Gao, Jiali; Major, Dan T; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu
2008-01-01
A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.
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...
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…
Enzyme kinetic characterization of protein tyrosine phosphatases
DEFF Research Database (Denmark)
Peters, Günther H.J.; Branner, S.; Møller, K. B.;
2003-01-01
Protein tyrosine phosphatases (PTPs) play a central role in cellular signaling processes, resulting in an increased interest in modulating the activities of PTPs. We therefore decided to undertake a detailed enzyme kinetic evaluation of various transmembrane and cytosolic PTPs (PTPalpha, PTPbeta...
Extracellular enzyme kinetics scale with resource availability
Sinsabaugh, Robert L.; Belnap, Jayne; Findlay, Stuart G.; Follstad Shah, Jennifer J.; Hill, Brian H.; Kuehn, Kevin A.; Kuske, Cheryl; Litvak, Marcy E.; Martinez, Noelle G.; Moorhead, Daryl L.; Warnock, Daniel D.
2014-01-01
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 assimilation of carbon, nitrogen and phosphorus by diverse aquatic and terrestrial microbial communities (1160 cases). Regression analyses were conducted by habitat (aquatic and terrestrial), enzyme class (hydrolases and oxidoreductases) and assay methodology (low affinity and high affinity substrates) to relate potential reaction rates to substrate availability. Across enzyme classes and habitats, the scaling relationships between apparent Vmax and apparent Km followed similar power laws with exponents of 0.44 to 0.67. These exponents, called elasticities, were not statistically distinct from a central value of 0.50, which occurs when the Km of an enzyme equals substrate concentration, a condition optimal for maintenance of steady state. We also conducted an ecosystem scale analysis of ten extracellular hydrolase activities in relation to soil and sediment organic carbon (2,000–5,000 cases/enzyme) that yielded elasticities near 1.0 (0.9 ± 0.2, n = 36). At the metabolomic scale, the elasticity of extracellular enzymatic reactions is the proportionality constant that connects the C:N:P stoichiometries of organic matter and ecoenzymatic activities. At the ecosystem scale, the elasticity of extracellular enzymatic reactions shows that organic matter ultimately limits effective enzyme binding sites. Our findings suggest that one mechanism by which microbial communities maintain homeostasis is regulating extracellular enzyme expression to optimize the short-term responsiveness of substrate acquisition. The analyses also show that, like elemental stoichiometry, the fundamental attributes of enzymatic reactions can be extrapolated from biochemical to community and ecosystem scales.
Continuum Kinetic and Multi-Fluid Simulations of Classical Sheaths
Cagas, Petr; Juno, James; Srinivasan, Bhuvana
2016-01-01
The kinetic study of plasma sheaths is critical, among other things, to understand the deposition of heat on walls, the effect of sputtering, and contamination of the plasma with detrimental impurities. The plasma sheath also provides a boundary condition and can often have a significant global impact on the bulk plasma. In this paper, kinetic studies of classical sheaths are performed with the continuum code, Gkeyll, that directly solves the Vlasov-Poisson/Maxwell equations. The code uses a novel version of the finite-element discontinuous Galerkin (DG) scheme that conserves energy in the continuous-time limit. The electrostatic field is computed using the Poisson equation. Ionization and scattering collisions are included, however, surface effects are neglected. The aim of this work is to introduce the continuum-kinetic method and compare its results to those obtained from an already established finite-volume multi-fluid model also implemented in Gkeyll. Novel boundary conditions on the fluids allow the she...
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.
An Operational Definition of the Steady State in Enzyme Kinetics.
Barnsley, E. A.
1990-01-01
The Briggs-Haldane assumption is used as the basis for the development of a kinetic model for enzyme catalysis. An alternative definition of the steady state and examples of realistic mechanisms are provided. (KR)
Enzyme kinetics in drug metabolism: fundamentals and applications.
Nagar, Swati; Argikar, Upendra A; Tweedie, Donald J
2014-01-01
Enzymes are protein catalysts that lower the energy barrier for a reaction and speed the rate of a chemical change. The kinetics of reactions catalyzed by enzymes, as well as several mechanisms underlying the kinetics, have been comprehensively studied and written in textbooks (1, 2). The importance of quantitative evaluation of enzymatic processes has been recognized in many fields of study, including biochemistry, molecular biology, and pharmaceutical sciences to name a few. In pharmaceutical sciences, the applications of enzyme kinetics range from hit finding efforts for new chemical entities on a pharmacological target to concentration effect relationships to large-scale biosynthesis. The study of the science of drug metabolism has two principal concepts-rate and extent. While understanding disposition pathways and identification of metabolites provides an insight into the extent of metabolism, kinetics of depletion of substrates (endogenous or exogenous) and formation of metabolites deals with the rate of metabolism. The current textbook specifically focuses on kinetics of drug-metabolizing enzymes, detailing specific enzyme classes, and discusses kinetics as they apply to drug transporters. This textbook also outlines additional factors that contribute to the kinetics of reactions catalyzed by these proteins such as variability in isoforms (pharmacogenomics) and experimental factors including key concepts such as alterations of substrate concentrations due to binding. Applications of these approaches in predicting kinetic parameters and alternative approaches for enzymes (systems biology) and transporters are also discussed. The final section focuses on real-life examples (case studies) to try and exemplify the applications of enzyme kinetic principles. This chapter provides a brief overview outlining some key concepts within each of the sections and the chapters within this textbook.
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…
Bioethanol from lignocellulose - pretreatment, enzyme immobilization and hydrolysis kinetics
DEFF Research Database (Denmark)
Tsai, Chien Tai
lignocellulose is the required high cellulase enzyme dosages that increase the processing costs. One method to decrease the enzyme dosage is to re-use BG, which hydrolyze the soluble substrate cellobiose. Based on the hypothesis that immobilized BG can be re-used, how many times the enzyme could be recycled......, the cost of enzyme is still the bottle neck, re-using the enzyme is apossible way to reduce the input of enzyme in the process. In the point view of engineering, the prediction of enzymatic hydrolysis kinetics under different substrate loading, enzyme combination is usful for process design. Therefore...... that more than 60% of enzymatic activity could be maintained under optimized immobilization condition. In order to evaluate stability, the immobilized enzymes were reused for the hydrolysis of Avicel. No significant loss of activity was observed up to 20th round. Similar glucose yields were obtained...
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.
New types of experimental data shape the use of enzyme kinetics for dynamic network modeling.
Tummler, Katja; Lubitz, Timo; Schelker, Max; Klipp, Edda
2014-01-01
Since the publication of Leonor Michaelis and Maude Menten's paper on the reaction kinetics of the enzyme invertase in 1913, molecular biology has evolved tremendously. New measurement techniques allow in vivo characterization of the whole genome, proteome or transcriptome of cells, whereas the classical enzyme essay only allows determination of the two Michaelis-Menten parameters V and K(m). Nevertheless, Michaelis-Menten kinetics are still commonly used, not only in the in vitro context of enzyme characterization but also as a rate law for enzymatic reactions in larger biochemical reaction networks. In this review, we give an overview of the historical development of kinetic rate laws originating from Michaelis-Menten kinetics over the past 100 years. Furthermore, we briefly summarize the experimental techniques used for the characterization of enzymes, and discuss web resources that systematically store kinetic parameters and related information. Finally, describe the novel opportunities that arise from using these data in dynamic mathematical modeling. In this framework, traditional in vitro approaches may be combined with modern genome-scale measurements to foster thorough understanding of the underlying complex mechanisms.
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.
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.…
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
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;
2001-01-01
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...
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
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...
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
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.
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...
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…
Energy Technology Data Exchange (ETDEWEB)
Rosa Correa, Albertina Xavier da [Centro de Ciencias Tecnologicas da Terra e do Mar, Universidade do Vale do Itajai, Rua Uruguai, 458, 88302-202 Itajai SC (Brazil); Roerig, Leonardo Rubi [Centro de Ciencias Tecnologicas da Terra e do Mar, Universidade do Vale do Itajai, Rua Uruguai, 458, 88302-202 Itajai SC (Brazil); Verdinelli, Miguel A. [Centro de Ciencias Tecnologicas da Terra e do Mar, Universidade do Vale do Itajai, Rua Uruguai, 458, 88302-202 Itajai SC (Brazil); Cotelle, Sylvie [Centre des Sciences de l' Environnement, Universite de Metz, 57000 Metz (France); Ferard, Jean-Francois [Centre des Sciences de l' Environnement, Universite de Metz, 57000 Metz (France); Radetski, Claudemir Marcos [Centro de Ciencias Tecnologicas da Terra e do Mar, Universidade do Vale do Itajai, Rua Uruguai, 458, 88302-202 Itajai SC (Brazil)]. E-mail: radetski@univali.br
2006-03-15
In this work, cadmium phytotoxicity and quantitative sensitivity relationships between different hierarchical endpoints in plants cultivated in a contaminated soil were studied. Thus, germination rate, biomass growth and antioxidative enzyme activity (i.e. superoxide dismutase, peroxidase, catalase and glutathione reductase) in three terrestrial plants (Avena sativa L., Brassica campestris L. cv. Chinensis, Lactuca sativa L. cv. hanson) were analyzed. Plant growth tests were carried out according to an International Standard Organization method and the results were analyzed by ANOVA followed by Williams' test. The concentration of Cd{sup 2+} that had the smallest observed significant negative effect (LOEC) on plant biomass was 6.25, 12.5 and 50 mg Cd/kg dry soil for lettuce, oat and Chinese cabbage, respectively. Activity of all enzymes studied increased significantly compared to enzyme activity in plant controls. For lettuce, LOEC values (mg Cd/kg dry soil) for enzymic activity ranged from 0.05 (glutathione reductase) to 0.39 (catalase). For oat, LOEC values (mg Cd/kg dry soil) ranged from 0.19 (for superoxide dismutase and glutathione reductase) to 0.39 (for catalase and peroxidase). For Chinese cabbage, LOEC values (mg Cd/kg dry soil) ranged from 0.19 (peroxidase, catalase and glutathione reductase) to 0.39 (superoxide dismutase). Classical (i.e. germination and biomass) and biochemical (i.e. enzyme activity) endpoints were compared to establish a sensitivity ranking, which was: enzyme activity > biomass > germination rate. For cadmium-soil contamination, the determination of quantitative sensitivity relationships (QSR) between classical and antioxidative enzyme biomarkers showed that the most sensitive plant species have, generally, the lowest QSR values.
Enzyme kinetics of hevamine, a chitinase from the rubber tree Hevea brasiliensis
Bokma, Evert; Barends, Thomas; Terwisscha van Scheltinga, Anke C.; Dijkstra, Bauke W.; Beintema, Jaap J.
2000-01-01
The enzyme kinetics of hevamine, a chitinase from the rubber tree Hevea brasiliensis, were studied in detail with a new enzyme assay. In this assay, the enzyme reaction products were derivatized by reductive coupling to a chromophore, Products mere separated by HPLC and the amount of product was cal
A Hands-On Classroom Simulation to Demonstrate Concepts in Enzyme Kinetics
Junker, Matthew
2010-01-01
A classroom exercise is described to introduce enzyme kinetics in an undergraduate biochemistry or chemistry course. The exercise is a simulation in which a student acts as an enzyme that "catalyzes" the unscrewing of a nut from a bolt. With other students assisting, the student enzyme carries out reactions with bolt-nut substrates under different…
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...
Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes
Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti
2016-08-01
Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.
A 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...
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...
ENZYME KINETICS FOR SYSTEMS BIOLOGY : WHEN, WHY AND HOW
Adamczyk, Malgorzata; van Eunen, Karen; Bakker, Barbara M.; Westerhoff, Hans V.; Jameson, D; Verma, M; Westerhoff, HV
2011-01-01
In vitro enzymatic assays of cell-free extracts offer an opportunity to assess in vivo enzyme concentrations. If performed under conditions that resemble the conditions in vivo, they may also reveal some of the capacities and properties of the same enzymes in vivo; we shall call this the ex vivo app
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.)
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…
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
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...
Enzyme kinetics determined by single-injection isothermal titration calorimetry.
Transtrum, Mark K; Hansen, Lee D; Quinn, Colette
2015-04-01
The purposes of this paper are (a) to examine the effect of calorimeter time constant (τ) on heat rate data from a single enzyme injection into substrate in an isothermal titration calorimeter (ITC), (b) to provide information that can be used to predict the optimum experimental conditions for determining the rate constant (k2), Michaelis constant (KM), and enthalpy change of the reaction (ΔRH), and (c) to describe methods for evaluating these parameters. We find that KM, k2 and ΔRH can be accurately estimated without correcting for the calorimeter time constant, τ, if (k2E/KM), where E is the total active enzyme concentration, is between 0.1/τ and 1/τ and the reaction goes to at least 99% completion. If experimental conditions are outside this domain and no correction is made for τ, errors in the inferred parameters quickly become unreasonable. A method for fitting single-injection data to the Michaelis-Menten or Briggs-Haldane model to simultaneously evaluate KM, k2, ΔRH, and τ is described and validated with experimental data. All four of these parameters can be accurately inferred provided the reaction time constant (k2E/KM) is larger than 1/τ and the data include enzyme saturated conditions.
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.
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
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...
Kinetics of soil enzyme activities under different ecosystems: An index of soil quality
Directory of Open Access Journals (Sweden)
Monty Kujur
2014-03-01
Full Text Available Soil microbial activity plays an important role in regulating biotransformation, nutrient cycling and hence the microbiological processes are at the center of many ecological functions. The kinetic parameters (Vmax and KmMichaelis constant of different enzymes (amylase, invertase, protease, urease, and dehydrogenase were determined in order to assess the metabolic response of soil. The maximum reaction velocity (Vmax represents a maximum rate of activity when all enzymes are saturated, which markedly increased in forest soil as compared to fresh mine spoil due to the gradual accumulation of soil organic matter. Smaller Km value was estimated in forest soil (FS as compared to fresh mine spoil (FMS, suggesting the greater affinity of soil enzymes for substrate in FS. The catalytic efficiency (Vmax /Km reflects an impression on microbial community composition with a change in soil enzymes. These enzyme characters (activities and kinetic parameters have greater significance as early and sensitive indicators of the changes in soil properties induced by different management systems. These parameters (Vmax and Km can be useful markers to assess changes in microbial activity of soil, since they represent quantity and affinity of enzymes respectively. The metabolic index (dehydrogenase activity/organic carbon (OC was found to be correlated with Vmax of dehydrogenase (r = 0.953; p < 0.01 and OC (r = 0.880; p < 0.01. Principal component analysis was able to discriminate seven different soil samples into seven independent clusters based on their enzyme activities and kinetic parameters. Indeed, the study revealed the importance of kinetics study of soil enzymes, which can be considered valid parameters to monitor the evolution of microbiological activity in soil, and hence an index of soil quality.
Penning, Trevor M
2016-07-01
Structure-function studies on steroid transforming enzymes often use site-directed mutagenesis to inform mechanisms of catalysis and effects on steroid binding, and data are reported in terms of changes in steady state kinetic parameters kcat, Km and kcat/Km. However, this dissection of function is limited since kcat is governed by the rate-determining step and Km is a complex macroscopic kinetic constant. Often site-directed mutagenesis can lead to a change in the rate-determining step which cannot be revealed by just reporting a decrease in kcat alone. These issues are made more complex when it is considered that many steroid transforming enzymes have more than one substrate and product. We present the case for using transient-kinetics performed with stopped-flow spectrometry to assign rate constants to discrete steps in these multi-substrate reactions and their use to interpret enzyme mechanism and the effects of disease and engineered mutations. We demonstrate that fluorescence kinetic transients can be used to measure ligand binding that may be accompanied by isomerization steps, revealing the existence of new enzyme intermediates. We also demonstrate that single-turnover reactions can provide a klim for the chemical step and Ks for steroid-substrate binding and that when coupled with kinetic isotope effect measurements can provide information on transition state intermediates. We also demonstrate how multiple turnover experiments can provide evidence for either "burst-phase" kinetics, which can reveal a slow product release step, or linear-phase kinetics, in which the chemical step can be rate-determining. With these assignments it becomes more straightforward to analyze the effects of mutations. We use examples from the hydroxysteroid dehydrogenases (AKR1Cs) and human steroid 5β-reductase (AKR1D1) to illustrate the utility of the approach, which are members of the aldo-keto reductase (AKR) superfamily.
