical and supercritical parameters for Gaussian channels.
Lectures on classical differential geometry
Struik, Dirk J
1988-01-01
Elementary, yet authoritative and scholarly, this book offers an excellent brief introduction to the classical theory of differential geometry. It is aimed at advanced undergraduate and graduate students who will find it not only highly readable but replete with illustrations carefully selected to help stimulate the student's visual understanding of geometry. The text features an abundance of problems, most of which are simple enough for class use, and often convey an interesting geometrical fact. A selection of more difficult problems has been included to challenge the ambitious student.Writ
Solar Activity and Classical Physics
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
This review of solar physics emphasizes several of the more conspicuous scientific puzzles posed by contemporary observational knowledge of the magnetic activity of the Sun. The puzzles emphasize how much classical physics we have yet to learn from the Sun. The physics of solar activity is based on the principles of Newton, Maxwell, Lorentz, Boltzmann, et. al., along with the principles of radiative transfer. In the large, these principles are expressed by magnetohydrodynamics. A brief derivation of the magnetohydrodynamic induction and momentum equations is provided, with a discussion of popular misconceptions.
The revision of classical stock model
Institute of Scientific and Technical Information of China (English)
YE Bai-qing; WANG Hong-li
2001-01-01
On the basis of the analysis of classical stock model, according to th e limitation of the model, the article puts forward the revision of classical mo del and enforces the applicability of the stock model.
Pseudoclassical fermionic model and classical solutions
International Nuclear Information System (INIS)
We study classical limit of fermionic fields seen as Grassmann variables and deduce the proper quantization prescription using Dirac's method for constrained systems and investigate quantum meaning of classical solutions for the Thirring model. (author)
Classical Electron Theory and Conservation Laws
Kiessling, Michael K. -H.
1999-01-01
It is shown that the traditional conservation laws for total charge, energy, linear and angular momentum, hold jointly in classical electron theory if and only if classical electron spin is included as dynamical degree of freedom.
The revision of classical stock model
Institute of Scientific and Technical Information of China (English)
叶柏青; 王洪利
2001-01-01
On the basis of the analysis of classical stock model, according to the limitation of the model, the article puts forward the revision of classical model and enforces the applicability of the stock model.
Lagrangian formalism and retarded classical electrodynamics
Jan, Xavier; Llosa, Josep; Molina, Alfred
1989-01-01
Unlike the 1/c2 approximation, where classical electrodynamics is described by the Darwin Lagrangian, here there is no Lagrangian to describe retarded (resp., advanced) classical electrodynamics up to 1/c3 for two-point charges with different masses.
Magnetically responsive enzyme powders
International Nuclear Information System (INIS)
Powdered enzymes were transformed into their insoluble magnetic derivatives retaining their catalytic activity. Enzyme powders (e.g., trypsin and lipase) were suspended in various liquid media not allowing their solubilization (e.g., saturated ammonium sulfate and highly concentrated polyethylene glycol solutions, ethanol, methanol, 2-propanol) and subsequently cross-linked with glutaraldehyde. Magnetic modification was successfully performed at low temperature in a freezer (−20 °C) using magnetic iron oxides nano- and microparticles prepared by microwave-assisted synthesis from ferrous sulfate. Magnetized cross-linked enzyme powders were stable at least for two months in water suspension without leakage of fixed magnetic particles. Operational stability of magnetically responsive enzymes during eight repeated reaction cycles was generally without loss of enzyme activity. Separation of magnetically modified cross-linked powdered enzymes from reaction mixtures was significantly simplified due to their magnetic properties. - Highlights: • Cross-linked enzyme powders were prepared in various liquid media. • Insoluble enzymes were magnetized using iron oxides particles. • Magnetic iron oxides particles were prepared by microwave-assisted synthesis. • Magnetic modification was performed under low (freezing) temperature. • Cross-linked powdered trypsin and lipase can be used repeatedly for reaction
Poole, P.
1984-01-01
Hydration induced conformation and dynamic changes are followed using a variety of experimental techniques applied to hen egg white lysozyme. These changes are completed just before the onset of enzyme activity, which occurs before all polar groups are hydrated, and before monolayer coverage is attained. We suggest that these hydration induced changes are necessary for the return of enzyme activity.
Doucet, Nicolas; Pelletier, Joelle,
2004-01-01
This brief technological report presents an overview of techniques and applications in the field of directed evolution of enzyme catalysts. These techniques allow for the creation of modified enzymes that are better adapted to many industrial contexts. Recent applications in organic synthesis as well as commercial, biomedical, and environmental usage of these modified catalysts will be presented.