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.
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....
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
van Eunen, Karen; Kiewiet, Jose A. L.; Westerhoff, Hans V.; Bakker, Barbara M.
2012-01-01
A decade ago, a team of biochemists including two of us, modeled yeast glycolysis and showed that one of the most studied biochemical pathways could not be quite understood in terms of the kinetic properties of the constituent enzymes as measured in cell extract. Moreover, when the same model was la
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…
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
Determining Enzyme Kinetics for Systems Biology with Nuclear Magnetic Resonance Spectroscopy
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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
Classical nucleation theory of homogeneous freezing of water: thermodynamic and kinetic parameters.
Ickes, Luisa; Welti, André; Hoose, Corinna; Lohmann, Ulrike
2015-02-28
The probability of homogeneous ice nucleation under a set of ambient conditions can be described by nucleation rates using the theoretical framework of Classical Nucleation Theory (CNT). This framework consists of kinetic and thermodynamic parameters, of which three are not well-defined (namely the interfacial tension between ice and water, the activation energy and the prefactor), so that any CNT-based parameterization of homogeneous ice formation is less well-constrained than desired for modeling applications. Different approaches to estimate the thermodynamic and kinetic parameters of CNT are reviewed in this paper and the sensitivity of the calculated nucleation rate to the choice of parameters is investigated. We show that nucleation rates are very sensitive to this choice. The sensitivity is governed by one parameter - the interfacial tension between ice and water, which determines the energetic barrier of the nucleation process. The calculated nucleation rate can differ by more than 25 orders of magnitude depending on the choice of parameterization for this parameter. The second most important parameter is the activation energy of the nucleation process. It can lead to a variation of 16 orders of magnitude. By estimating the nucleation rate from a collection of droplet freezing experiments from the literature, the dependence of these two parameters on temperature is narrowed down. It can be seen that the temperature behavior of these two parameters assumed in the literature does not match with the predicted nucleation rates from the fit in most cases. Moreover a comparison of all possible combinations of theoretical parameterizations of the dominant two free parameters shows that one combination fits the fitted nucleation rates best, which is a description of the interfacial tension coming from a molecular model [Reinhardt and Doye, J. Chem. Phys., 2013, 139, 096102] in combination with the activation energy derived from self-diffusion measurements [Zobrist
Hoang Thi Thu, Duyen; Razavi, Bahar S.
2016-04-01
Earthworms boost microbial activities and consequently form hotspots in soil. The distribution of enzyme activities inside the earthworm biopores is completely unknown. For the first time, we analyzed enzyme kinetics and visualized enzyme distribution inside and outside biopores by in situ soil zymography. Kinetic parameters (Vmax and Km) of 6 enzymes β-glucosidase (GLU), cellobiohydrolase (CBH), xylanase (XYL), chitinase (NAG), leucine aminopeptidase (LAP) and acid phosphatase (APT) were determined in biopores formed by Lumbricus terrestris L.. The spatial distributions of GLU, NAG and APT become visible via zymograms in comparison between earthworm-inhabited and earthworm-free soil. Zymography showed heterogeneous distribution of hotspots in the rhizosphere and biopores. The hotspot areas were 2.4 to 14 times larger in the biopores than in soil without earthworms. The significantly higher Vmax values for GLU, CBH, XYL, NAG and APT in biopores confirmed the stimulation of enzyme activities by earthworms. For CBH, XYL and NAG, the 2- to 3-fold higher Km values in biopores indicated different enzyme systems with lower substrate affinity compared to control soil. The positive effects of earthworms on Vmax were cancelled by the Km increase for CBH, XYL and NAG at a substrate concentration below 20 μmol g-1 soil. The change of enzyme systems reflected a shift in dominant microbial populations toward species with lower affinity to holo-celluloses and to N-acetylglucosamine, and with higher affinity to proteins as compared to the biopores-free soil. We conclude that earthworm biopores are microbial hotspots with much higher and dense distribution of enzyme activities compared to bulk soil. References Spohn M, Kuzyakov Y. (2014) Spatial and temporal dynamics of hotspots of enzyme activity in soil as affected by living and dead roots - a soil zymography analysis, Plant Soil 379: 67-77. Blagodatskaya, E., Kuzyakov, Y., 2013. Review paper: Active microorganisms in soil
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.
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)
Garima Srivastava
Full Text Available β-Amylase finds application in food and pharmaceutical industries. Functionalized graphene sheets were customised as a matrix for covalent immobilization of Fenugreek β-amylase using glutaraldehyde as a cross-linker. The factors affecting the process were optimized using Response Surface Methodology based Box-Behnken design of experiment which resulted in 84% immobilization efficiency. Scanning and Transmission Electron Microscopy (SEM, TEM and Fourier Tansform Infrared (FTIR spectroscopy were employed for the purpose of characterization of attachment of enzyme on the graphene. The enzyme kinetic studies were carried out for obtaining best catalytic performance and enhanced reusability. Optimum temperature remained unchanged, whereas optimum pH showed shift towards acidic range for immobilized enzyme. Increase in thermal stability of immobilized enzyme and non-toxic nature of functionalized graphene can be exploited for production of maltose in food and pharmaceutical industries.
Application of A Microfluidic Tool for the Determination of Enzyme Kinetics
DEFF Research Database (Denmark)
Ringborg, Rolf H.
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 many enzymes...... alreadyexist and can be found in common text books. These models do however require mutant specific data and must be collected with the target reaction. In this thesis a novel way of collecting kinetic data is created, this is carried out by combining existing technology and enables the analysis of aqueous...
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 ...
Adewale, Peter; Dumont, Marie-Josée; Ngadi, Michael
2015-11-01
The use of ultrasonic processing was evaluated for its ability to achieve adequate mixing while providing sufficient activation energy for the enzymatic transesterification of waste tallow. The effects of ultrasonic parameters (amplitude, cycle and pulse) and major reaction factors (molar ratio and enzyme concentration) on the reaction kinetics of biodiesel generation from waste tallow bio-catalyzed by immobilized lipase [Candida antarctica lipase B (CALB)] were investigated. Three sets of experiments namely A, B, and C were conducted. In experiment set A, two factors (ultrasonic amplitude and cycle) were investigated at three levels; in experiment set B, two factors (molar ratio and enzyme concentration) were examined at three levels; and in experiment set C, two factors (ultrasonic amplitude and reaction time) were investigated at five levels. A Ping Pong Bi Bi kinetic model approach was employed to study the effect of ultrasonic amplitude on the enzymatic transesterification. Kinetic constants of transesterification reaction were determined at different ultrasonic amplitudes (30%, 35%, 40%, 45%, and 50%) and enzyme concentrations (4, 6, and 8 wt.% of fat) at constant molar ratio (fat:methanol); 1:6, and ultrasonic cycle; 5 Hz. Optimal conditions for ultrasound-assisted biodiesel production from waste tallow were fat:methanol molar ratio, 1:4; catalyst level 6% (w/w of fat); reaction time, 20 min (30 times less than conventional batch processes); ultrasonic amplitude 40% at 5 Hz. The kinetic model results revealed interesting features of ultrasound assisted enzyme-catalyzed transesterification (as compared to conventional system): at ultrasonic amplitude 40%, the reaction activities within the system seemed to be steady after 20 min which means the reaction could proceed with or without ultrasonic mixing. Reversed phase high performance liquid chromatography indicated the biodiesel yield to be 85.6±0.08%.
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.
KINETIC STUDY OF THE ENZYME CONVERSION OF STEAM EXPLODED PAULOWNIA TOMENTOSA TO GLUCOSE
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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.
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
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
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.
Hirashio, S; Taguchi, T; Naito, T; Maki, K; Ogata, S; Taniyama, K; Taniguchi, Y; Yorioka, N
2009-05-01
A 38-year-old man underwent renal biopsy because of proteinuria. It revealed swelling and vacuolation of glomerular epithelial cells, as well as myelin-like structures characteristic of Fabry's disease. Detection of decreased plasma activity of alpha-galactosidase A confirmed the diagnosis. Enzyme replacement therapy was provided with recombinant agalsidase-beta, resulting in improvement of his symptoms. When renal biopsy was repeated, specific staining for globotriaosylceramide showed that renal deposits were decreased by enzyme therapy.
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.
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.
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
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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.
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)
Kinetic theory of the eigenmodes of classical fluids and neutron scattering
Cohen, E.G.D.; Schepper, I.M. de; Zuilhof, M.J.
1984-01-01
The lowest lying eigenmodes of a classical fluid have been approximately determined for a wide range of densities and wavenumbers. The most important eigenmodes are direct extensions of the three hydrodynamic heat and sound modes to much larger wavenumbers. A new and consistent interpretation of neu
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.
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
Bahr, J.M.
1990-01-01
This paper extends a four-step derivation procedure, previously presented for cases of transport affected by surface reactions, to transport problems involving homogeneous reactions. Derivations for these classes of reactions are used to illustrate the manner in which mathematical differences between reaction classes are reflected in the mathematical derivation procedures required to identify kinetically influenced terms. Simulation results for a case of transport affected by a single solution phase complexation reaction and for a case of transport affected by a precipitation-dissolution reaction are used to demonstrate the nature of departures from equilibrium-controlled transport as well as the use of kinetically influenced terms in determining criteria for the applicability of the local equilibrium assumption. A final derivation for a multireaction problem demonstrates the application of the generalized procedure to a case of transport affected by reactions of several classes. -from Author
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.
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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.
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.
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...
Directory of Open Access Journals (Sweden)
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.
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
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...
Liuni, Peter; Olkhov-Mitsel, Ekaterina; Orellana, Arturo; Wilson, Derek J
2013-04-01
Kinetic isotope effect (KIE) measurements are a powerful tool for studying enzyme mechanisms; they can provide insights into microscopic catalytic processes and even structural constraints for transition states. However, KIEs have not come into widespread use in enzymology, due in large part to the requirement for prohibitively cumbersome experimental procedures and daunting analytical frameworks. In this work, we introduce time-resolved electrospray ionization mass spectrometry (TRESI-MS) as a straightforward, precise, and inexpensive method for measuring KIEs. Neither radioisotopes nor large amounts of material are needed and kinetic measurements for isotopically "labeled" and "unlabeled" species are acquired simultaneously in a single "competitive" assay. The approach is demonstrated first using a relatively large isotope effect associated with yeast alcohol dehydrogenase (YADH) catalyzed oxidation of ethanol. The measured macroscopic KIE of 2.19 ± 0.05 is consistent with comparable measurements in the literature but cannot be interpreted in a way that provides insights into isotope effects in individual microscopic steps. To demonstrate the ability of TRESI-MS to directly measure intrinsic KIEs and to characterize the precision of the technique, we measure a much smaller (12)C/(13)C KIE associated specifically with presteady state acylation of chymotrypsin during hydrolysis of an ester substrate.
Parametric constraints on the dynamic behavior of immobilized enzyme kinetics in a microreactor
Directory of Open Access Journals (Sweden)
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.
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 ...
Schokker, E.P.
1997-01-01
The kinetics of heat inactivation of the extracellular proteinase from Pseudomonas fluorescens 22F was studied. It was established, by making use of kinetic modelling, that heat inactivation in the temperature range 35 - 70 °C was most likely caused by intermolecular autoproteolysis, where unfolded
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
Computer controlled automated assay for comprehensive studies of enzyme kinetic parameters.
Directory of Open Access Journals (Sweden)
Felix Bonowski
Full Text Available Stability and biological activity of proteins is highly dependent on their physicochemical environment. The development of realistic models of biological systems necessitates quantitative information on the response to changes of external conditions like pH, salinity and concentrations of substrates and allosteric modulators. Changes in just a few variable parameters rapidly lead to large numbers of experimental conditions, which go beyond the experimental capacity of most research groups. We implemented a computer-aided experimenting framework ("robot lab assistant" that allows us to parameterize abstract, human-readable descriptions of micro-plate based experiments with variable parameters and execute them on a conventional 8 channel liquid handling robot fitted with a sensitive plate reader. A set of newly developed R-packages translates the instructions into machine commands, executes them, collects the data and processes it without user-interaction. By combining script-driven experimental planning, execution and data-analysis, our system can react to experimental outcomes autonomously, allowing outcome-based iterative experimental strategies. The framework was applied in a response-surface model based iterative optimization of buffer conditions and investigation of substrate, allosteric effector, pH and salt dependent activity profiles of pyruvate kinase (PYK. A diprotic model of enzyme kinetics was used to model the combined effects of changing pH and substrate concentrations. The 8 parameters of the model could be estimated from a single two-hour experiment using nonlinear least-squares regression. The model with the estimated parameters successfully predicted pH and PEP dependence of initial reaction rates, while the PEP concentration dependent shift of optimal pH could only be reproduced with a set of manually tweaked parameters. Differences between model-predictions and experimental observations at low pH suggest additional protonation
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)
Berberan-Santos, Mario N
2009-01-01
A different view of Henri-Michaelis-Menten (HMM) enzyme kinetics is presented. In the first part of the paper, a simplified but useful description that stresses the cyclic nature of the catalytic process is introduced. The time-dependence of the substrate concentration after the initial transient phase is derived in a simple way that dispenses the mathematical technique known as quasi-steady-state approximation. In the second part of the paper an exact one-dimensional formulation of HMM kinetics is obtained. The whole problem is condensed in a single one-variable evolution equation that is a second-order non-linear differential equation, and the control parameters are reduced to three dimensionless quantities: enzyme efficiency, substrate reduced initial concentration, and enzyme reduced initial concentration. The exact solution of HMM kinetics is obtained as a set of Maclaurin series. From the same equation, a number of approximate solutions, some known, some new, are derived in a systematic way that allows ...
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...
Magnus, Jørgen Barsett; Oldiges, Marco; Takors, Ralf
2009-01-01
The enzyme targets for the rational optimization of a Corynebacterium glutamicum strain constructed for valine production are identified by analyzing the control of flux in the valine/leucine pathway. The control analysis is based on measurements of the intracellular metabolite concentrations and on a kinetic model of the reactions in the investigated pathway. Data-driven and model-based methods are used and evaluated against each other. The approach taken gives a quantitative evaluation of the flux control and it is demonstrated how the understanding of flux control is used to reach specific recommendations for strain optimization. The flux control coefficients (FCCs) with respect to the valine excretion rate were calculated, and it was found that the control is distributed mainly between the acetohydroxyacid synthase enzyme (FCC = 0.32), the branched chain amino acid transaminase (FCC = 0.27), and the exporting translocase (FCC = 0.43). The availability of the precursor pyruvate has substantial influence on the valine flux, whereas the cometabolites are less important as demonstrated by the calculation of the respective response coefficients. The model is further used to make in-silico predictions of the change in valine flux following a change in enzyme level. A doubling of the enzyme level of valine translocase will result in an increase in valine flux of 31%. By optimizing the enzyme levels with respect to valine flux it was found that the valine flux can be increased by a factor 2.5 when the optimal enzyme levels are implemented.
Directory of Open Access Journals (Sweden)
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
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.
Razavi, Bahar S.; Blagodatskaya, Evgenia; Kuzyakov, Yakov
2015-01-01
The temperature sensitivity of enzymes responsible for organic matter decomposition in soil is crucial for predicting the effects of global warming on the carbon cycle and sequestration. We tested the hypothesis that differences in temperature sensitivity of enzyme kinetic parameters Vmax and Km will lead to a canceling effect: strong reduction of temperature response of catalytic reactions. Short-term temperature response of Vmax and Km of three hydrolytic enzymes responsible for decomposition of cellulose (β-glucosidase, cellobiohydrolase) and hemicelluloses (xylanase) were analyzed in situ from 0 to 40°C. The apparent activation energy varied between enzymes from 20.7 to 35.2 kJ mol−1 corresponding to the Q10 values of the enzyme activities of 1.4–1.9 (with Vmax-Q10 1.0–2.5 and Km-Q10 0.94–2.3). Temperature response of all tested enzymes fitted well to the Arrhenius equation. Despite that, the fitting of Arrhenius model revealed the non-linear increase of two cellulolytic enzymes activities with two distinct thresholds at 10–15°C and 25–30°C, which were less pronounced for xylanase. The nonlinearity between 10 and 15°C was explained by 30–80% increase in Vmax. At 25–30°C, however, the abrupt decrease of enzyme-substrate affinity was responsible for non-linear increase of enzyme activities. Our study is the first demonstrating nonlinear response of Vmax and Km to temperature causing canceling effect, which was most strongly pronounced at low substrate concentrations and at temperatures above 15°C. Under cold climate, however, the regulation of hydrolytic activity by canceling in response to warming is negligible because canceling was never observed below 10°C. The canceling, therefore, can be considered as natural mechanism reducing the effects of global warming on decomposition of soil organics at moderate temperatures. The non-linearity of enzyme responses to warming and the respective thresholds should therefore be investigated for
Estimating the turnover number in enzyme kinetic reactions using transient and stationary state data
Directory of Open Access Journals (Sweden)
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
Polygalacturonase enzymes hydrolyze the polygalacturonic acid chains found in pectin. Interest in polygalacturonase enzymes continues as they are useful in a number of industrial processes and conversely, detrimental, as they are involved in maceration of economically important crops. While a good...
Tryon, E; Kuby, S A
1984-01-01
From a study of the steady-state kinetics (at pH 7.6, 30 degrees C) of the reduction of cytochrome c, a 'ping-pong' mechanism may be postulated for the crystalline NADPH-cytochrome c reductase from ale yeast, Saccharomyces cerevisiae [1], a result derivable from a three-substrate ordered system with a rapid equilibrium random sequence in substrates, NADPH and FAD, followed by reactions of the third substrate, Cyt C3+. On this basis, estimates for the kinetic parameters were made together with the inhibitor dissociation constants for NADP+ (competitive with respect to NADPH as variable substrate, but noncompetitive with respect to cytochrome c3+ as the variable substrate). A noncompetitive type of inhibition was also found for cytochrome c2+ with NADPH as variable substrate, in confirmation of the proposed mechanism. With 2,6-dichloroindophenol as the acceptor, in place of cytochrome c3+, a value for KNADPH could be estimated which agreed with that estimated above, with cytochrome c3+ as the acceptor, again, in confirmation of the postulated mechanism. The reactions with molecular O2 catalyzed by the enzyme with NADPH as the reductant have been studied polarographically, and its Km for O2 estimated to be about 0.15 mmol/l at pH 7.6, 25 degrees C. The product of the reaction appears to be H2O2, which acts as a noncompetitive inhibitor for NADPH (Ki = 0.5 mmol/l), and tentatively an enzyme ternary complex containing oxygen and FADoh (semiquinone of FAD) may be assumed to be the kinetically important intermediate, which may be postulated to be in quasi-equilibrium with an enzyme ternary complex containing Oo2 (superoxide) and FAD.
House, Chloe; Meades, Glen; Linenberger, Kimberly J.
2016-01-01
Presented is a guided inquiry activity designed to be conducted with prenursing students using an analogous system to help develop a conceptual understanding of factors impacting enzyme kinetics and the various types of enzyme inhibition. Pre- and postconceptual understanding evaluations and effectiveness of implementation surveys were given to…
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
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 decreased...
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
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…
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
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
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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.
Pey, Angel L
2013-12-01
Many inborn errors of amino acids metabolism are caused by single point mutations affecting the ability of proteins to fold properly (i.e., protein homeostasis), thus leading to enzyme loss-of-function. Mutations may affect protein homeostasis by altering intrinsic physical properties of the polypeptide (folding thermodynamics, and rates of folding/unfolding/misfolding) as well as the interaction of partially folded states with elements of the protein homeostasis network (such as molecular chaperones and proteolytic machineries). Understanding these mutational effects on protein homeostasis is required to develop new therapeutic strategies aimed to target specific features of the mutant polypeptide. Here, I review recent work in three different diseases of protein homeostasis associated to inborn errors of amino acids metabolism: phenylketonuria, inherited homocystinuria and primary hyperoxaluria type I. These three different genetic disorders involve proteins operating in different cell organelles and displaying different structural complexities. Mutations often decrease protein kinetic stability of the native state (i.e., its half-life for irreversible denaturation), which can be studied using simple kinetic models amenable to biophysical and biochemical characterization. Natural ligands and pharmacological chaperones are shown to stabilize mutant enzymes, thus supporting their therapeutic application to overcome protein kinetic destabilization. The role of molecular chaperones in protein folding and misfolding is also discussed as well as their potential pharmacological modulation as promising new therapeutic approaches. Since current available treatments for these diseases are either burdening or only successful in a fraction of patients, alternative treatments must be considered covering studies from protein structure and biophysics to studies in animal models and patients.
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.
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...
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
effects and interactions between different factors on the gelation rates and gel properties were examined in response surface designs in which enzyme dosage (0.125–2.0 U mL−1 for HRP; 0.125–10 U mL−1 for laccase), substrate concentration (1.0–4.0%), temperature (25–55 °C), pH (3.5–5.5), and H2O2 (0...
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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.
Characterization and kinetic parameters of ethylene-forming enzyme from avocado fruit.
McGarvey, D J; Christoffersen, R E
1992-03-25
Biosynthesis of the phytohormone ethylene in higher plants proceeds via the following pathway: S-adenosylmethionine----1-aminocyclopropane-1-carboxylic acid (ACC)----ethylene. Ethylene-forming enzyme (EFE), the enzyme responsible for the oxidation of ACC to ethylene, has been only partially characterized in vitro. We have obtained authentic EFE activity in vitro from extracts of avocado fruit (Persea americana Mill. cv Hass). Ammonium sulfate fractionation revealed the presence of two EFE activities, which we designate as EFE1 and EFE2. EFE1 activity utilizes ACC and O2 as substrates and requires Fe(II) and ascorbate as cofactors. The enzyme has a relatively low Km (32 microM) for ACC, discriminates diastereomers of 1-amino-2-ethyl-cyclopropane-1-carboxylic acid, and is inhibited competitively by 2-aminoisobutyric acid, thus confirming its identity with authentic EFE. Activity is retained in a 100,000 x g supernatant and has a pH optimum of 7.5-8.0, suggesting a cytosolic localization.
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.
Kinetics of enzyme-catalyzed hydrolysis of steam-exploded sugarcane bagasse.
Aguiar, Rodrigo Souza; Silveira, Marcos Henrique Luciano; Pitarelo, Ana Paula; Corazza, Marcos Lucio; Ramos, Luiz Pereira
2013-11-01
This work presents the experimental kinetic data and the fractal modeling of sugarcane bagasse steam treatment and enzymatic hydrolysis. Sugarcane bagasse (50 wt% moisture) was pretreated by autohydrolysis at 210 °C for 4 min. Acid catalysis involved the use of 9.5mg g(-1) of H2SO4 or H3PO4 in relation to the substrate dry mass at these same pretreatment conditions. Unwashed, water-washed and alkali-washed substrates were hydrolyzed at 2.0 wt% using 8 and 15 FPU g(-1) (108.22 and 199.54 mg/g) total solids of a Celluclast 1.5 L and Novozym 188 mixture (Novozymes). The fractal kinetic modeling was used to describe the effect of pretreatment and both washing processes on substrate accessibility. Water and/or alkali washing was not strictly necessary to achieve high hydrolysis efficiencies. Also, the fractal model coefficients revealed that H3PO4 was a better pretreatment catalyst under the experimental conditions used in this study, resulting in the most susceptible substrates for enzymatic hydrolysis.
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...
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
Bezerra, Rui M F; Fraga, Irene; Dias, Albino A
2013-01-01
Enzyme kinetic parameters are usually determined from initial rates nevertheless, laboratory instruments only measure substrate or product concentration versus reaction time (progress curves). To overcome this problem we present a methodology which uses integrated models based on Michaelis-Menten equation. The most severe practical limitation of progress curve analysis occurs when the enzyme shows a loss of activity under the chosen assay conditions. To avoid this problem it is possible to work with the same experimental points utilized for initial rates determination. This methodology is illustrated by the use of integrated kinetic equations with the well-known reaction catalyzed by alkaline phosphatase enzyme. In this work nonlinear regression was performed with the Solver supplement (Microsoft Office Excel). It is easy to work with and track graphically the convergence of SSE (sum of square errors). The diagnosis of enzyme inhibition was performed according to Akaike information criterion.
Kim, Hyojin; Seo, Kyung-Ah; Kim, Hyunmi; Lee, Hye Suk; Lee, Choong-Hwan; Shin, Jae-Gook; Liu, Kwang-Hyeon
2007-04-01
KR-32570 (5-(2-Methoxy-5-chlorophenyl)furan-2-ylcarbonyl)guanidine) is a new cardioprotective agent for preventing ischemia-reperfusion injury. Human liver microsomal incubation of KR-32570 in the presence of NADPH resulted in the formation of two metabolites, hydroxy-KR-32570 and O-desmethyl-KR-32570. In this study, a kinetic analysis of the metabolism of two metabolites from KR-32570 was performed in human liver microsomes, and recombinant CYP1A2, and CYP3A4. The metabolism for hydroxy- and O-desmethyl-KR-32570 formation from KR-32570 by human liver microsomes was best described by a Michaelis-Menten equation and a Hill equation, respectively. The Cl(int) values of hydroxy- and O-desmethyl-KR-32570 formation were similar to each other (0.03 vs 0.04 microL/min/pmol CYP, respectively). CYP3A4 mediated the formation of hydroxy-KR-32570 from KR-32570 with Cl(int) = 0.24 microL/min/pmol CYP3A4. The intrinsic clearance for O-desmethyl-KR-32570 formation by CYP1A2 was 0.83 AL/min/pmol CYP1A2. These findings suggest that CYP3A4 and CYP1A2 enzymes are major enzymes contributing to the metabolism of KR-32570.
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.
Gan, Jinping; Qu, Qinling; He, Bing; Shyu, Wen C; Rodrigues, A David; He, Kan
2008-08-01
Troglitazone (TGZ) induced hepatotoxicity has been linked to cytochrome P450 (CYP)-catalyzed reactive metabolite formation. Therefore, the kinetics and CYP specificity of reactive metabolite formation were studied using dansyl glutathione (dGSH) as a trapping agent after incubation of TGZ with human liver microsomes (HLM) and recombinant human CYP proteins. CYP2C8 exhibited the highest rate of TGZ adduct (TGZ-dGS) formation, followed by CYP3A4, CYP3A5, and CYP2C19. The involvement of CYP2C8 and CYP3A4 was confirmed with CYP form-selective chemical inhibitors. The impact of TGZ concentration on the rate of TGZ-dGS formation was also evaluated. In this instance, two distinctly different profiles were observed with recombinant CYP3A4 and CYP2C8. It is concluded that both CYP3A4/5 and CYP2C8 play a major role in the formation of TGZ adduct in HLM. However, the contribution of these CYPs varies depending on their relative expression and the concentration of TGZ. PMID:19356091
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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…
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
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...
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)
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...... evolutionary origin in this family of PRTases. Only the N-terminal two thirds of the polypeptide chain folds as a traditional type I PRTase with a five-stranded β-sheet surrounded by helices. The C-terminal third adopts an unusual three-helix bundle structure that together with the nucleobase-binding loop......H-range and the kinetic and ligand binding properties depend on both pH and the presence/absence of phosphate in the buffers. A slow hydrolysis of PRPP to ribose 5-phosphate and pyrophosphate, catalyzed by the enzyme may be facilitated by elements in the C-terminal three-helix bundle part of the protein....
Directory of Open Access Journals (Sweden)
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.
Energy Technology Data Exchange (ETDEWEB)
Tsao, G T
1976-02-01
This project deals with acidic and enzymatic hydrolysis of cellulosic materials. Highlights of the first eight months of out project are as follows. (1) Essentially homogeneous C/sub 1/, C/sub x/, and Cellobiase enzyme have been isolated from Cellulase-Onozuka of Trichodeima viride origin. Besides the 3 major components, one protein of a molecular weight of 10,000 was purified, which has strong C/sub x/ activity and also another (M.W. 23,000) with strong C/sub 1/ activity. (2) Kinetics of Cellobiase has been investigated and its kinetics constant accurately determined. Immobilization of this enzyme on porous glass was successful. (3) Absorption of SO/sub 2/ at atmospheric pressure increased digestibility of delignated cellulose but not the natural materials such as corn stalk. A pressurizable absorption unit is being built. (4) Kinetics models for purified C/sub 1/ and C/sub x/ are postulated and equations derived. Experimental tests will be made when sufficient quantities of purified C/sub 1/ and C/sub x/ enzyme are prepared. (5) A lignin digesting, white-rot fungus, Pleurotus ostreatus, has cultivated in our laboratory. It has grown well and heavy. (6) A number of electron micrographs were made with untreated cellulosic materials, which showed that the method of drying the specimens for electromicroscopy is important. Ordinary drying procedures will alter their physical structures. A technique, critical point drying, is being practiced, which will not change the structure. (auth)
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
Leong, Sze Ying; Oey, Indrawati
2014-03-01
The objective of this research was to study the enzyme kinetics and thermostability of endogenous ascorbic acid oxidase (AAO) in carrot purée (Daucus carota cv. Nantes) after being treated with pulsed electric field (PEF) processing. Various PEF treatments using electric field strength between 0.2 and 1.2kV/cm and pulsed electrical energy between 1 and 520kJ/kg were conducted. The enzyme kinetics and the kinetics of AAO thermal inactivation (55-70°C) were described using Michaelis-Menten model and first order reaction model, respectively. Overall, the estimated Vmax and KM values were situated in the same order of magnitude as the untreated carrot purée after being exposed to pulsed electrical energy between 1 and 400kJ/kg, but slightly changed at pulsed electrical energy above 500kJ/kg. However, AAO presented different thermostability depending on the electric field strength applied. After PEF treatment at the electric field strength between 0.2 and 0.5kV/cm, AAO became thermolabile (i.e. increase in inactivation rate (k value) at reference temperature) but the temperature dependence of k value (Ea value) for AAO inactivation in carrot purée decreased, indicating that the changes in k values were less temperature dependent. It is obvious that PEF treatment affects the temperature stability of endogenous AAO. The changes in enzyme kinetics and thermostability of AAO in carrot purée could be related to the resulting carrot purée composition, alteration in intracellular environment and the effective concentration of AAO released after being subjected to PEF treatment.
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...
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.
Girgih, Abraham T; He, Rong; Aluko, Rotimi E
2014-05-01
Four novel peptide sequences (WVYY, WYT, SVYT, and IPAGV) identified from an enzymatic digest of hemp seed proteins were used for enzyme inhibition kinetics and molecular docking studies. Results showed that WVYY (IC50 = 0.027 mM) was a more potent (p < 0.05) ACE-inhibitory peptide than WYT (IC50 = 0.574 mM). However, WYT (IC50 = 0.054 mM) and SVYT (IC50 = 0.063 mM) had similar renin-inhibitory activity, which was significantly better than that of IPAGV (IC50 = 0.093 mM). Kinetics studies showed that WVYY had a lower inhibition constant (Ki) of 0.06 mM and hence greater affinity for ACE when compared to the 1.83 mM obtained for WYT. SVYT had lowest Ki value of 0.89 mM against renin, when compared to the values obtained for WYT and IPAGV. Molecular docking results showed that the higher inhibitory activities of WVYY and SVYT were due to the greater degree of noncovalent bond-based interactions with the enzyme protein, especially formation of higher numbers of hydrogen bonds with active site residues.
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...