Magnetically responsive enzyme powders
Energy Technology Data Exchange (ETDEWEB)
Pospiskova, Kristyna, E-mail: kristyna.pospiskova@upol.cz [Regional Centre of Advanced Technologies and Materials, Palacky University, Slechtitelu 11, 783 71 Olomouc (Czech Republic); Safarik, Ivo, E-mail: ivosaf@yahoo.com [Regional Centre of Advanced Technologies and Materials, Palacky University, Slechtitelu 11, 783 71 Olomouc (Czech Republic); Department of Nanobiotechnology, Institute of Nanobiology and Structural Biology of GCRC, Na Sadkach 7, 370 05 Ceske Budejovice (Czech Republic)
2015-04-15
Powdered enzymes were transformed into their insoluble magnetic derivatives retaining their catalytic activity. Enzyme powders (e.g., trypsin and lipase) were suspended in various liquid media not allowing their solubilization (e.g., saturated ammonium sulfate and highly concentrated polyethylene glycol solutions, ethanol, methanol, 2-propanol) and subsequently cross-linked with glutaraldehyde. Magnetic modification was successfully performed at low temperature in a freezer (−20 °C) using magnetic iron oxides nano- and microparticles prepared by microwave-assisted synthesis from ferrous sulfate. Magnetized cross-linked enzyme powders were stable at least for two months in water suspension without leakage of fixed magnetic particles. Operational stability of magnetically responsive enzymes during eight repeated reaction cycles was generally without loss of enzyme activity. Separation of magnetically modified cross-linked powdered enzymes from reaction mixtures was significantly simplified due to their magnetic properties. - Highlights: • Cross-linked enzyme powders were prepared in various liquid media. • Insoluble enzymes were magnetized using iron oxides particles. • Magnetic iron oxides particles were prepared by microwave-assisted synthesis. • Magnetic modification was performed under low (freezing) temperature. • Cross-linked powdered trypsin and lipase can be used repeatedly for reaction.
Enzyme and microbial sensors for environmental monitoring
Wollenberger, U.; Neumann, B.; Scheller, Frieder W.
1993-03-01
Biosensors employing the biocatalyst on a different level of integration have been developed for monitoring environmental pollution. These probes range from laboratory specimen to commercial detectors applied to analyzers. This paper presents a selection of recent developments on amperometric enzyme and microbial biosensors. A monoenzymatic bulk type carbon electrode is described for biosensing organic hydroperoxides in aqueous solutions. Here, peroxidase is immobilized within the electrode body and the direct electron transfer between electrode and enzyme is measured. Both, reversible and irreversible inhibitors of acetylcholinesterase have been quantified by using a kinetically controlled acetylcholine enzyme sequence electrode. The inhibitory effect of pesticides such as butoxycarboxime, dimethoate, and trichlorfon could be quantified within 6 min in micrometers olar concentrations. Different multi-enzyme electrodes have been developed for the determination of inorganic phosphate. These sensors represent examples of sequentially acting enzymes in combination with enzymatic analyte recycling. Using this type of amplification nanomolar concentrations could be measured. A very fast responding microbial sensor for biological oxygen demand has been developed by immobilizing Trichosporon cutaneum onto an oxygen electrode. With this whole cell sensor waste water can be assayed with a sample frequency of 20 per hour and a working stability of more than 30 days.
Technics of classical and digital photography comparsion
Kvapilová, Kamila
2012-01-01
This bachelor work is aimed at basic principles of taking photos by classical and digital camera. Describes methods for achieving of required photos by digital way and also classical taking photos on cine-film. Compares the technology of classical and digital photography from the beginning, which is getting the camera and accessories. It also describes the construction and control of the camera. Processing of photo compares the quality of digital and classic photo.
Markkinointiviestintäsuunnitelma : Classic Coffee Oy
Eerola, Laura
2015-01-01
Opinnäytetyön aiheena oli laatia markkinointiviestintäsuunnitelma kalenterivuodelle 2016 vuosikellon muodossa, toimintansa jo vakiinnuttaneelle Classic Coffee Oy:lle. Classic Coffee Oy on vuonna 2011 perustettu, Tampereella toimiva kahvila-alan yritys joka tarjoaa lounaskahvilatoiminnan lisäksi laadukkaita konditoria-palveluita, yritys- ja kokoustarjoiluja sekä tilavuokrausta. Classic Coffee Oy:llä on yksi kahvila, Classic Coffee Tampella. Kahvila sijaitsee Tampellassa, Tampereen keskustan vä...
The new-classical contribution to macroeconomics
D. LAIDLER
2013-01-01
This work is devoted to assessing New-Classical ideas, and to asking what of lasting importance this school of macroeconomics has contributed since the early 1970s. It deals in turn with the relationship between New-Classical Economics and Monetarism, the relative explanatory power of these two bodies of doctrine over empirical evidence, and the claims of New-Classical Economics to embody a superior analytic method. The author argues that, although the particular ways in which New-Classical M...
Physiological characteristics of classical ballet.
Schantz, P G; Astrand, P O
1984-10-01
The aerobic and anaerobic energy yield during professional training sessions ("classes") of classical ballet as well as during rehearsed and performed ballets has been studied by means of oxygen uptake, heart rate, and blood lactate concentration determinations on professional ballet dancers from the Royal Swedish Ballet in Stockholm. The measured oxygen uptake during six different normal classes at the theatre averaged about 35-45% of the maximal oxygen uptake, and the blood lactate concentration averaged 3 mM (N = 6). During 10 different solo parts of choreographed dance (median length = 1.8 min) representative for moderately to very strenuous dance, an average oxygen uptake (measured during the last minute) of 80% of maximum and blood lactate concentration of 10 mM was measured (N = 10). In addition, heart rate registrations from soloists in different ballets during performance and final rehearsals frequently indicated a high oxygen uptake relative to maximum and an average blood lactate concentration of 11 mM (N = 5). Maximal oxygen uptake, determined in 1971 (N = 11) and 1983 (N = 13) in two different groups of dancers, amounted to on the average 51 and 56 ml X min-1 X kg-1 for the females and males, respectively. In conclusion, classical ballet is a predominantly intermittent type of exercise. In choreographed dance each exercise period usually lasts only a few minutes, but can be very demanding energetically, while during the dancers' basic training sessions, the energy yield is low. PMID:6513765
Curiel, Erik
2014-01-01
In the early 1970s it is was realized that there is a striking formal analogy between the Laws of black-hole mechanics and the Laws of classical thermodynamics. Before the discovery of Hawking radiation, however, it was generally thought that the analogy was only formal, and did not reflect a deep connection between gravitational and thermodynamical phenomena. It is still commonly held that the surface gravity of a stationary black hole can be construed as a true physical temperature and its area as a true entropy only when quantum effects are taken into account; in the context of classical general relativity alone, one cannot cogently construe them so. Does the use of quantum field theory in curved spacetime offer the only hope for taking the analogy seriously? I think the answer is `no'. To attempt to justify that answer, I shall begin by arguing that the standard argument to the contrary is not physically well founded, and in any event begs the question. Looking at the various ways that the ideas of "tempe...