Jensen, Kaj Frank; Hansen, Michael Riis; Jensen, Kristine Steen; Christoffersen, Stig; Poulsen, Jens-Christian Navarro; Mølgaard, Anne; Kadziola, Anders
2015-04-14
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-phosphoribosyl-α-1-pyrophosphate (PRPP) and adenine or the product adenosine monophosphate (AMP) or the inhibitor adenosine diphosphate (ADP) in each active site. The individual subunit adopts an overall structure that resembles a 6-oxopurine phosphoribosyltransferase (PRTase) more than known APRTases implying that APRT functionality in Crenarchaeotae has its evolutionary origin in this family of PRTases. Only the N-terminal two-thirds of the polypeptide chain folds as a traditional type I PRTase with a five-stranded β-sheet surrounded by helices. The C-terminal third adopts an unusual three-helix bundle structure that together with the nucleobase-binding loop undergoes a conformational change upon binding of adenine and phosphate resulting in a slight contraction of the active site. The inhibitor ADP binds like the product AMP with both the α- and β-phosphates occupying the 5'-phosphoribosyl binding site. The enzyme shows activity over a wide pH range, and the kinetic and ligand binding properties depend on both pH and the presence/absence of phosphate in the buffers. A slow hydrolysis of PRPP to ribose 5-phosphate and pyrophosphate, catalyzed by the enzyme, may be facilitated by elements in the C-terminal three-helix bundle part of the protein. PMID:25790177
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
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)
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…
Knecht, W; Bergjohann, U; Gonski, S; Kirschbaum, B; Löffler, M
1996-08-15
Human mitochondrial dihydroorotate dehydrogenase (the fourth enzyme of pyrimidine de novo synthesis) has been overproduced by means of a recombinant baculovirus that contained the human cDNA fragment for this protein. After virus infection and protein expression in Trichoplusia ni cells (BTI-Tn-5B1-4), the subcellular distribution of the recombinant dihydroorotate dehydrogenase was determined by two distinct enzyme-activity assays and by Western blot analysis with anti-(dihydroorotate dehydrogenase) Ig. The targeting of the recombinant protein to the mitochondria of the insect cells was verified. The activity of the recombinant enzyme in the mitochondria of infected cells was about 740-fold above the level of dihydroorotate dehydrogenase in human liver mitochondria. In a three-step procedure, dihydroorotate dehydrogenase was purified to a specific activity of greater than 50 U/mg. Size-exclusion chromatography showed a molecular mass of 42 kDa and confirmed the existence of the fully active enzyme as a monomeric species. Fluorimetric cofactor analysis revealed the presence of FMN in recombinant dihydroorotate dehydrogenase. By kinetics analysis, Km values for dihydroorotate and ubiquinone-50 were found to be 4 microM and 9.9 microM, respectively, while Km values for dihydroorotate and decylubiquinone were 9.4 microM and 13.7 microM, respectively. The applied expression system will allow preparation of large quantities of the enzyme for structure and function studies. Purified recombinant human dihytdroorotate dehydrogenase was tested for its sensitivity to a reported inhibitor A77 1726 (2-hydroxyethyliden-cyanoacetic acid 4-trifluoromethyl anilide), which is the active metabolite of the isoxazole derivative leflunomide [5-methyl-N-(4-trifluoromethyl-phenyl)-4-isoxazole carboximide]. An IC50 value of 1 microM was determined for A77 1726. Detailed kinetics experiments revealed uncompetitive inhibition with respect to dihydroorotate (Kiu = 0.94 microM) and non
Directory of Open Access Journals (Sweden)
Marius Schmidt
2014-03-01
Full Text Available With recent technological advances at synchrotrons [Graber et al., J. Synchrotron Radiat. 18, 658–670 (2011], it is feasible to rapidly collect time-resolved crystallographic data at multiple temperature settings [Schmidt et al., Acta Crystallogr. D 69, 2534–2542 (2013], from which barriers of activation can be extracted. With the advent of fourth generation X-ray sources, new opportunities emerge to investigate structure and dynamics of biological macromolecules in real time [M. Schmidt, Adv. Condens. Matter Phys. 2013, 1–10] in crystals and potentially from single molecules in random orientation in solution [Poon et al., Adv. Condens. Matter Phys. 2013, 750371]. Kinetic data from time-resolved experiments on short time-scales must be interpreted in terms of chemical kinetics [Steinfeld et al., Chemical Kinetics and Dynamics, 2nd ed. (Prentience Hall, 1985] and tied to existing time-resolved experiments on longer time-scales [Schmidt et al., Acta Crystallogr. D 69, 2534–2542 (2013; Jung et al., Nat. Chem. 5, 212–220 (2013]. With this article, we will review and outline steps that are required to routinely determine the energetics of reactions in biomolecules in crystal and solution with newest X-ray sources. In eight sections, we aim to describe concepts and experimental details that may help to inspire new approaches to collect and interpret these data.
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.
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...... stability criteria for the classic explicit and fully implicit methods. The Crank-Nicolson method turns out to be only conditionally stable in contrast to the current thought regarding this method....
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
Haseba, Takeshi; Kameyama, Kouji; Mashimo, Keiko; Ohno, Youkichi
2012-01-01
ADH 1 and ADH 3 are major two ADH isozymes in the liver, which participate in systemic alcohol metabolism, mainly distributing in parenchymal and in sinusoidal endothelial cells of the liver, respectively. We investigated how these two ADHs contribute to the elimination kinetics of blood ethanol by administering ethanol to mice at various doses, and by measuring liver ADH activity and liver contents of both ADHs. The normalized AUC (AUC/dose) showed a concave increase with an increase in ethanol dose, inversely correlating with β. CL(T) (dose/AUC) linearly correlated with liver ADH activity and also with both the ADH-1 and -3 contents (mg/kg B.W.). When ADH-1 activity was calculated by multiplying ADH-1 content by its V(max)/mg (4.0) and normalized by the ratio of liver ADH activity of each ethanol dose to that of the control, the theoretical ADH-1 activity decreased dose-dependently, correlating with β. On the other hand, the theoretical ADH-3 activity, which was calculated by subtracting ADH-1 activity from liver ADH activity and normalized, increased dose-dependently, correlating with the normalized AUC. These results suggested that the elimination kinetics of blood ethanol in mice was dose-dependently changed, accompanied by a shift of the dominant metabolizing enzyme from ADH 1 to ADH 3.
Directory of Open Access Journals (Sweden)
Takeshi Haseba
2012-01-01
Full Text Available ADH 1 and ADH 3 are major two ADH isozymes in the liver, which participate in systemic alcohol metabolism, mainly distributing in parenchymal and in sinusoidal endothelial cells of the liver, respectively. We investigated how these two ADHs contribute to the elimination kinetics of blood ethanol by administering ethanol to mice at various doses, and by measuring liver ADH activity and liver contents of both ADHs. The normalized AUC (AUC/dose showed a concave increase with an increase in ethanol dose, inversely correlating with β. CLT (dose/AUC linearly correlated with liver ADH activity and also with both the ADH-1 and -3 contents (mg/kg B.W.. When ADH-1 activity was calculated by multiplying ADH-1 content by its Vmax/mg (4.0 and normalized by the ratio of liver ADH activity of each ethanol dose to that of the control, the theoretical ADH-1 activity decreased dose-dependently, correlating with β. On the other hand, the theoretical ADH-3 activity, which was calculated by subtracting ADH-1 activity from liver ADH activity and normalized, increased dose-dependently, correlating with the normalized AUC. These results suggested that the elimination kinetics of blood ethanol in mice was dose-dependently changed, accompanied by a shift of the dominant metabolizing enzyme from ADH 1 to ADH 3.
Whitelaw, Douglas A; Tonkin, Rochelle; Meints, Carla E; Wolthers, Kirsten R
2015-10-15
Herein, we compare the kinetic properties of CPR from Arabidopsis thaliana (ATR2), with CPR from Artemisia annua (aaCPR) and human CPR (hCPR). While all three CPR forms elicit comparable rates for cytochrome c(3+) turnover, NADPH reduction of the FAD cofactor is ∼50-fold faster in aaCPR and ATR2 compared to hCPR, with a kobs of ∼500 s(-1) (6 °C). Stopped-flow analysis of the isolated FAD-domains reveals that NADP(+)-FADH2 charge-transfer complex formation is also significantly faster in the plant enzymes, but the rate of its decay is comparable for all three proteins. In hCPR, transfer of a hydride ion from NADPH to FAD is tightly coupled to subsequent FAD to FMN electron transfer, indicating that the former catalytic event is slow relative to the latter. In contrast, interflavin electron transfer is slower than NADPH hydride transfer in aaCPR and ATR2, occurring with an observed rate constant of ∼50 s(-1). Finally, the transfer of electrons from FMN to cytochrome c(3+) is rapid (>10(3) s(-1)) in all three enzymes and does not limit catalytic turnover. In combination, the data reveal differences in rate-determining steps between plant CPR and their mammalian equivalent in mediating the flux of reducing equivalents from NADPH to external electron acceptors. PMID:26361974
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。
Directory of Open Access Journals (Sweden)
Rinku Pandey
Full Text Available Organochlorine insecticide hexachlorocyclohexane (HCH has recently been classified as a 'Persistent Organic pollutant' by the Stockholm Convention. The LinB haloalkane dehalogenase is a key upstream enzyme in the recently evolved Lin pathway for the catabolism of HCH in bacteria. Here we report a sequence-structure-function analysis of ten naturally occurring and thirteen synthetic mutants of LinB. One of the synthetic mutants was found to have ∼80 fold more activity for β- and δ-hexachlorocyclohexane. Based on detailed biophysical calculations, molecular dynamics and ensemble docking calculations, we propose that the latter variant is more active because of alterations to the shape of its active site and increased conformational plasticity.
Clayman, Dee L.
1995-01-01
Appraises several databases devoted to classical literature. Thesaurus Linguae Graecae (TLG) contains the entire extant corpus of ancient Greek literature, including works on lexicography and historiography, extending into the 15th century. Other works awaiting completion are the Database of Classical Bibliography and a CD-ROM pictorial dictionary…
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.
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
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.
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
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
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...... 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...... 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 training with a volume reduction did not increase the content...
Schwinger, Julian Seymour; Milton, K A; Tsai, W Y
1998-01-01
This text for the graduate classical electrodynamics course was left unfinished upon Julian Schwinger's death in 1994, but was completed by his coauthors, who have brilliantly recreated the excitement of Schwinger's novel approach. Classical Electrodynamics captures Schwinger's inimitable lecturing style, in which everything flows inexorably from what has gone before. An essential resource for both physicists and their students, the book includes a "Reader's Guide", which describes the major themes in each chapter, suggests a possible path through the book, and identifies topics for inclusion
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
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
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
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.
Takayanagi, Toshiaki
2013-12-01
The basic model for chronic hepatitis B virus (HBV) or hepatitis C virus (HCV) infection during therapy enables us to analyze short-term viral kinetics. However, the model is not useful for analyzing long-term viral kinetics. Here, I suggest a new model that was obtained by introducing Michaelis-Menten kinetics into the basic model. The new model can exhibit long-term viral kinetics without rebound and oscillation, unlike the basic model. The value of the parameter K in the new model is analogous to the Michaelis constant Km and is predicted to be approximately less than 10(10)/ml.
Wessjohann, Ludger A; Keim, Jeanette; Weigel, Benjamin; Dippe, Martin
2013-04-01
Chemospecific and regiospecific modifications of natural products by methyl, prenyl, or C-glycosyl moieties are a challenging and cumbersome task in organic synthesis. Because of the availability of an increasing number of stable and selective transferases and cofactor regeneration processes, enzyme-assisted strategies turn out to be promising alternatives to classical synthesis. Two categories of alkylating enzymes become increasingly relevant for applications: firstly prenyltransferases and terpene synthases (including terpene cyclases), which are used in the production of terpenoids such as artemisinin, or meroterpenoids like alkylated phenolics and indoles, and secondly methyltransferases, which modify flavonoids and alkaloids to yield products with a specific methylation pattern such as 7-O-methylaromadendrin and scopolamine.
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)
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.
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
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...
Forward design of a complex enzyme cascade reaction
Hold, Christoph; Billerbeck, Sonja; Panke, Sven
2016-01-01
Enzymatic reaction networks are unique in that one can operate a large number of reactions under the same set of conditions concomitantly in one pot, but the nonlinear kinetics of the enzymes and the resulting system complexity have so far defeated rational design processes for the construction of such complex cascade reactions. Here we demonstrate the forward design of an in vitro 10-membered system using enzymes from highly regulated biological processes such as glycolysis. For this, we adapt the characterization of the biochemical system to the needs of classical engineering systems theory: we combine online mass spectrometry and continuous system operation to apply standard system theory input functions and to use the detailed dynamic system responses to parameterize a model of sufficient quality for forward design. This allows the facile optimization of a 10-enzyme cascade reaction for fine chemical production purposes. PMID:27677244
Classical and quantum free motions in the tomographic probability representation
Man'ko, Vladimir I
2011-01-01
Based on a geometric picture, the example of free particle motion for both classical and quantum domains is considered in the tomographic probability representation. Wave functions and density operators as well as optical and symplectic tomograms are obtained as solutions of kinetic classical and quantum equations for the state tomograms. The difference of tomograms of free particle for classical and quantum states is discussed.
Sucharitakul, J.; Tongsook, C.; Pakotiprapha, D.; Berkel, van W.J.H.; Chaiyen, P.
2013-01-01
3-Hydroxybenzoate 6-hydroxylase (3HB6H) from Rhodococcus jostii RHA1 is an NADH-specific flavoprotein monooxygenase that catalyzes the para-hydroxylation of 3-hydroxybenzoate (3HB) to form 2,5-dihydroxybenzoate (2,5-DHB). Based on results from stopped-flow spectrophotometry, the reduced enzyme-3HB c
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...
Multiple alternative substrate kinetics.
Anderson, Vernon E
2015-11-01
The specificity of enzymes for their respective substrates has been a focal point of enzyme kinetics since the initial characterization of metabolic chemistry. Various processes to quantify an enzyme's specificity using kinetics have been utilized over the decades. Fersht's definition of the ratio kcat/Km for two different substrates as the "specificity constant" (ref [7]), based on the premise that the important specificity existed when the substrates were competing in the same reaction, has become a consensus standard for enzymes obeying Michaelis-Menten kinetics. The expansion of the theory for the determination of the relative specificity constants for a very large number of competing substrates, e.g. those present in a combinatorial library, in a single reaction mixture has been developed in this contribution. The ratio of kcat/Km for isotopologs has also become a standard in mechanistic enzymology where kinetic isotope effects have been measured by the development of internal competition experiments with extreme precision. This contribution extends the theory of kinetic isotope effects to internal competition between three isotopologs present at non-tracer concentrations in the same reaction mix. This article is part of a special issue titled: Enzyme Transition States from Theory and Experiment.
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.
Institute of Scientific and Technical Information of China (English)
Abdelfattah Z M Salem; German Buenda-Rodrguez; Mona M M Elghandour; Mara A Mariezcurrena Berasain; Francisco J Pea Jimnez; Alberto B Pliego; Juan C V Chagoyn; Mara A Cerrillo; Miguel A Rodrguez
2015-01-01
Anin vitro gas production (GP) technique was used to investigate the effects of combining different doses ofSalix babylonicaextract (SB) with exogenous ifbrolytic enzymes (EZ) based on xylanase (X) and celulase (C), or their mixture (XC; 1:1 v/v) onin vitrofermentation characteristics of a total mixed ration of corn silage and concentrate mixture (50:50, w/w)as substrate. Four levels of SB (0, 0.6, 1.2 and 1.8 mL g–1 dry matter (DM))andfour supplemental styles of EZ (1 µL g–1 DM; control (no enzymes), X, C and XC (1:1, v/v) were used in a 4×4 factorial arrangement.In vitro GP (mL g–1 DM) were recorded at 2, 4, 6, 8, 10, 12, 24, 36, 48 and 72 h of incubation. After 72 h, the incubation process was stopped and supernatant pH was determined, and then ifltered to determine dry matter degradability (DMD). Fermentation parameters, such as the 24 h gas yield (GY24),in vitro organic matter digestibility (OMD), metabolizable energy (ME), short chain fatty acid concentrations (SCFA), and microbial crude protein production (MCP) were also estimated. Results indicated that there was a SB´EZ interaction (P0.05) on OMD, pH, ME, GY24, SCFA and MP. The combination of SB with EZ increased (P<0.001) OMD, ME, SCFA, PF72 and GP24, whereas there was no impact on pH. It could be concluded that addition of SB extract, C, and X effectively improved thein vitro rumen fermentation, and the combination of enzyme with SB extract at the level of 1.2 mL g–1 was more effective than the other treatments.