Entanglement-Enhanced Classical Communication
Herrera-Martí, David A
2008-01-01
This thesis will be focused on the classical capacity of quantum channels, one of the first areas treated by quantum information theorists. The problem is fairly solved since some years. Nevertheless, this work will give me a reason to introduce a consistent formalism of the quantum theory, as well as to review fundamental facts about quantum non-locality and how it can be used to enhance communication. Moreover, this reflects my dwelling in the spirit of classical information theory, and it is intended to be a starting point towards a thorough study of how quantum technologies can help to shape the future of telecommunications. Whenever it was possible, heuristic reasonings were introduced instead of rigorous mathematical proofs. This finds an explanation in that I am a self-taught neophyte in the field, and just about every time I came across a new concept, physical arguments were always more compelling to me than just maths. The technical content of the thesis is twofold. On one hand, a quadratic classific...
Kinetic coefficients for quark-antiquark plasma with quantal treatment of color
International Nuclear Information System (INIS)
We discuss the near-equilibrium state of the q-bar q plasma treated as a system of classical particles with quantized color charges. The matrix of the kinetic coefficients is calculated (in the relaxation approximation of the transport equation) and compared with its classical version. The color Ohm law is recovered but the structure of the kinetic matrix is different. 5 refs. (author)
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...... 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 as...
Collection of problems in classical mechanics
Kotkin, G L; ter Haar, D
1971-01-01
Collection of Problems in Classical Mechanics presents a set of problems and solutions in physics, particularly those involving mechanics. The coverage of the book includes 13 topics relevant to classical mechanics, such as integration of one-dimensional equations of motion; the Hamiltonian equations of motion; and adiabatic invariants. The book will be of great use to physics students studying classical mechanics.
Classical approximations of relativistic quantum physics
Johnson, Glenn Eric
2016-01-01
A correspondence of classical to quantum physics studied by Schr\\"{o}\\-dinger and Ehrenfest applies without the necessity of technical conjecture that classical observables are associated with Hermitian Hilbert space operators. This correspondence provides appropriate nonrelativistic classical interpretations to realizations of relativistic quantum physics that are incompatible with the canonical formalism. Using this correspondence, Newtonian mechanics for a $1/r$ potential provides approxim...
Diminuendo: Classical Music and the Academy
Asia, Daniel
2010-01-01
How is the tradition of Western classical music faring on university campuses? Before answering this question, it is necessary to understand what has transpired with classical music in the wider culture, as the relationship between the two is so strong. In this article, the author discusses how classical music has taken a big cultural hit in…
Quantum electrodynamics in a classical approximation, 1
International Nuclear Information System (INIS)
Quantum electrodynamics is formulated in a classical approximation. A quantum mechanical proper-time is employed as a useful parameter, which enables us to elucidate the relationship between quantum electrodynamics and classical electrodynamics. The classical motion of a charged particle is realized as an asymptotic limit of quantum electrodynamics. (author)
Gorban, A. N.; Karlin, I. V.
2003-01-01
Nonlinear kinetic equations are reviewed for a wide audience of specialists and postgraduate students in physics, mathematical physics, material science, chemical engineering and interdisciplinary research. Contents: The Boltzmann equation, Phenomenology and Quasi-chemical representation of the Boltzmann equation, Kinetic models, Discrete velocity models, Direct simulation, Lattice Gas and Lattice Boltzmann models, Minimal Boltzmann models for flows at low Knudsen number, Other kinetic equati...
Quaternary Structure Analyses of an Essential Oligomeric Enzyme.
Soares da Costa, Tatiana P; Christensen, Janni B; Desbois, Sebastien; Gordon, Shane E; Gupta, Ruchi; Hogan, Campbell J; Nelson, Tao G; Downton, Matthew T; Gardhi, Chamodi K; Abbott, Belinda M; Wagner, John; Panjikar, Santosh; Perugini, Matthew A
2015-01-01
Here, we review recent studies aimed at defining the importance of quaternary structure to a model oligomeric enzyme, dihydrodipicolinate synthase. This will illustrate the complementary and synergistic outcomes of coupling the techniques of analytical ultracentrifugation with enzyme kinetics, in vitro mutagenesis, macromolecular crystallography, small angle X-ray scattering, and molecular dynamics simulations, to demonstrate the role of subunit self-association in facilitating protein dynamics and enzyme function. This multitechnique approach has yielded new insights into the molecular evolution of protein quaternary structure. PMID:26412653
Directory of Open Access Journals (Sweden)
Keith F. Tipton
2014-05-01
Full Text Available Data on enzyme activities and kinetics have often been reported with insufficient experimental detail to allow their repetition. This paper discusses the objectives and recommendations of the Standards for Reporting Enzyme Data (STRENDA project to define minimal experimental standards for the reporting enzyme functional data.