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.
Haataja, Tatu J K; Koski, M Kristian; Hiltunen, J Kalervo; Glumoff, Tuomo
2011-05-01
All of the peroxisomal β-oxidation pathways characterized thus far house at least one MFE (multifunctional enzyme) catalysing 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 Drosophila melanogaster MFE-2 (DmMFE-2), complements the Saccharomyces cerevisiae MFE-2 deletion strain, and the recombinant protein displays both MFE-2 enzymatic activities in vitro. The resolved crystal structure is the first one for a full-length MFE-2 revealing the assembly of domains, and the data can also be transferred to structure-function studies for other MFE-2 proteins. The structure explains the necessity of dimerization. The lack of substrate channelling is proposed based on both the structural features, as well as by the fact that hydration and dehydrogenation activities of MFE-2, if produced as separate enzymes, are equally efficient in catalysis as the full-length MFE-2.
Institute of Scientific and Technical Information of China (English)
苏平; 周明
2012-01-01
To comparatively study the differences on structures and functions of phycocyanin lyase CpcE/F from different cyanobacteria, CpcE/F from Anabaena sp. PCC 7120 were cloned and expressed greatly. The reconstitution of PCB and CpcA from Mastigocladus laminosus PCC 7603 in vitro using the overexpressed lyase Anabaena sp. PCC 7120 CpcE/F showed that CpcE/F from Anabaena sp. PCC 7120 is the specific enzyme for biosynthesis of α-PC, furthermore, the enzyme kinetics of PcE/F lyase were studied preliminarily.%为了比较研究不同藻种中藻蓝蛋白裂合酶CpcE/F的结构与功能的差异,对Anabaena sp.PCC 7120中的CpcE/F进行克隆,并进行大量表达,将表达的裂合酶CpcE/F用于藻蓝胆素(PCB)与Mastigocladus laminosus PCC 7603藻蓝蛋白α-亚基(α-PC)脱辅基蛋白(CpcA)的体外重组,得到天然活性的α-PC,从而表明CpcE/F所编码的蛋白质是α-PC生物合成的裂合酶,并对CpcE/F的酶动力学进行了初步研究.
Classicalization of Quantum Variables
Koide, T
2014-01-01
A systematic procedure to extract classical degrees of freedom in quantum mechanics is formulated using the stochastic variational method. With this classicalization, a hybrid model constructed from quantum and classical variables (quantum-classical hybrids) is derived systematically. In this procedure, conservation laws such as energy are maintained, and Eherefest`s theorem is still satisfied with modification. The criterion for the applicability of quantum-classical hybrids is also investigated.
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
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...
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
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
Kantsadi, Anastassia L; Bokor, Éva; Kun, Sándor; Stravodimos, George A; Chatzileontiadou, Demetra S M; Leonidas, Demetres D; Juhász-Tóth, Éva; Szakács, Andrea; Batta, Gyula; Docsa, Tibor; Gergely, Pál; Somsák, László
2016-11-10
C-β-d-Glucopyranosyl pyrrole derivatives were prepared in the reactions of pyrrole, 2-, and 3-aryl-pyrroles with O-peracetylated β-d-glucopyranosyl trichloroacetimidate, while 2-(β-d-glucopyranosyl) indole was obtained by a cross coupling of O-perbenzylated β-d-glucopyranosyl acetylene with N-tosyl-2-iodoaniline followed by spontaneous ring closure. An improved synthesis of O-perbenzoylated 2-(β-d-glucopyranosyl) imidazoles was achieved by reacting C-glucopyranosyl formimidates with α-aminoketones. The deprotected compounds were assayed with isoforms of glycogen phosphorylase (GP) to show no activity of the pyrroles against rabbit muscle GPb. The imidazoles proved to be the best known glucose derived inhibitors of not only the muscle enzymes (both a and b) but also of the pharmacologically relevant human liver GPa (Ki = 156 and 26 nM for the 4(5)-phenyl and -(2-naphthyl) derivatives, respectively). An X-ray crystallographic study of the rmGPb-imidazole complexes revealed structural features of the strong binding, and also allowed to explain the absence of inhibition for the pyrrole derivatives. PMID:27522507
Quantum computing classical physics.
Meyer, David A
2002-03-15
In the past decade, quantum algorithms have been found which outperform the best classical solutions known for certain classical problems as well as the best classical methods known for simulation of certain quantum systems. This suggests that they may also speed up the simulation of some classical systems. I describe one class of discrete quantum algorithms which do so--quantum lattice-gas automata--and show how to implement them efficiently on standard quantum computers.
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....
Entanglement in Classical Optics
Ghose, Partha
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 between separable and nonseparable states in classical wave optics where no discreteness is involved. The influence of the Pancharatnam phase on a classical Bell-like state is deived. Finally, to what extent classical polarization optics can be used to simulate quantum information processing tasks is also discussed. This should be of great practical importance because coherence and entanglement are robust in classical optics but not in quantum systems.
Bacon, Rendi Murphree; Biggerstaff, Brad J; Schriefer, Martin E; Gilmore, Robert D; Philipp, Mario T; Steere, Allen C; Wormser, Gary P; Marques, Adriana R; Johnson, Barbara J B
2003-04-15
In a study of US patients with Lyme disease, immunoglobulin (Ig) G and IgM antibody responses to recombinant Borrelia burgdorferi antigen VlsE1 (rVlsE1), IgG responses to a synthetic peptide homologous to a conserved internal sequence of VlsE (C6), and IgM responses to a synthetic peptide comprising the C-terminal 10 amino acid residues of a B. burgdorferi outer-surface protein C (pepC10) were evaluated by kinetic enzyme-linked immunoassay. At 99% specificity, the overall sensitivities for detecting IgG antibody to rVlsE1 or C6 in samples from patients with diverse manifestations of Lyme disease were equivalent to that of 2-tiered testing. When data were considered in parallel, 2 combinations (IgG responses to either rVlsE1 or C6 in parallel with IgM responses to pepC10) maintained high specificity (98%) and were significantly more sensitive than 2-tiered analysis in detecting antibodies to B. burgdorferi in patients with acute erythema migrans. In later stages of Lyme disease, the sensitivities of the in parallel tests and 2-tiered testing were high and statistically equivalent.
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
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)
Measuring the Enzyme Activity of Arabidopsis Deubiquitylating Enzymes.
Kalinowska, Kamila; Nagel, Marie-Kristin; Isono, Erika
2016-01-01
Deubiquitylating enzymes, or DUBs, are important regulators of ubiquitin homeostasis and substrate stability, though the molecular mechanisms of most of the DUBs in plants are not yet understood. As different ubiquitin chain types are implicated in different biological pathways, it is important to analyze the enzyme characteristic for studying a DUB. Quantitative analysis of DUB activity is also important to determine enzyme kinetics and the influence of DUB binding proteins on the enzyme activity. Here, we show methods to analyze DUB activity using immunodetection, Coomassie Brilliant Blue staining, and fluorescence measurement that can be useful for understanding the basic characteristic of DUBs.
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.
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...
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. ...
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...
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...
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.
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
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.
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
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
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.
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...... 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...
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.
Enzymes: principles and biotechnological applications.
Robinson, Peter K
2015-01-01
Enzymes are biological catalysts (also known as biocatalysts) that speed up biochemical reactions in living organisms, and which can be extracted from cells and then used to catalyse a wide range of commercially important processes. This chapter covers the basic principles of enzymology, such as classification, structure, kinetics and inhibition, and also provides an overview of industrial applications. In addition, techniques for the purification of enzymes are discussed.
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.
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.
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
On Noncommutative Classical Mechanics
Djemai, A E F
2003-01-01
In this work, I investigate the noncommutative Poisson algebra of classical observables corresponding to a proposed general Noncommutative Quantum Mechanics, \\cite{1}. I treat some classical systems with various potentials and some Physical interpretations are given concerning the presence of noncommutativity at large scales (Celeste Mechanics) directly tied to the one present at small scales (Quantum Mechanics) and its possible relation with UV/IR mixing.
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...
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)
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
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...
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
Moonlighting enzymes in parasitic protozoa.
Collingridge, Peter W; Brown, Robert W B; Ginger, Michael L
2010-08-01
Enzymes moonlight in a non-enzymatic capacity in a diverse variety of cellular processes. The discovery of these non-enzymatic functions is generally unexpected, and moonlighting enzymes are known in both prokaryotes and eukaryotes. Importantly, this unexpected multi-functionality indicates that caution might be needed on some occasions in interpreting phenotypes that result from the deletion or gene-silencing of some enzymes, including some of the best known enzymes from classic intermediary metabolism. Here, we provide an overview of enzyme moonlighting in parasitic protists. Unequivocal and putative examples of moonlighting are discussed, together with the possibility that the unusual biological characteristics of some parasites either limit opportunities for moonlighting to arise or perhaps contribute to the evolution of novel proteins with clear metabolic ancestry.
Kinetic theory and transport phenomena
Soto, Rodrigo
2016-01-01
This textbook presents kinetic theory, which is a systematic approach to describing nonequilibrium systems. The text is balanced between the fundamental concepts of kinetic theory (irreversibility, transport processes, separation of time scales, conservations, coarse graining, distribution functions, etc.) and the results and predictions of the theory, where the relevant properties of different systems are computed. The book is organised in thematic chapters where different paradigmatic systems are studied. The specific features of these systems are described, building and analysing the appropriate kinetic equations. Specifically, the book considers the classical transport of charges, the dynamics of classical gases, Brownian motion, plasmas, and self-gravitating systems, quantum gases, the electronic transport in solids and, finally, semiconductors. Besides these systems that are studied in detail, concepts are applied to some modern examples including the quark–gluon plasma, the motion of bacterial suspen...
Enzyme technology: Key to selective biorefining
DEFF Research Database (Denmark)
Meyer, Anne S.
2014-01-01
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...... point and then improve the functional traits by targeted mutation of the protein. The talk will display some of our recent hypotheses related to enzyme action, recently obtained results within knowledge-based enzyme improvements as well as cast light on research methods used in optimizing enzyme...
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, ...
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
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.
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.
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
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
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.)
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…
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...
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.
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 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
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)
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)
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.
Mecanica Clasica (Classical Mechanics)
H. C. Rosu
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 Mechanics Laboratory
Brosing, Juliet W.
2006-12-01
At Pacific University we have included a lab with our upper division Classical Mechanics class. We do a combination of physical labs (air resistance, harmonic motion, amusement park physics), Maple labs (software), and projects. Presentation of some of the labs, results and challenges with this course will be included.
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…
Children's Classics. Fifth Edition.
Jordan, Alice M.
"Children's Classics," a 1947 article by Alice M. Jordan reprinted from "The Horn Book Magazine," examines the dynamics and appeal of some of the most famous books for young readers, including "Alice in Wonderland,""The Wind in the Willows,""Robinson Crusoe," and "Andersen's Fairy Tales." Paul Hein's annotated bibliography, a revision of Jordan's…
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.)
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
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.
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, ...
Classical Weyl Transverse Gravity
Oda, Ichiro
2016-01-01
We study various classical aspects of the Weyl transverse (WTDiff) gravity in a general space-time dimension. First of all, we clarify a classical equivalence among three kinds of gravitational theories, those are, the conformally-invariant scalar tensor gravity, Einstein's general relativity and the WTDiff gravity via the gauge fixing procedure. Secondly, we show that in the WTDiff gravity the cosmological constant is a mere integration constant as in unimodular gravity, but it does not receive any radiative corrections unlike the unimodular gravity. A key point in this proof is to construct a covariantly conserved energy-momentum tensor, which is achieved on the basis of this equivalence relation. Thirdly, we demonstrate that the Noether current for the Weyl transformation is identically vanishing, thereby implying that the Weyl symmetry existing in both the conformally-invariant scalar tensor gravity and the WTDiff gravity is a "fake" symmetry. We find it possible to extend this proof to all matter fields,...
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.
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.
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...
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
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…
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.
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...
Classical Maxwellian polarization entanglement
Carroll, John E
2015-01-01
An explanation of polarization entanglement is presented using Maxwells classical electromagnetic theory.Two key features are required to understand these classical origins.The first is that all waves diffract and weakly diffracting waves,with a principal direction of propagation in the laboratory frame, travel along that direction at speeds ever so slightly less than c.This allows nontrivial Lorentz transformations that can act on selected forward F waves or selected waves R traveling in the opposite direction to show that both can arise from a single zero momentum frame where all the waves are transverse to the original principal direction.Such F and R waves then both belong to a single relativistic entity where correlations between the two are unremarkable.The second feature requires the avoidance of using the Coulomb gauge.Waves, tending to plane waves in the limit of zero diffraction,can then be shown to be composed of two coupled sets of E and B fields that demonstrate the classical entanglement of F an...
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
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.
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....
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…
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...
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
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.
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.
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)
吕欢; 罗明琍; 方飞; 吴新荣
2012-01-01
Objective To establish an optimized inhibitory reaction system for the research of Folium Mori extracts in inhibiting alpha-glucosidase activity and to investigate the enzyme kinetics. Methods We studied the inhibitive effects of Folium Mori extracts on alpha-glucosidase by using enzyme-inhibitor model and optimized the reaction system by optimizing the substrate concentration, the amount of enzyme and the reaction time. We also investigated the inhibitory kinetic characteristics of extracts by using Lineweaver-Burk method. Results The optimized reaction system consisted of 40 mg/mL of the substrate concentration, 0.2 mL of enzyme and 25 min for reaction time. Inhibitory kinetic results indicated that the extracts were mixed competitive inhibitors, but the positive drug was noncompetitive inhibitor. Conclusion Folium Mori extracts have inhibitory effect on a- glucosidase activity, and the inhibitory type is in mixed competitive inhibition, which are expected to be used to develop as anti-diabetes drugs.%目的 研究桑叶提取物抑制α-葡萄糖苷酶活性反应体系的条件优化及酶动力学.方法 采用酶-抑制剂模型法,优化底物浓度、酶用量和反应时间,确定最佳反应体系,研究桑叶提取物对α-葡萄糖苷酶的抑制作用,并采用双倒数作图法研究桑叶提取物的酶抑制动力学特性.结果 当蔗糖浓度为40 mg/mL,酶用量为0.2mL(约1.6 U/mL),反应时间为25 min时为最佳反应体系；酶抑制动力学实验表明,桑叶提取物的抑制类型为混合型竞争性抑制,阳性对照为非竞争性抑制.结论 桑叶提取物对α-葡萄糖苷酶活性有抑制作用；桑叶提取物对α-葡萄糖苷酶抑制活性为混合性竞争性抑制,可以用于开发降糖药物.
Probability representation of classical states
Man'ko, OV; Man'ko, [No Value; Pilyavets, OV
2005-01-01
Probability representation of classical states described by symplectic tomograms is discussed. Tomographic symbols of classical observables which are functions on phase-space are studied. Explicit form of kernel of commutative star-product of the tomographic symbols is obtained.
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
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.
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...
Classical Physics and Quantum Loops
Energy Technology Data Exchange (ETDEWEB)
Barry R. Holstein; John F. Donoghue
2004-05-01
The standard picture of the loop expansion associates a factor of h-bar with each loop, suggesting that the tree diagrams are to be associated with classical physics, while loop effects are quantum mechanical in nature. We discuss examples wherein classical effects arise from loop contributions and display the relationship between the classical terms and the long range effects of massless particles.
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…
Nucleosynthesis in classical novae
José, Jordi; Hernanz, Margarita; Iliadis, Christian
2006-10-01
Classical novae are dramatic stellar explosions with an energy release that is only overcome by supernovae and gamma-ray bursts. These unique cataclysmic events constitute a crucible where different scientific disciplines merge, including astrophysics, nuclear and atomic physics, cosmochemistry, high-energy physics or computer science. In this review, we focus on the nucleosynthesis accompanying nova outbursts. Theoretical predictions are compared with the elemental abundances inferred from observations of the nova ejecta as well as with the isotopic abundance ratios measured in meteorites. Special emphasis is given to the interplay between nova outbursts and the Galactic abundance pattern and on the synthesis of radioactive nuclei for which γ-ray signals are expected. Finally, we analyze the key role played by nuclear physics in our understanding of the nova phenomenon by means of recent experiments and a thorough account of the impact of nuclear uncertainties.