Prediction of radiation inactivation of presonicated a-amylase in terms of kinetic parameters
International Nuclear Information System (INIS)
Full text: In-vitro radiation inactivation of enzyme amylase denies display of optimum enzyme function owing to alterations in active site. Certain extent of enzyme activity seems to be protected in case of radiation inactivated enzyme, prior-exposed to ultrasonic frequencies. The present investigation, exploring trends of changes in kinetic parameters and its dependence on ultrasonic frequencies and gamma doses, will be discussed to highlight the functional status of active site under situation
Introducing Newton and classical physics
Rankin, William
2002-01-01
The rainbow, the moon, a spinning top, a comet, the ebb and flood of the oceans ...a falling apple. There is only one universe and it fell to Isaac Newton to discover its secrets. Newton was arguably the greatest scientific genius of all time, and yet he remains a mysterious figure. Written and illustrated by William Rankin, "Introducting Newton and Classical Physics" explains the extraordinary ideas of a man who sifted through the accumulated knowledge of centuries, tossed out mistaken beliefs, and single-handedly made enormous advances in mathematics, mechanics and optics. By the age of 25, entirely self-taught, he had sketched out a system of the world. Einstein's theories are unthinkable without Newton's founding system. He was also a secret heretic, a mystic and an alchemist, the man of whom Edmund Halley said "Nearer to the gods may no man approach!". This is an ideal companion volume to "Introducing Einstein".
Classical electromagnetism in a nutshell
Garg, Anupam
2012-01-01
This graduate-level physics textbook provides a comprehensive treatment of the basic principles and phenomena of classical electromagnetism. While many electromagnetism texts use the subject to teach mathematical methods of physics, here the emphasis is on the physical ideas themselves. Anupam Garg distinguishes between electromagnetism in vacuum and that in material media, stressing that the core physical questions are different for each. In vacuum, the focus is on the fundamental content of electromagnetic laws, symmetries, conservation laws, and the implications for phenomena such as radiation and light. In material media, the focus is on understanding the response of the media to imposed fields, the attendant constitutive relations, and the phenomena encountered in different types of media such as dielectrics, ferromagnets, and conductors. The text includes applications to many topical subjects, such as magnetic levitation, plasmas, laser beams, and synchrotrons.
Scientific Realism and Classical Physics
Singh, Virendra
2008-01-01
We recount the successful long career of classical physics, from Newton to Einstein, which was based on the philosophy of scientific realism. Special emphasis is given to the changing status and number of ontological entitities and arguments for their necessity at any time. Newton, initially, began with (i) point particles, (ii) aether, (iii) absolute space and (iv) absolute time. The electromagnetic theory of Maxwell and Faraday introduced `fields' as a new ontological entity not reducible to earlier ones. Their work also unified electricity, magnetism and optics. Repeated failure to observe the motion of earth through aether led Einstein to modify the Newtonian absolute space and time concepts to a fused Minkowski space-time and the removal of aether from basic ontological entities in his special theory of relativity. Later Einstein in his attempts to give a local theory of gravitation was led to further modify flat Minkowski space-time to the curved Riemannian space time. This reduced gravitational phenome...
Hydrogen: Beyond the Classic Approximation
International Nuclear Information System (INIS)
The classical nucleus approximation is the most frequently used approach for the resolution of problems in condensed matter physics.However, there are systems in nature where it is necessary to introduce the nuclear degrees of freedom to obtain a correct description of the properties.Examples of this, are the systems with containing hydrogen.In this work, we have studied the resolution of the quantum nuclear problem for the particular case of the water molecule.The Hartree approximation has been used, i.e. we have considered that the nuclei are distinguishable particles.In addition, we have proposed a model to solve the tunneling process, which involves the resolution of the nuclear problem for configurations of the system away from its equilibrium position
Classic ballet dancers postural patterns
Directory of Open Access Journals (Sweden)
Joseani Paulini Neves Simas
2008-06-01
Full Text Available The aim of this study was to evaluate classic ballet practice and its influence on postural patterns and (a identify the most frequent postural changes; (b determine the postural pattern; (c verify the existence of association of practice time and postural changes. The investigation was carried out in two stages: one, description in which 106 dancers participated; the other, causal comparative in which 50 dancers participated; and (a questionnaire; (b a checkerboard; (c postural chart; (d measure tape; (e camera and (f pedoscope were used as instrument. Descriptive and inferential statistics was used for analysis. The results revealed the most frequent postural changes such as hyperlordosis, unleveled shoulders and pronated ankles. Ballet seems to have negative implications in the postural development , affecting especially the vertebral spine, trunk and feet. The practice time was not a parameter to indicate the increase in postural changes. In conclusion, ballet may be associated with postural changes and determining a characteristic postural pattern.
DOE Fundamentals Handbook: Classical Physics
International Nuclear Information System (INIS)
The Classical Physics Fundamentals Handbook was developed to assist nuclear facility operating contractors provide operators, maintenance personnel, and the technical staff with the necessary fundamentals training to ensure a basic understanding of physical forces and their properties. The handbook includes information on the units used to measure physical properties; vectors, and how they are used to show the net effect of various forces; Newton's Laws of motion, and how to use these laws in force and motion applications; and the concepts of energy, work, and power, and how to measure and calculate the energy involved in various applications. This information will provide personnel with a foundation for understanding the basic operation of various types of DOE nuclear facility systems and equipment
Casimir Effect - The Classical Limit
International Nuclear Information System (INIS)
The temperature dependence of the Casimir effect for the radiation field confined between two conducting plates is analysed; The Casimir energy is shown to decline exponentially with temperature while the Casimir entropy which is defined in the text is shown to approach a limit which depends only on the geometry of the constraining plates. The result is shown to hold, for a scalar field, for arbitrary geometry. The high temperature (T) expansion is shown to be ''robust'', i.e. it does not have any nonvanishing correction to the ''classical' result where the latter is defined by the validity of the Rayleigh - Jeans law. We show that validity of the Rayleigh - Jeans law implies the vanishing of the Casimir energy, hence the high temperature Casimir force, for a wide variety of geometries, is purely entropic
Classical Concepts in Quantum Programming
Ömer, Bernhard
2005-07-01
The rapid progress of computer technology has been accompanied by a corresponding evolution of software development, from hardwired components and binary machine code to high level programming languages, which allowed to master the increasing hardware complexity and fully exploit its potential. This paper investigates, how classical concepts like hardware abstraction, hierarchical programs, data types, memory management, flow of control, and structured programming can be used in quantum computing. The experimental language QCL will be introduced as an example, how elements like irreversible functions, local variables, and conditional branching, which have no direct quantum counterparts, can be implemented, and how nonclassical features like the reversibility of unitary transformation or the nonobservability of quantum states can be accounted for within the framework of a procedural programming language.
Bettini, Alessandro
2016-01-01
This first volume covers the mechanics of point particles, gravitation, extended systems (starting from the two-body system), the basic concepts of relativistic mechanics and the mechanics of rigid bodies and fluids. The four-volume textbook, which covers electromagnetism, mechanics, fluids and thermodynamics, and waves and light, is designed to reflect the typical syllabus during the first two years of a calculus-based university physics program. Throughout all four volumes, particular attention is paid to in-depth clarification of conceptual aspects, and to this end the historical roots of the principal concepts are traced. Writings by the founders of classical mechanics, G. Galilei and I. Newton, are reproduced, encouraging students to consult them. Emphasis is also consistently placed on the experimental basis of the concepts, highlighting the experimental nature of physics. Whenever feasible at the elementary level, concepts relevant to more advanced courses in modern physics are included. Each chapter b...
Classical Syllogisms in Logic Teaching
DEFF Research Database (Denmark)
Øhrstrøm, Peter; Sandborg-Petersen, Ulrik; Thorvaldsen, Steinar;
2013-01-01
test persons have a tendency correctly to assess valid syllogisms as such more often than correctly assessing invalid syllogisms as such. It is also investigated to what extent the students have improved their skills in practical reasoning by attending the logic courses. Finally, some open questions......This paper focuses on the challenges of introducing classical syllogisms in university courses in elementary logic and human reasoning. Using a program written in Prolog+CG, some empirical studies have been carried out involving three groups of students in Denmark; one group of philosophy students...... and two groups of students of informatics. The skills of the students in syllogistic reasoning before and after the logic courses have been studied and are discussed. The empirical observations made with the program make it possible to identify syllogisms which are found difficult by the students, and...
Theoretical physics 1 classical mechanics
Nolting, Wolfgang
2016-01-01
This textbook offers a clear and comprehensive introduction to classical mechanics, one of the core components of undergraduate physics courses. The book starts with a thorough introduction to the mathematical tools needed, to make this textbook self-contained for learning. The second part of the book introduces the mechanics of the free mass point and details conservation principles. The third part expands the previous to mechanics of many particle systems. Finally the mechanics of the rigid body is illustrated with rotational forces, inertia and gyroscope movement. Ideally suited to undergraduate students in their first year, the book is enhanced throughout with learning features such as boxed inserts and chapter summaries, with key mathematical derivations highlighted to aid understanding. The text is supported by numerous worked examples and end of chapter problem sets. About the Theoretical Physics series Translated from the renowned and highly successful German editions, the eight volumes of this series...
Institute of Scientific and Technical Information of China (English)
王周俊; 李翔; 王琛琛; 唐颐; 张亚红
2011-01-01
通过在毛细管内层层组装纳米沸石并固定脂肪酶来构建纳米沸石修饰的固定化酶微反应器通道,将纳米沸石良好的生物相容性和高的酶固定能力与微反应器反应效率高和扩散传质快等优点相结合,以对硝基苯棕榈酸酯的水解作为探针反应,对该微反应器内固定化酶催化水解反应动力学进行了研究和计算,并与普通反应器内同样的反应进行比较.通过对比米氏方程参数,证实在微反应器内酶催化水解反应效率比普通反应器内提高3倍以上,并可提高酶和反应底物的亲和能力.%Nanozeolite modified microchannel reactors were constructed by assembling zeolite nanocrystals into capillary using layer-by-layer assemble method. And then lipase CRL was immobilized on the nanozeolites assembled in the microreactors. The nanozeolite modified microreactors could incorporate excellent biocaptibility and large external area of nanozeolites and high efficiency and fast mass diffusion of microreactors together.Hydrolysis of 4-nitrophenyl palmitate (4-NPP) was carried out as a probe reaction to study the hydrolysis kinetics catalyzed by immobilized CRL in the microreactors. By comparing the characteristic parameters (Km and Vmax) of Michaelis-Menten equation, it is found that efficiency of enzymatic hydrolysis in such nanozeolite modified microchannel reactors could be 3 or more times higher than that of the same reaction in conventional reactors. In addition, affinity between enzyme and substrates is also enhanced in the nanozeolite modified microchannel reactors.