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.
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
Institute of Scientific and Technical Information of China (English)
曹冬洁; 王相友; 王娟
2016-01-01
rate of fruit and vegetable can provide important theoretical guidance and design basis for the storage and preservation method. Although the storage time is an important factor to affect the respiration rate of fruits and vegetables, there are few models to consider the storage time. A theoretical model of respiration rate ofAgaricus bisporusrelated to storage time, based on the enzyme kinetics equation, was established. The effect of storage time on the respiration rate ofAgaricus bisporus was studied at 5℃ and 20% oxygen concentration under the controlled atmosphere storage, and the respiration models ofAgaricus bisporusbased on this were established, with the coefficients of determination of 0.9766 and 0.9331 respectively. The difference between the model and the measured value was not significant (P>0.05), the absolute error of the respiration rate was less than 5 mL/(kg·h), and the relative error was 0.06%-24.95%. After that, the effects of storage temperature (5, 10, 15 and 20℃) on the respiration rate were studied as well as the established model parameters. Based on the model, the temperature dependence of the model parameters was evaluated using an Arrhenius plot, and the model incorporating temperature and time was established, whose coefficients of determination were 0.9073 and 0.9350 respectively. The difference between the model and the measured value was not significant (P>0.05), the absolute error of the respiration rate was less than 17 mL/(kg·h), and the relative error was 1.00%-25.25%. The verification tests showed that, the respiration of Agaricus bisporusin terms of time and temperature during the storage was well described by the obtained models, and agreed well with the experiment data. The respiration rate model can provide the important theoretical basis for the prediction of respiratory rate and the research of storage quality in the process of storage and transportation of fruits and vegetables.%为了给气调贮藏设计提供理论
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.
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.
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.
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 ...
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: ……
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...
The Classical Electron Problem
Gill, T L; Lindesay, J
2001-01-01
In this paper, we construct a parallel image of the conventional Maxwell theory by replacing the observer-time by the proper-time of the source. This formulation is mathematically, but not physically, equivalent to the conventional form. The change induces a new symmetry group which is distinct from, but closely related to the Lorentz group, and fixes the clock of the source for all observers. The new wave equation contains an additional term (dissipative), which arises instantaneously with acceleration. This shows that the origin of radiation reaction is not the action of a "charge" on itself but arises from inertial resistance to changes in motion. This dissipative term is equivalent to an effective mass so that classical radiation has both a massless and a massive part. Hence, at the local level the theory is one of particles and fields but there is no self-energy divergence (nor any of the other problems). We also show that, for any closed system of particles, there is a global inertial frame and unique (...
Aniello, P.; Ciaglia, F. M.; Di Cosmo, F.; Marmo, G.; Pérez-Pardo, J. M.
2016-10-01
We propose a new point of view regarding the problem of time in quantum mechanics, based on the idea of replacing the usual time operator T with a suitable real-valued function T on the space of physical states. The proper characterization of the function T relies on a particular relation with the dynamical evolution of the system rather than with the infinitesimal generator of the dynamics (Hamiltonian). We first consider the case of classical hamiltonian mechanics, where observables are functions on phase space and the tools of differential geometry can be applied. The idea is then extended to the case of the unitary evolution of pure states of finite-level quantum systems by means of the geometric formulation of quantum mechanics. It is found that T is a function on the space of pure states which is not associated with any self-adjoint operator. The link between T and the dynamical evolution is interpreted as defining a simultaneity relation for the states of the system with respect to the dynamical evolution itself. It turns out that different dynamical evolutions lead to different notions of simultaneity, i.e., the notion of simultaneity is a dynamical notion.
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...
Extended symmetrical classical electrodynamics.
Fedorov, A V; Kalashnikov, E G
2008-03-01
In this paper, we discuss a modification of classical electrodynamics in which "ordinary" point charges are absent. The modified equations contain additional terms describing the induced charges and currents. The densities of the induced charges and currents depend on the vector k and the vectors of the electromagnetic field, E and B . It is shown that the vectors E and B can be defined in terms of two four-potentials and the components of k are the components of a four-tensor of the third rank. The Lagrangian of the modified electrodynamics is defined. The conditions are derived at which only one four-potential determines the behavior of the electromagnetic field. It is also shown that static modified electrodynamics can describe the electromagnetic field in the inner region of an electric monopole. In the outer region of the electric monopole the electric field is governed by the Maxwell equations. It follows from boundary conditions at the interface between the inner and outer regions of the monopole that the vector k has a discrete spectrum. The electric and magnetic fields, energy, and angular momentum of the monopole are found for different eigenvalues of k .
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 ...
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...
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...
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...
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
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.
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
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
Marklof, Jens
2010-03-01
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 stochastic process is the renormalization dynamics on the space of lattices, a powerful technique that has recently been successfully applied also to other open problems in mathematical physics, including KAM theory and quantum chaos. This lecture is based on joint work with Andreas Strömbergsson, Uppsala.
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.
Innovation: the classic traps.
Kanter, Rosabeth Moss
2006-11-01
Never a fad, but always in or out of fashion, innovation gets rediscovered as a growth enabler every half dozen years. Too often, though, grand declarations about innovation are followed by mediocre execution that produces anemic results, and innovation groups are quietly disbanded in cost-cutting drives. Each managerial generation embarks on the same enthusiastic quest for the next new thing. And each generation faces the same vexing challenges- most of which stem from the tensions between protecting existing revenue streams critical to current success and supporting new concepts that may be crucial to future success. In this article, Harvard Business School professor Rosabeth Moss Kanter reflects on the four major waves of innovation enthusiasm she's observed over the past 25 years. She describes the classic mistakes companies make in innovation strategy, process, structure, and skills assessment, illustrating her points with a plethora of real-world examples--including AT&T Worldnet, Timberland, and Ocean Spray. A typical strategic blunder is when managers set their hurdles too high or limit the scope of their innovation efforts. Quaker Oats, for instance, was so busy in the 1990s making minor tweaks to its product formulas that it missed larger opportunities in distribution. A common process mistake is when managers strangle innovation efforts with the same rigid planning, budgeting, and reviewing approaches they use in their existing businesses--thereby discouraging people from adapting as circumstances warrant. Companies must be careful how they structure fledgling entities alongside existing ones, Kanter says, to avoid a clash of cultures and agendas--which Arrow Electronics experienced in its attempts to create an online venture. Finally, companies commonly undervalue and underinvest in the human side of innovation--for instance, promoting individuals out of innovation teams long before their efforts can pay off. Kanter offers practical advice for avoiding
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.
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.
The equilibrium classical scatter spectrum of waves
Guruprasad, V
2016-01-01
Regardless of the unspecific notions of photons as light complexes, radiation bundles or wave packets, the radiation from a single state transition is at most a single continuous wave train that starts and ends with the transition. The radiation equilibrium spectrum must be the superposition sum of the spectra of such wave trains. A classical equipartition of wave trains cannot diverge since they would be finite in number, whereas standing wave modes are by definition infinite, which had doomed Rayleigh's theory, and concern only the total radiation. Wave trains are the microscopic entities of radiation interacting with matter, that correspond to molecules in kinetic theory. Their quantization came from matter transitions in Einstein's 1917 derivation of Planck's law. The spectral scatter of wave trains by Doppler shifts, which cause the wavelength displacements in Wien's law used for the frequency dependence in Einstein's derivation, is shown to yield the shape of the Planck spectrum. A Lorentz transform pro...
Classic writings on instructional technology
Ely, Donald P.; Plomp, Tjeerd
1996-01-01
This paper describes the selection process of 17 articles for inclusion in the book, "Classic Writings on Instructional Technology." The book brings together original "classic" educational technology articles into one volume to document the history of the field through its literature. It is also an
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…
Teaching and Demonstrating Classical Conditioning.
Sparrow, John; Fernald, Peter
1989-01-01
Discusses classroom demonstrations of classical conditioning and notes tendencies to misrepresent Pavlov's procedures. Describes the design and construction of the conditioner that is used for demonstrating classical conditioning. Relates how students experience conditioning, generalization, extinction, discrimination, and spontaneous recovery.…
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
Classic African American Children's Literature
McNair, Jonda C.
2010-01-01
The purpose of this article is to assert that there are classic African American children's books and to identify a sampling of them. The author presents multiple definitions of the term classic based on the responses of children's literature experts and relevant scholarship. Next, the manner in which data were collected and analyzed in regard to…
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 ...
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 subst......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...
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.
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...
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.
Plasmon mass scale in classical nonequilibrium gauge theory
Lappi, Tuomas
2016-01-01
Classical lattice Yang-Mills calculations provide a good way to understand different nonequilibrium phenomena in nonperturbatively overoccupied systems. Above the Debye scale the classical theory can be matched smoothly to kinetic theory. The aim of this work is to study the limits of this quasiparticle picture by determining the plasmon mass in classical real time Yang-Mills theory on a lattice in 3 spatial dimensions. We compare three methods to determine the plasmon mass: a hard thermal loop expression in terms of the particle distribution, an effective dispersion relation constructed from fields and their time derivatives, and by measuring oscillations between electric and magnetic field modes after artificially introducing a homogeneous color electric field. We find that a version of the dispersion relation that uses electric fields and their time derivatives agrees with the other methods within 50%.
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.
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
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...
From Classical to Quantum Transistor
Directory of Open Access Journals (Sweden)
Sanjeev Kumar
2009-05-01
Full Text Available In this article the classical transistor and the basic physics underlying the operation of single electron transistor are presented; a brief history of transistor and current technological issues are discussed.
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)
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.
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
Classical Transitions for Flux Vacua
Deskins, J Tate; Yang, I-Sheng
2012-01-01
We present the simplest model for classical transitions in flux vacua. A complex field with a spontaneously broken U(1) symmetry is embedded in $M_2\\times S_1$. We numerically construct different winding number vacua, the vortices interpolating between them, and simulate the collisions of these vortices. We show that classical transitions are generic at large boosts, independent of whether or not vortices miss each other in the compact $S_1$.
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.
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...
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...
14. Enzymes as Biocatalysts for Lipid-based Bioproducts Processing
DEFF Research Database (Denmark)
Cheong, Ling-Zhi; Guo, Zheng; Fedosov, Sergey;
2012-01-01
Bioproducts are materials, chemicals and energy derived from renewable biological resources such as agriculture, forestry, and biologically-derived wastes. To date, the use of enzymes as biocatalysts for lipid-based bioproducts processing has shown marked increase. This is mainly due to the fact...... that cost benefit derived from enzymatic processing such as enzyme specificity, higher product purity and lesser or none toxic waste disposal has surpassed the cost of biocatalysts itself. This chapter provided insights into distinct enzymes characteristics essential in industrial processing especially...... 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...
Examinations of the Chemical Step in Enzyme Catalysis.
Singh, P; Islam, Z; Kohen, A
2016-01-01
Advances in computational and experimental methods in enzymology have aided comprehension of enzyme-catalyzed chemical reactions. The main difficulty in comparing computational findings to rate measurements is that the first examines a single energy barrier, while the second frequently reflects a combination of many microscopic barriers. We present here intrinsic kinetic isotope effects and their temperature dependence as a useful experimental probe of a single chemical step in a complex kinetic cascade. Computational predictions are tested by this method for two model enzymes: dihydrofolate reductase and thymidylate synthase. The description highlights the significance of collaboration between experimentalists and theoreticians to develop a better understanding of enzyme-catalyzed chemical conversions.
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
Orphan enzymes in ether lipid metabolism.
Watschinger, Katrin; Werner, Ernst R
2013-01-01
Ether lipids are an emerging class of lipids which have so far not been investigated and understood in every detail. They have important roles as membrane components of e.g. lens, brain and testis, and as mediators such as platelet-activating factor. The metabolic enzymes for biosynthesis and degradation have been investigated to some extent. As most involved enzymes are integral membrane proteins they are tricky to handle in biochemical protocols. The sequence of some ether lipid metabolising enzymes has only recently been reported and other sequences still remain obscure. Defined enzymes without assigned sequence are known as orphan enzymes. One of these enzymes with uncharacterised sequence is plasmanylethanolamine desaturase, a key enzyme for the biosynthesis of one of the most abundant phospholipids in our body, the plasmalogens. This review aims to briefly summarise known functions of ether lipids, give an overview on their metabolism including the most prominent members, platelet-activating factor and the plasmalogens. A special focus is set on the description of orphan enzymes in ether lipid metabolism and on the successful strategies how four previous orphans have recently been assigned a sequence. Only one of these four was characterised by classical protein purification and sequencing, whereas the other three required alternative strategies such as bioinformatic candidate gene selection and recombinant expression or development of an inhibitor and multidimensional metabolic profiling.
Bisphenol A degradation in water by ligninolytic enzymes.
Gassara, Fatma; Brar, Satinder K; Verma, M; Tyagi, R D
2013-08-01
Many endocrine disruptor compounds, such as bisphenol A (BPA) are used today and released into the environment at low doses but they are barely degraded in wastewater treatment plants. One of the potential alternatives to effectively degrade endocrine disruptor compounds is based on the use of the oxidative action of extracellular fungal enzymes. The aim of this work is to study the ability of free and encapsulated enzymes (manganese peroxidase, lignin peroxidase and laccase) to degrade BPA. Higher degradation of BPA (90%) by ligninolytic enzymes encapsulated on polyacrylamide hydrogel and pectin after 8h was obtained. The degradation of BPA while using the free enzyme (26%) was lower than the value obtained with encapsulated enzymes. The presence of pectin in the formulation significantly (p>0.05) enhanced the activity of enzymes. Kinetics of BPA degradation showed an increase in Vm, while Km remained constant when enzymes were encapsulated. Hence, encapsulation protected the enzymes from non-competitive inhibition.
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.
Classical approach in atomic physics
Energy Technology Data Exchange (ETDEWEB)
Solov' ev, E.A. [Bogoliubov Laboratory of Theoretical Physics, Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation)
2011-12-15
The application of a classical approach to various quantum problems - the secular perturbation approach to quantization of a hydrogen atom in external fields and a helium atom, the adiabatic switching method for calculation of a semiclassical spectrum of a hydrogen atom in crossed electric and magnetic fields, a spontaneous decay of excited states of a hydrogen atom, Gutzwiller's approach to Stark problem, long-lived excited states of a helium atom discovered with the help of Poincare section, inelastic transitions in slow and fast electron-atom and ion-atom collisions - is reviewed. Further, a classical representation in quantum theory is discussed. In this representation the quantum states are treated as an ensemble of classical states. This approach opens the way to an accurate description of the initial and final states in classical trajectory Monte Carlo (CTMC) method and a purely classical explanation of tunneling phenomenon. The general aspects of the structure of the semiclassical series such as renormalization group symmetry, criterion of accuracy and so on are reviewed as well. (author)
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...
Substrate-dependent kinetics in tyrosinase-based biosensing: amperometry vs. spectrophotometry
Rassaei, L.; Cui, J.; Goluch, E.D.; Lemay, S.G.
2012-01-01
Despite the broad use of enzymes in electroanalytical biosensors, the influence of enzyme kinetics on the function of prototype sensors is often overlooked or neglected. In the present study, we employ amperometry as an alternative or complementary method to study the kinetics of tyrosinase, whose
Novel enzymes for the degradation of cellulose
Directory of Open Access Journals (Sweden)
Horn Svein
2012-07-01
Full Text Available Abstract The bulk terrestrial biomass resource in a future bio-economy will be lignocellulosic biomass, which is recalcitrant and challenging to process. Enzymatic conversion of polysaccharides in the lignocellulosic biomass will be a key technology in future biorefineries and this technology is currently the subject of intensive research. We describe recent developments in enzyme technology for conversion of cellulose, the most abundant, homogeneous and recalcitrant polysaccharide in lignocellulosic biomass. In particular, we focus on a recently discovered new type of enzymes currently classified as CBM33 and GH61 that catalyze oxidative cleavage of polysaccharides. These enzymes promote the efficiency of classical hydrolytic enzymes (cellulases by acting on the surfaces of the insoluble substrate, where they introduce chain breaks in the polysaccharide chains, without the need of first “extracting” these chains from their crystalline matrix.