Drying of liquid food droplets. Enzyme inactivation and multicomponent diffusion.
Meerdink, G.
1993-01-01
In this thesis the drying of liquid food droplets is studied from three different points of view: drying kinetics, enzyme inactivation and multicomponent diffusion. Mathematical models are developed and validated experimentally.Drying experiments are performed with suspended droplets and with free f
Hilbert space theory of classical electrodynamics
Indian Academy of Sciences (India)
RAJAGOPAL A K; GHOSE PARTHA
2016-06-01
Classical electrodynamics is reformulated in terms of wave functions in the classical phase space of electrodynamics, following the Koopman–von Neumann–Sudarshan prescription for classical mechanics on Hilbert spaces sans the superselection rule which prohibits interference effects in classical mechanics. This is accomplished by transforming from a set of commutingobservables in one Hilbert space to another set of commuting observables in a larger Hilbert space. This is necessary to clarify the theoretical basis of the much recent work on quantum-like features exhibited by classical optics. Furthermore, following Bondar et al, {\\it Phys. Rev.} A 88, 052108 (2013), it is pointed out that quantum processes that preserve the positivity or nonpositivity of theWigner function can be implemented by classical optics. This may be useful in interpreting quantum information processing in terms of classical optics.
Kinetic Initial Conditions for Inflation
Handley, W J; Lasenby, A N; Hobson, M P
2014-01-01
We consider the classical evolution of the inflaton field $\\phi(t)$ and the Hubble parameter $H(t)$ in homogeneous and isotropic single-field inflation models. Under an extremely broad assumption, we show that the universe generically emerges from an initial singularity in a non-inflating state where the kinetic energy of the inflaton dominates its potential energy, $\\dot{\\phi}^2 \\gg V(\\phi)$. In this kinetically-dominated regime, the dynamical equations admit simple analytic solutions for $\\phi(t)$ and $H(t)$, which are independent of the form of $V(\\phi)$. In such models, these analytic solutions thus provide a simple way of setting the initial conditions from which to start the (usually numerical) integration of the coupled equations of motion for $\\phi(t)$ and $H(t)$. We illustrate this procedure by applying it to spatially-flat models with polynomial and exponential potentials, and determine the background evolution in each case; generically $H(t)$ and $|\\phi(t)|$ as well as their time derivatives decrea...
Empiricism or self-consistent theory in chemical kinetics?
International Nuclear Information System (INIS)
To give theoretical background for mechanochemical kinetics, we need first of all to find a possibility to predict the kinetic parameters for real chemical processes by determining rate constants and reaction orders without developing strictly specialized and, to a great extent, artificial models, i.e. to derive the kinetic law of mass action from 'first principles'. However, the kinetic law of mass action has had only an empirical basis from the first experiments of Gulberg and Waage until now, in contrast to the classical law of mass action for chemical equilibrium rigorously derived in chemical thermodynamics from equilibrium condition. Nevertheless, in this paper, an attempt to derive the kinetic law of mass action from 'first principles' is made in macroscopic formulation. It has turned out to be possible owing to the methods of thermodynamics of irreversible processes that were unknown in Gulberg and Waage's time
A simplification of the unified gas kinetic scheme
Chen, Songze; Xu, Kun
2016-01-01
Unified gas kinetic scheme (UGKS) is an asymptotic preserving scheme for the kinetic equations. It is superior for transition flow simulations, and has been validated in the past years. However, compared to the well known discrete ordinate method (DOM) which is a classical numerical method solving the kinetic equations, the UGKS needs more computational resources. In this study, we propose a simplification of the unified gas kinetic scheme. It allows almost identical numerical cost as the DOM, but predicts numerical results as accurate as the UGKS. Based on the observation that the equilibrium part of the UGKS fluxes can be evaluated analytically, the equilibrium part in the UGKS flux is not necessary to be discretized in velocity space. In the simplified scheme, the numerical flux for the velocity distribution function and the numerical flux for the macroscopic conservative quantities are evaluated separately. The simplification is equivalent to a flux hybridization of the gas kinetic scheme for the Navier-S...
Geometric dynamics of Vlasov kinetic theory and its moments
Tronci, Cesare
2008-01-01
The Vlasov equation of kinetic theory is introduced and the Hamiltonian structure of its moments is presented. Then we focus on the geodesic evolution of the Vlasov moments. As a first step, these moment equations generalize the Camassa-Holm equation to its multi-component version. Subsequently, adding electrostatic forces to the geodesic moment equations relates them to the Benney equations and to the equations for beam dynamics in particle accelerators. Next, we develop a kinetic theory for self assembly in nano-particles. Darcy's law is introduced as a general principle for aggregation dynamics in friction dominated systems (at different scales). Then, a kinetic equation is introduced for the dissipative motion of isotropic nano-particles. The zeroth-moment dynamics of this equation recovers the classical Darcy's law at the macroscopic level. A kinetic-theory description for oriented nano-particles is also presented. At the macroscopic level, the zeroth moments of this kinetic equation recover the magnetiz...
Enzymes in Analytical Chemistry.
Fishman, Myer M.