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.
New Approaches to Classical Liberalism
Directory of Open Access Journals (Sweden)
Nicolas Maloberti
2012-01-01
Full Text Available This article focuses on the following three novel and original philosophical approaches to classical liberalism: Den Uyl and Rasmussen's perfectionist argument from meta-norms, Gaus's justificatory model, and Kukathas's conscience-based theory of authority. None of these three approaches are utilitarian or consequentialist in character. Neither do they appeal to the notion of a rational bargain as it is typical within contractarianism. Furthermore, each of these theories rejects the idea that classical liberalism should be grounded on considerations of interpersonal justice such as those that are central to the Lockean tradition. It is argued that these three theories, despite their many attractive features, fail to articulate in a convincing manner some central classical liberal concerns.
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.
Overview of Classical Swine Fever (Hog Cholera, Classical Swine fever)
Classical swine fever is a contagious often fatal disease of pigs clinically characterized by high body temperature, lethargy, yellowish diarrhea, vomits and purple skin discoloration of ears, lower abdomen and legs. It was first described in the early 19th century in the USA. Later, a condition i...
Kinetic ELISA in Microfluidic Channels
Directory of Open Access Journals (Sweden)
Debashis Dutta
2011-06-01
Full Text Available In this article, we describe the kinetic ELISA of Blue Tongue and Epizootic Hemorrhagic Disease viral antibodies in microfluidic channels by monitoring the rate of generation of the enzyme reaction product under static conditions. It has been shown that this format of the immunoassay allows very reliable quantitation of the target species using inexpensive glass microchips and a standard epifluorescence microscope system coupled to a CCD camera. For the viral antibodies assayed here, the limit of detection (LOD for the analyte concentration in our microchips was established to be 3–5 times lower than that obtained on commercial microwell plates using a fiftieth of the sample volume and less than a third of the incubation time. Our analyses further show that when compared to the end-point ELISA format, the kinetic mode of this assay yields an improvement in the LOD by over an order of magnitude in microfluidic devices. This benefit is primarily realized as the observed variation in the background fluorescence (signal at the start of the enzyme reaction period was significantly larger than that in the rate of signal generation upon repeating these assays in different microchannels/microchips. Because the kinetic ELISA results depend only on the latter quantity, the noise level in them was substantially lower compared to that in its end-point counterpart in which the absolute fluorescence measurements are of greater significance. While a similar benefit was also recorded through implementation of kinetic ELISAs on the microwell platform, the improvement in LOD registered in that system was not as significant as was observed in the case of microfluidic assays.
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
to 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......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...
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.
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.
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
On Classical and Quantum Cryptography
Volovich, I V; 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.
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…
Supersymmetric classical mechanics: free case
Energy Technology Data Exchange (ETDEWEB)
Rodrigues, R. de Lima [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)]|[Paraiba Univ., Cajazeiras, PB (Brazil). Dept. de Ciencias Exatas e da Natureza]. E-mail: rafael@cfp.ufpb.br; Almeida, W. Pires de [Paraiba Univ., Cajazeiras, PB (Brazil). Dept. de Ciencias Exatas e da Natureza; Fonseca Neto, I. [Paraiba Univ., Campina Grande, PB (Brazil). Dept. de Fisica
2001-06-01
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, {phi}(t;{theta}). (author)
Relative Clauses in Classical Nahuatl
Langacker, Ronald W.
1975-01-01
Jane Rosenthal's paper on relative clauses in Classical Nahuatl is discussed, and it is argued that she misses an important generalization. An alternative analysis to a class of relative pronouns and new rules for the distribution of relative pronouns are proposed. (SC)
Minimum signals in classical physics
Institute of Scientific and Technical Information of China (English)
邓文基; 许基桓; 刘平
2003-01-01
The bandwidth theorem for Fourier analysis on any time-dependent classical signal is shown using the operator approach to quantum mechanics. Following discussions about squeezed states in quantum optics, the problem of minimum signals presented by a single quantity and its squeezing is proposed. It is generally proved that all such minimum signals, squeezed or not, must be real Gaussian functions of time.
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.
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
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.
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…
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)
No return to classical reality
Jennings, David; Leifer, Matthew
2016-01-01
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, non-commutativity, 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 understanding - the intrinsically quantum mechanical aspects of nature. The most famous of these is Bell's theorem, but we also review two more recent results in this area. Firstly, Hardy's theorem shows that even a finite-dimensional quantum system must contain an infinite amount of information, and secondly, the Pusey-Barrett-Rudolph theorem shows that the wave function must be an objective property of an individual quantum system. Besides being of foundational interest, results of this sort now find surprising practical applications in areas such as quantum information science and the simulation of quantum systems.
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.
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...
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.
Kinetic properties of cyanase.
Anderson, P M; Little, R M
1986-04-01
Cyanase is an inducible enzyme in Escherichia coli that catalyzes the hydrolysis of cyanate. Bicarbonate is required for activity, perhaps as a substrate, and the initial product of the reaction is carbamate, which spontaneously breaks down to ammonia and bicarbonate [Anderson, P. M. (1980) Biochemistry 19, 2882]. The purpose of this study was to characterize the kinetic properties of cyanase. Initial velocity studies showed that both cyanate and bicarbonate act as competitive substrate inhibitors. A number of monovalent anions act as inhibitors. Azide and acetate appear to act as competitive inhibitors with respect to cyanate and bicarbonate, respectively. Chloride, bromide, nitrate, nitrite, and formate also inhibit, apparently as the result of binding at either substrate site. Malonate and several other dicarboxylic dianions at very low concentrations display "slow-binding", reversible inhibition which can be prevented by saturating concentrations of either substrate. The results are consistent with a rapid equilibrium random mechanism in which bicarbonate acts as a substrate, bicarbonate and cyanate bind at adjacent anion-binding sites, and both substrates can bind at the other substrate anion binding site to give a dead-end complex.
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.
DEFF Research Database (Denmark)
Baum, Andreas
the understanding of the structural properties of the extracted pectin. Secondly, enzyme kinetics of biomass converting enzymes was examined in terms of measuring enzyme activity by spectral evolution profiling utilizing FTIR. Chemometric multiway methods were used to analyze the tensor datasets enabling the second......-order calibration advantage (reference Theory of Analytical chemistry). As PAPER 3 illustrates the method is universally applicable without the need of any external standards and was exemplified by performing quantitative enzyme activity determinations for glucose oxidase, pectin lyase and a cellolytic enzyme blend...... (Celluclast 1.5L). In PAPER 4, the concept is extended to quantify enzyme activity of two simultaneously acting enzymes, namely pectin lyase and pectin methyl esterase. By doing so the multiway methods PARAFAC, TUCKER3 and NPLS were compared and evaluated towards accuracy and precision....
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...
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.
Coupled Classical and Quantum Oscillators
McDermott, R M; Dermott, Rachael M. Mc; Redmount, Ian H.
2004-01-01
Some of the most enduring questions in physics--including the quantum measurement problem and the quantization of gravity--involve the interaction of a quantum system with a classical environment. Two linearly coupled harmonic oscillators provide a simple, exactly soluble model for exploring such interaction. Even the ground state of a pair of identical oscillators exhibits effects on the quantum nature of one oscillator, e.g., a diminution of position uncertainty, and an increase in momentum uncertainty and uncertainty product, from their unperturbed values. Interaction between quantum and classical oscillators is simulated by constructing a quantum state with one oscillator initially in its ground state, the other in a coherent or Glauber state. The subsequent wave function for this state is calculated exactly, both for identical and distinct oscillators. The reduced probability distribution for the quantum oscillator, and its position and momentum expectation values and uncertainties, are obtained from thi...
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 Equations for Quantum Systems
Gell-Mann, Murray; Gell-Mann, Murray; Hartle, James B.
1993-01-01
The origin of the phenomenological deterministic laws that approximately govern the quasiclassical domain of familiar experience is considered in the context of the quantum mechanics of closed systems such as the universe as a whole. We investigate the requirements for coarse grainings to yield decoherent sets of histories that are quasiclassical, i.e. such that the individual histories obey, with high probability, effective classical equations of motion interrupted continually by small fluctuations and occasionally by large ones. We discuss these requirements generally but study them specifically for coarse grainings of the type that follows a distinguished subset of a complete set of variables while ignoring the rest. More coarse graining is needed to achieve decoherence than would be suggested by naive arguments based on the uncertainty principle. Even coarser graining is required in the distinguished variables for them to have the necessary inertia to approach classical predictability in the presence of t...
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.
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)
A Companion to Classical Receptions
Directory of Open Access Journals (Sweden)
A. De Villiers
2012-03-01
Full Text Available This recent addition to the excellent Blackwell Companions series looks at the various forms of classical reception currently being researched as well as those deemed to have future importance. The diversity and volume of the themes and approaches contained in this book are truly impressive. As Hardwick and Stray state in their introduction, this collection “has been constructed on the basis that the activators of reception are many and varied and that we all gain from encountering examples from outside our own immediate areas of knowledge” (p. 4. Throughout the book they stay true to this motto and traditional approaches to classical reception are not given prominence over more recent (sometimes contentious approaches such as film studies, cultural politics and photography. The same goes for the various cultures involved and there is even a chapter on Greek drama in South Africa.
Lorentz invariance in chiral kinetic theory.
Chen, Jing-Yuan; Son, Dam T; Stephanov, Mikhail A; Yee, Ho-Ung; Yin, Yi
2014-10-31
We show that Lorentz invariance is realized nontrivially in the classical action of a massless spin-1/2 particle with definite helicity. We find that the ordinary Lorentz transformation is modified by a shift orthogonal to the boost vector and the particle momentum. The shift ensures angular momentum conservation in particle collisions and implies a nonlocality of the collision term in the Lorentz-invariant kinetic theory due to side jumps. We show that 2/3 of the chiral-vortical effect for a uniformly rotating particle distribution can be attributed to the magnetic moment coupling required by the Lorentz invariance. We also show how the classical action can be obtained by taking the classical limit of the path integral for a Weyl particle. PMID:25396362
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...
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...
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...
Stability and Catalytic Kinetics of Horseradish Peroxidase Confined in Nanoporous SBA-15
DEFF Research Database (Denmark)
Ikemoto, Hediki; Chi, Qijin; Ulstrup, Jens
2010-01-01
temperature. Details of the enzyme kinetics including the apparent Michaelis constant (KM) and maximum rate (Vmax) were determined. Both thermal stability and stability, towards the denaturing agents guanidinium chloride and urea, of free and immobilized enzymes were compared next. The thermal stability...... of the immobilized enzyme is significantly improved in comparison with free HRP. The catalytic kinetics is slowed down notably, but Vmax is much more robust to heat than the free enzyme. The stability resistance of the enzyme towards the denaturing agents depends on the chemical nature of the denaturing agents...... and interactions between enzyme and silica nanopore walls. Guanidinium chloride showed similar attenuation of the catalytic activity of immobilized and free enzyme. In contrast, the immobilized HRP was much more resistant to urea than the free enzyme. The different behaviour of free and immobilized enzyme is most...
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.
Logical, conditional, and classical probability
Quznetsov, G. A.
2005-01-01
The propositional logic is generalized on the real numbers field. the logical function with all properties of the classical probability function is obtained. The logical analog of the Bernoulli independent tests scheme is constructed. The logical analog of the Large Number Law is deduced from properties of these functions. The logical analog of thd conditional probability is defined. Consistency encured by a model on a suitable variant of the nonstandard analysis.
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; ...
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.
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...
Quantum manifolds with classical limit
Hohmann, Manuel; Wohlfarth, Mattias N R
2008-01-01
We propose a mathematical model of quantum spacetime as an infinite-dimensional manifold locally homeomorphic to an appropriate Schwartz space. This extends and unifies both the standard function space construction of quantum mechanics and the manifold structure of spacetime. In this picture we demonstrate that classical spacetime emerges as a finite-dimensional manifold through the topological identification of all quantum points with identical position expectation value. We speculate on the possible relevance of this geometry to quantum field theory and gravity.
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.
Chemical and Biological Kinetics
Emanuel', N. M.
1981-10-01
Examples of the application of the methods and ideas of chemical kinetics in various branches of chemistry and biology are considered and the results of studies on the kinetics and mechanisms of autoxidation and inhibited and catalysed oxidation of organic substances in the liquid phase are surveyed. Problems of the kinetics of the ageing of polymers and the principles of their stabilisation are discussed and certain trends in biological kinetics (kinetics of tumour growth, kinetic criteria of the effectiveness of chemotherapy, problems of gerontology, etc.) are considered. The bibliography includes 281 references.
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 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...
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...
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 ...
Sulfide toxicity kinetics of a uasb reactor
Directory of Open Access Journals (Sweden)
D. R. Paula Jr.
2009-12-01
Full Text Available The effect of sulfide toxicity on kinetic parameters of anaerobic organic matter removal in a UASB (up-flow anaerobic sludge blanket reactor is presented. Two lab-scale UASB reactors (10.5 L were operated continuously during 12 months. The reactors were fed with synthetic wastes prepared daily using glucose, ammonium acetate, methanol and nutrient solution. One of the reactors also received increasing concentrations of sodium sulfide. For both reactors, the flow rate of 16 L.d-1 was held constant throughout the experiment, corresponding to a hydraulic retention time of 15.6 hours. The classic model for non-competitive sulfide inhibition was applied to the experimental data for determining the overall kinetic parameter of specific substrate utilization (q and the sulfide inhibition coefficient (Ki. The application of the kinetic parameters determined allows prediction of methanogenesis inhibition and thus the adoption of operating parameters to minimize sulfide toxicity in UASB reactors.
Quantum-Classical Correspondence: Dynamical Quantization and the Classical Limit
Energy Technology Data Exchange (ETDEWEB)
Turner, L [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)
2004-11-12
In only 150 pages, not counting appendices, references, or the index, this book is one author's perspective of the massive theoretical and philosophical hurdles in the no-man's-land separating the classical and quantum domains of physics. It ends with him emphasizing his own theoretical contribution to this area. In his own words, he has attempted to answer: 1. How can we obtain the quantum dynamics of open systems initially described by the equations of motion of classical physics (quantization process) 2. How can we retrieve classical dynamics from the quantum mechanical equations of motion by means of a classical limiting process (dequantization process). However, this monograph seems overly ambitious. Although the publisher's description refers to this book as an accessible entre, we find that this author scrambles too hastily over the peaks of information that are contained in his large collection of 272 references. Introductory motivating discussions are lacking. Profound ideas are glossed over superficially and shoddily. Equations morph. But no new convincing understanding of the physical world results. The author takes the viewpoint that physical systems are always in interaction with their environment and are thus not isolated and, therefore, not Hamiltonian. This impels him to produce a method of quantization of these stochastic systems without the need of a Hamiltonian. He also has interest in obtaining the classical limit of the quantized results. However, this reviewer does not understand why one needs to consider open systems to understand quantum-classical correspondence. The author demonstrates his method using various examples of the Smoluchowski form of the Fokker--Planck equation. He then renders these equations in a Wigner representation, uses what he terms an infinitesimality condition, and associates with a constant having the dimensions of an action. He thereby claims to develop master equations, such as the Caldeira
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...
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
2015-01-01
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 init
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
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
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 ...
Intuitionism vs. classicism a mathematical attack on classical logic
Haverkamp, Nick
2015-01-01
In the early twentieth century, the Dutch mathematician L.E.J. Brouwer launched a powerful attack on the prevailing mathematical methods and theories. He developed a new kind of constructive mathematics, called intuitionism, which seems to allow for a rigorous refutation of widely accepted mathematical assumptions including fundamental principles of classical logic. Following an intense mathematical debate esp. in the 1920s, Brouwer's revolutionary criticism became a central philosophical concern in the 1970s, when Michael Dummett tried to substantiate it with meaning-theoretic considerations.