1980-01-01
Presents tabular information concerning recent research in the field of enzymes in analytic chemistry, with methods, substrate or reaction catalyzed, assay, comments and references listed. The table refers to 128 references. Also listed are 13 general citations. (CS)
Membrane Assisted Enzyme Fractionation
DEFF Research Database (Denmark)
Yuan, Linfeng
difference. In this thesis, separations using crossflow elecro-membrane filtration (EMF) of amino acids, bovine serum albumin (BSA) and industrial enzymes from Novozymes were performed. The main objective of this study was to investigate the technological feasibility of EMF in the application of industrial...... enzyme fractionation, such as removal of a side activity from the main enzyme activity. As a proof-of-concept, amino acids were used as model solution to test the feasibility of EMF in the application of amphoteric molecule separation. A single amino acid was used to illustrate the effect of an electric...... TMP on the separation performance were very small in the investigated range. The mass transport of each enzyme can be well explained by the Extended-Nernst-Planck equation. Better separation was observed at lower feed concentration, higher solution pH in the investigated range and with a polysulfone...
A kinetic model for the burst phase of processive cellulases
DEFF Research Database (Denmark)
Præstgaard, Eigil; Olsen, Jens Elmerdahl; Murphy, Leigh;
2011-01-01
negligible. Here, we propose an explicit kinetic model for this behavior, which uses classical burst phase theory as the starting point. The model is tested against calorimetric measurements of the activity of the cellobiohydrolase Cel7A from Trichoderma reesei on amorphous cellulose. A simple version of the...
The theories of unmixing kinetics of solid solutions
International Nuclear Information System (INIS)
In this paper, some general thermodynamical results on concentration fluctuations and on the driving force of unmixing are briefly recalled. The cluster kinetics approach, in its classical form is presented. The cooperative models are described. A brief survey is made of the problem of coarsening and the recent developments of the stochastic description of unmixing (Ising model) are given
Enzyme with rhamnogalacturonase activity.
Kofod, L.V.; Andersen, L N; Dalboge, H; Kauppinen, M.S.; Christgau, S; Heldt-Hansen, H.P.; Christophersen, C.; Nielsen, P.M.; Voragen, A. G. J.; Schols, H.A.
1998-01-01
An enzyme exhibiting rhamnogalacturonase activity, capable of cleaving a rhamnogalacturonan backbone in such a manner that galacturonic acids are left as the non-reducing ends, and which exhibits activity on hairy regions from a soy bean material and/or on saponified hairy regions from a sugar beet material. The enzyme has the amino acid sequence of SEQ ID NO:2 and is encoded by the DNA sequence of SEQ ID NO:1
Overproduction of ligninolytic enzymes
Energy Technology Data Exchange (ETDEWEB)
Elisashvili, Vladimir; Kachlishvili, Eva; Torok, Tamas
2014-06-17
Methods, compositions, and systems for overproducing ligninolytic enzymes from the basidiomycetous fungus are described herein. As described, the method can include incubating a fungal strain of Cerrena unicolor IBB 303 in a fermentation system having growth medium which includes lignocellulosic material and then cultivating the fungal strain in the fermentation system under conditions wherein the fungus expresses the ligninolytic enzymes. In some cases, the lignocellulosic material is mandarin peel, ethanol production residue, walnut pericarp, wheat bran, wheat straw, or banana peel.
The Kinetics of Carrier Transport Inhibition
DEFF Research Database (Denmark)
Rosenberg, T.; Wilbrandt, Robert Walter
1962-01-01
The kinetical treatment of enzymatic carrier transports as given in previous communications has been extended to conditions of inhibition. Various possible types of inhibitors have been considered differing in the site of attack (enzyme or carrier), in the mode of action (competing with the...... substrate for the enzyme or the carrier or for both, competing with the carrier for the enzyme, or non-competitive) and in the ability of penetrating the membrane. Experiments are reported on the inhibition of glucose and fructose transport across the human red cell membrane by phlorizine, phloretine and......, with the result that a certain asymmetry of inhibition (stronger inhibition of exit than of entrance) is to be expected. This asymmetry was termed “first order asymmetry”. In experiments with each of the three inhibitors an asymmetry of inhibition in the expected direction was observed which however...
Kinetics of Inhibition of Polyphenol Oxidase Obtained from Tobacco Nicotiana Tobacum
Institute of Scientific and Technical Information of China (English)
刘卫群; 饶学明; 潘继承; 周海梦
2004-01-01
In this study, the kinetics of inhibition of polyphenol oxidase by L-cysteine has been investigated.The inhibition of tobacco polyphenol oxidase was studied using the progress-of-substrate-reaction method proposed by Tsou, following the substrate reaction during irreversible inhibition of the enzyme activity. Analysis of the inhibition kinetics shows that inhibition occurs by an irreversible and non-complexation reaction. The microscopic rate constants were determined for reaction of the inhibitor both with the free enzyme and with the enzyme-substrate complex. The results show that the presence of the substrate has a significant protective effect of the enzyme against inactivation by L-cysteine.
Evaluation method for the drying performance of enzyme containing formulations
DEFF Research Database (Denmark)
Sloth, Jakob; Bach, P.; Jensen, Anker Degn;
2008-01-01
A method is presented for fast and cheap evaluation of the performance of enzyme containing formulations in terms of preserving the highest enzyme activity during spray drying. The method is based on modeling the kinetics of the thermal inactivation reaction which occurs during the drying process....... Relevant kinetic parameters are determined from differential scanning calorimeter (DSC) experiments and the model is used to simulate the severity of the inactivation reaction for temperatures and moisture levels relevant for spray drying. After conducting experiments and subsequent simulations for a...... number of different formulations it may be deduced which formulation performs best. This is illustrated by a formulation design study where 4 different enzyme containing formulations are evaluated. The method is validated by comparison to pilot scale spray dryer experiments....
Linking Protein Motion to Enzyme Catalysis
Directory of Open Access Journals (Sweden)
Priyanka Singh
2015-01-01
Full Text Available Enzyme motions on a broad range of time scales can play an important role in various intra- and intermolecular events, including substrate binding, catalysis of the chemical conversion, and product release. The relationship between protein motions and catalytic activity is of contemporary interest in enzymology. To understand the factors influencing the rates of enzyme-catalyzed reactions, the dynamics of the protein-solvent-ligand complex must be considered. The current review presents two case studies of enzymes—dihydrofolate reductase (DHFR and thymidylate synthase (TSase—and discusses the role of protein motions in their catalyzed reactions. Specifically, we will discuss the utility of kinetic isotope effects (KIEs and their temperature dependence as tools in probing such phenomena.
Religious ecstasy in classical Sufism
Directory of Open Access Journals (Sweden)
Göran Ogén
1982-01-01
Full Text Available The purpose of this essay is to shed some light on the phenomenon of religious ecstasy as met within Islamic mysticism and there particularly during its classical period. In this case, the expression "classical Sufism" refers to the period of Sufi history from about 850 A.D. until circa 1100 A.D. In the Sufi vocabulary there is even a rather differentiated terminology concerning these ecstatic experiences or states; whether different descriptions of one and the same experience are involved or whether the terms actually describe different experiences is a question that we must set aside for the present. There are, however, Sufis expressing the opinion that these different states of mind are based on one single experience in spite of the difference in terms. A generic term for these experiences or states is not to be found in the Sufi terminology however, so the problem of which of these phenomena must be present in order for ecstasy to be evidenced—or which of them would be sufficient— does not therefore arise for the Sufis. So instead of speaking of religious ecstasy in general, they either refer to the single specific terms in question or else use the plural of one of the words employed to designate one of the terms we include in "religious ecstasy". They thus speak of "ecstasies", mawagid from the singular form wagd—if one should at all attempt a translation of this plural. This plural is a genuine Sufi construction and does not otherwise seem to occur in the Arabic language, except as a later borrowing. Psalmody based on the Koranic vocabulary remains the main procedure for putting oneself in ecstasy. If we add 'and listening to psalmody', we then obtain a fairly satisfactory picture of the external conditions for the Sufis' ecstasy until the eleventh century, when various innovations begin to appear. As far as the darwiš-dance is concerned, it is not until the thirteenth century with Rumi that it becomes transformed from an expression
Kinetic study of enzymatic hydrolysis of potato starch
Óscar Fernando Castellanos Domínguez; Pardo, M; P. Rivera; G. González
2010-01-01
This article describes the kinetic study of potato starch enzymatic hydrolysis using soluble enzymes (Novo Nordisk). Different assays divided into four groups were used: reaction time (with which it was possible to reduce the 48-72 hour duration reported in the literature to 16 hours with comparable productivity levels); selecting the set of enzymes to be used (different types were evaluated - BAN and Termamyl as alfa-amylases during dextrinisation stage, and AMG, Promozyme and Fungamyl for s...
Illustrating the Effect of pH on Enzyme Activity Using Gibbs Energy Profiles
Bearne, Stephen L.
2014-01-01
Gibbs energy profiles provide students with a visual representation of the energy changes that occur during enzyme catalysis, making such profiles useful as teaching and learning tools. Traditional kinetic topics, such as the effect of pH on enzyme activity, are often not discussed in terms of Gibbs energy profiles. Herein, the symbolism of Gibbs…
DEFF Research Database (Denmark)
Cruys-Bagger, Nicolaj; Guilin, Ren; Tatsumi, Hirosuke; Baumann, Martin; Spodsberg, Nikolaj; Delcomyn Andersen, Heidi; Gorton, Lo; Borch, Kim; Westh, Peter
2012-01-01
An amperometric enzyme biosensor for continuous detection of cellobiose has been implemented as an enzyme assay for cellulases. We show that the initial kinetics for cellobiohydrolase I, Cel7A from Trichoderma reesei, acting on different types of cellulose substrates, semi-crystalline and amorphous...
Dynamics of Radical-Mediated Enzyme Catalyses
Warncke, Kurt
1997-11-01
An emergent class of enzymes harnesses the extreme reactivity of electron-deficient free radical species to perform some of the most difficult reactions in biology. The regio- and stereo-selectivity achieved by these enzymes defies long-held ideas that radical reactions are non-specific. The common primary step in these catalyses is metal- or metallocenter-assisted generation of an electron-deficient organic "initiator radical". The initiator radical abstracts a hydrogen atom from the substrate, opening a new reaction channel for rearrangement to the product. Our aim is to elucidate the detailed molecular mechanisms of the radical pair separation and radical rearrangement steps. Radical pair separation and substrate radical rearrangement are tracked by using time-resolved (10-7 to 10-3 s) techniques of pulsed-electron paramagnetic resonance spectroscopy (FT-EPR, ESEEM). Synchronous time-evolution of the reactions is attained by triggering with a visible laser pulse. Transient non-Boltzmann population of the states of the spin-coupled systems, and resultant electron spin polarization, facilitates study at or near room temperature under conditions where the enzymes are operative. The systems examined include ethanolamine deaminase, a vitamin B12 coenzyme-dependent enzyme, ribonucleotide reductase and photosynthetic reaction centers. The electronic and nuclear structural and kinetic information obtained from the pulsed-EPR studies is used to address how the initiator radicals are stabilized against deleterious recombination with the metal, and to distinguish the participation of concerted versus sequential rearrangement pathways.