Nanomaterials with enzyme-like characteristics (nanozymes): next-generation artificial enzymes.
Wei, Hui; Wang, Erkang
2013-07-21
Over the past few decades, researchers have established artificial enzymes as highly stable and low-cost alternatives to natural enzymes in a wide range of applications. A variety of materials including cyclodextrins, metal complexes, porphyrins, polymers, dendrimers and biomolecules have been extensively explored to mimic the structures and functions of naturally occurring enzymes. Recently, some nanomaterials have been found to exhibit unexpected enzyme-like activities, and great advances have been made in this area due to the tremendous progress in nano-research and the unique characteristics of nanomaterials. To highlight the progress in the field of nanomaterial-based artificial enzymes (nanozymes), this review discusses various nanomaterials that have been explored to mimic different kinds of enzymes. We cover their kinetics, mechanisms and applications in numerous fields, from biosensing and immunoassays, to stem cell growth and pollutant removal. We also summarize several approaches to tune the activities of nanozymes. Finally, we make comparisons between nanozymes and other catalytic materials (other artificial enzymes, natural enzymes, organic catalysts and nanomaterial-based catalysts) and address the current challenges and future directions (302 references).
Van den Ende, Wim; Clerens, Stefan; Vergauwen, Rudy; Boogaerts, David; Le Roy, Katrien; Arckens, Lutgarde; Van Laere, André
2006-01-01
Inulin-type fructans are the simplest and most studied fructans and have become increasingly popular as prebiotic health-improving compounds. A natural variation in the degree of polymerization (DP) of inulins is observed within the family of the Asteraceae. Globe thistle (Echinops ritro), artichoke (Cynara scolymus), and Viguiera discolor biosynthesize fructans with a considerably higher DP than Cichorium intybus (chicory), Helianthus tuberosus (Jerusalem artichoke), and Dahlia variabilis. The higher DP in some species can be explained by the presence of special fructan:fructan 1-fructosyl transferases (high DP 1-FFTs), different from the classical low DP 1-FFTs. Here, the RT-PCR-based cloning of a high DP 1-FFT cDNA from Echinops ritro is described, starting from peptide sequence information derived from the purified native high DP 1-FFT enzyme. The cDNA was successfully expressed in Pichia pastoris. A comparison is made between the mass fingerprints of the native, heterodimeric enzyme and its recombinant, monomeric counterpart (mass fingerprints and kinetical analysis) showing that they have very similar properties. The recombinant enzyme is a functional 1-FFT lacking invertase and 1-SST activities, but shows a small intrinsic 1-FEH activity. The enzyme is capable of producing a high DP inulin pattern in vitro, similar to the one observed in vivo. Depending on conditions, the enzyme is able to produce fructo-oligosaccharides (FOS) as well. Therefore, the enzyme might be suitable for both FOS and high DP inulin production in bioreactors. Alternatively, introduction of the high DP 1-FFT gene in chicory, a crop widely used for inulin extraction, could lead to an increase in DP which is useful for a number of specific industrial applications. 1-FFT expression analysis correlates well with high DP fructan accumulation in vivo, suggesting that the enzyme is responsible for high DP fructan formation in planta. PMID:16449376
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.
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.
Activity assessment of microbial fibrinolytic enzymes.
Kotb, Essam
2013-08-01
Conversion of fibrinogen to fibrin inside blood vessels results in thrombosis, leading to myocardial infarction and other cardiovascular diseases. In general, there are four therapy options: surgical operation, intake of antiplatelets, anticoagulants, or fibrinolytic enzymes. Microbial fibrinolytic enzymes have attracted much more attention than typical thrombolytic agents because of the expensive prices and the side effects of the latter. The fibrinolytic enzymes were successively discovered from different microorganisms, the most important among which is the genus Bacillus. Microbial fibrinolytic enzymes, especially those from food-grade microorganisms, have the potential to be developed as functional food additives and drugs to prevent or cure thrombosis and other related diseases. There are several assay methods for these enzymes; this may due to the insolubility of substrate, fibrin. Existing assay methods can be divided into three major groups. The first group consists of assay of fibrinolytic activity with natural proteins as substrates, e.g., fibrin plate methods. The second and third groups of assays are suitable for kinetic studies and are based on the determination of hydrolysis of synthetic peptide esters. This review will deal primarily with the microorganisms that have been reported in literature to produce fibrinolytic enzymes and the first review discussing the methods used to assay the fibrinolytic activity.
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...
Classical trajectories and quantum tunneling
Ivlev, B I
2003-01-01
The problem of inter-band tunneling in a semiconductor (Zener breakdown) in a nonstationary and homogeneous electric field is solved exactly. Using the exact analytical solution, the approximation based on classical trajectories is studied. A new mechanism of enhanced tunneling through static non-one-dimensional barriers is proposed in addition to well known normal tunneling solely described by a trajectory in imaginary time. Under certain conditions on the barrier shape and the particle energy, the probability of enhanced tunneling is not exponentially small even for non-transparent barriers, in contrast to the case of normal tunneling.
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
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...... using historical data on composers and employ a unique instrumental variable – a measure of birth centrality, calculated as the average distance between a composer’s birthplace and the birthplace of his peers. I find a strong causal impact of peer group size on the number of important compositions...
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
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.
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.
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)
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.
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.
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.
Microtubule dynamics. II. Kinetics of self-assembly
DEFF Research Database (Denmark)
Flyvbjerg, H.; Jobs, E.
1997-01-01
Inverse scattering theory describes the conditions necessary and sufficient to determine an unknown potential from known scattering data. No similar theory exists for when and how one may deduce the kinetics of an unknown chemical reaction from quantitative information about its final state and its...... various initial concentrations of monomers. Distinct mathematical properties of the kinetics of the unknown reaction pathway are found. These properties are shown to restrict the kinetics to a single model that generalizes Oosawa's classical nucleation-polymerization model. The methods used here...
Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects
DEFF Research Database (Denmark)
Wedberg, Nils Hejle Rasmus Ingemar
) in water and organic solvents. The effects of solvent on structural and dynamical enzyme properties are studied, and special attention is given to how enzyme properties in organic solvents are affected by the hydration level, which is shown to be related to the water activity. In experimental studies......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...
About the modern house - and the classical
DEFF Research Database (Denmark)
Hauberg, Jørgen
2010-01-01
In text and illustrations describes the classical house and the classical city, represented by Andrea Palladio (1508-80), and the modern house, the modern city and building task, represented by Le Corbusier (1857-1965).......In text and illustrations describes the classical house and the classical city, represented by Andrea Palladio (1508-80), and the modern house, the modern city and building task, represented by Le Corbusier (1857-1965)....
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.
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...
Classical equations for quantum systems
Energy Technology Data Exchange (ETDEWEB)
Gell-Mann, M. (Theoretical Astrophysics Group (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico 87545) (United States) (Santa Fe Institute, 1660 Old Pecos Trail, Santa Fe, New Mexico 87501); Hartle, J.B. (Department of Physics, University of California enSanta Barbara, Santa Barbara, (California) 93106)
1993-04-15
The origin of the phenomenological deterministic laws that approximately govern the quasiclassical domain of familiar experience is considered in the context of the quantum mechanics of closed systems such as the universe as a whole. A formulation of quantum mechanics is used that predicts probabilities for the individual members of a set of alternative coarse-grained histories that [ital decohere], which means that there is negligible quantum interference between the individual histories in the set. We investigate the requirements for coarse grainings to yield decoherent sets of histories that are quasiclassical, i.e., such that the individual histories obey, with high probability, effective classical equations of motion interrupted continually by small fluctuations and occasionally by large ones. We discuss these requirements generally but study them specifically for coarse grainings of the type that follows a distinguished subset of a complete set of variables while ignoring the rest. More coarse graining is needed to achieve decoherence than would be suggested by naive arguments based on the uncertainty principle. Even coarser graining is required in the distinguished variables for them to have the necessary inertia to approach classical predictability in the presence of the noise consisting of the fluctuations that typical mechanisms of decoherence produce. We describe the derivation of phenomenological equations of motion explicitly for a particular class of models.
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...
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...
Fluctuations in classical sum rules.
Elton, John R; Lakshminarayan, Arul; Tomsovic, Steven
2010-10-01
Classical sum rules arise in a wide variety of physical contexts. Asymptotic expressions have been derived for many of these sum rules in the limit of long orbital period (or large action). Although sum-rule convergence may well be exponentially rapid for chaotic systems in a global phase-space sense with time, individual contributions to the sums may fluctuate with a width which diverges in time. Our interest is in the global convergence of sum rules as well as their local fluctuations. It turns out that a simple version of a lazy baker map gives an ideal system in which classical sum rules, their corrections, and their fluctuations can be worked out analytically. This is worked out in detail for the Hannay-Ozorio sum rule. In this particular case the rate of convergence of the sum rule is found to be governed by the Pollicott-Ruelle resonances, and both local and global boundaries for which the sum rule may converge are given. In addition, the width of the fluctuations is considered and worked out analytically, and it is shown to have an interesting dependence on the location of the region over which the sum rule is applied. It is also found that as the region of application is decreased in size the fluctuations grow. This suggests a way of controlling the length scale of the fluctuations by considering a time dependent phase-space volume, which for the lazy baker map decreases exponentially rapidly with time.
Institute of Scientific and Technical Information of China (English)
MAO LuYuan; CAI RuXiu; HUANG Bo; ZOU GuoLin; ZHOU Hui; GAO ChengZhuo
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:
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)
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.
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…
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.
Simplification of the unified gas kinetic scheme.
Chen, Songze; Guo, Zhaoli; Xu, Kun
2016-08-01
The unified gas kinetic scheme (UGKS) is an asymptotic preserving (AP) scheme for kinetic equations. It is superior for transition flow simulation 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. 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 equilibrium part of the UGKS flux is calculated by analytical solution instead of the numerical quadrature in velocity space. The simplification is equivalent to a flux hybridization of the gas kinetic scheme for the Navier-Stokes (NS) equations and the conventional discrete ordinate method. Several simplification strategies are tested, through which we can identify the key ingredient of the Navier-Stokes asymptotic preserving property. Numerical tests show that, as long as the collision effect is built into the macroscopic numerical flux, the numerical scheme is Navier-Stokes asymptotic preserving, regardless the accuracy of the microscopic numerical flux for the velocity distribution function. PMID:27627418
Simplification of the unified gas kinetic scheme
Chen, Songze; Guo, Zhaoli; Xu, Kun
2016-08-01
The unified gas kinetic scheme (UGKS) is an asymptotic preserving (AP) scheme for kinetic equations. It is superior for transition flow simulation 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. 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 equilibrium part of the UGKS flux is calculated by analytical solution instead of the numerical quadrature in velocity space. The simplification is equivalent to a flux hybridization of the gas kinetic scheme for the Navier-Stokes (NS) equations and the conventional discrete ordinate method. Several simplification strategies are tested, through which we can identify the key ingredient of the Navier-Stokes asymptotic preserving property. Numerical tests show that, as long as the collision effect is built into the macroscopic numerical flux, the numerical scheme is Navier-Stokes asymptotic preserving, regardless the accuracy of the microscopic numerical flux for the velocity distribution function.
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...
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...
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
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...
A kinetic model for the burst phase of processive cellulases
DEFF Research Database (Denmark)
Præstgaard, Eigil; Olsen, Jens Elmerdahl; Murphy, Leigh;
2011-01-01
is 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...
Mass, Momentum and Kinetic Energy of a Relativistic Particle
Zanchini, Enzo
2010-01-01
A rigorous definition of mass in special relativity, proposed in a recent paper, is recalled and employed to obtain simple and rigorous deductions of the expressions of momentum and kinetic energy for a relativistic particle. The whole logical framework appears as the natural extension of the classical one. Only the first, second and third laws of…
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
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
Hydrogen Beyond the Classic Approximation
Scivetti, I
2003-01-01
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
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 databases and knowledge organization
DEFF Research Database (Denmark)
Hjørland, Birger
2015-01-01
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......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...... into (ranked) sets of relevant documents, whereas the latter aims to increase the “selection power” of users. The Boolean retrieval model is valuable in providing users with the power to make informed searches and have full control over what is found and what is not. These issues may have significant...
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.
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
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.
Classical scattering from oscillating targets
Energy Technology Data Exchange (ETDEWEB)
Papachristou, P.K.; Diakonos, F.K.; Constantoudis, V.; Schmelcher, P.; Benet, L
2002-12-30
We study planar classical scattering from an oscillating heavy target whose dynamics defines a five-dimensional phase space. Although the system possesses no periodic orbits, and thus topological chaos is not present, the scattering functions display a variety of structures on different time scales. These structures are due to scattering events with a strong energy transfer from the projectile to the moving disk resulting in low-velocity peaks. We encounter initial conditions for which the projectile exhibits infinitely many bounces with the oscillating disk. Our numerical investigations are supported by analytical results on a specific model with a simple time-law. The observed properties possess universal character for scattering off oscillating targets.
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...
Inflation and classical scale invariance
Racioppi, Antonio
2014-01-01
BICEP2 measurement of primordial tensor modes in CMB suggests that cosmological inflation is due to a slowly rolling inflaton taking trans-Planckian values and provides further experimental evidence for the absence of large $M_{\\rm P}$ induced operators. We show that classical scale invariance solves the problem and allows for a remarkably simple scale-free inflaton model without any gauge group. Due to trans-Planckian inflaton values and VEVs, a dynamically induced Coleman-Weinberg-type inflaton potential of the model can predict tensor-to-scalar ratio $r$ in a large range. Precise determination of $r$ in future experiments will allow to test the proposed field-theoretic framework.
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
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.
From classical to quantum fields
Baulieu, Laurent; Sénéor, Roland
2017-01-01
Quantum Field Theory has become the universal language of most modern theoretical physics. This introductory textbook shows how this beautiful theory offers the correct mathematical framework to describe and understand the fundamental interactions of elementary particles. The book begins with a brief reminder of basic classical field theories, electrodynamics and general relativity, as well as their symmetry properties, and proceeds with the principles of quantisation following Feynman's path integral approach. Special care is used at every step to illustrate the correct mathematical formulation of the underlying assumptions. Gauge theories and the problems encountered in their quantisation are discussed in detail. The last chapters contain a full description of the Standard Model of particle physics and the attempts to go beyond it, such as grand unified theories and supersymmetry. Written for advanced undergraduate and beginning graduate students in physics and mathematics, the book could also serve as a re...
Classical Cosmology Through Animation Stories
Mijic, Milan; Kang, E. Y. E.; Longson, T.; State LA SciVi Project, Cal
2010-05-01
Computer animations are a powerful tool for explanation and communication of ideas, especially to a younger generation. Our team completed a three part sequence of short, computer animated stories about the insight and discoveries that lead to the understanding of the overall structure of the universe. Our principal characters are Immanuel Kant, Henrietta Leavitt, and Edwin Hubble. We utilized animations to model and visualize the physical concepts behind each discovery and to recreate the characters, locations, and flavor of the time. The animations vary in length from 6 to 11 minutes. The instructors or presenters may wish to utilize them separately or together. The animations may be used for learning classical cosmology in a visual way in GE astronomy courses, in pre-college science classes, or in public science education setting.
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...
DEFF Research Database (Denmark)
Yuhong, Huang; Busk, Peter Kamp; Lange, Lene
2015-01-01
and hemicellulose-degrading enzymes of classical fungal enzyme producers with those of Fusarium species. The results indicated that Fusarium species are robust cellulose and hemicellulose degraders. Wheat bran, carboxymethylcellulose and xylan-based growth media induced a broad spectrum of lignocellulolytic enzymes...
Resonance Van Hove singularities in wave kinetics
Shi, Yi-Kang; Eyink, Gregory L.
2016-10-01
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 of degeneracy δ of the critical points. Following Van Hove, we show that non-degenerate singularities lead to finite phase measures for D > 2 but produce divergences when D ≤ 2 and possible breakdown of wave kinetics if the collision integral itself becomes too large (or even infinite). Similar divergences and possible breakdown can occur for degenerate singularities, when D - δ ≤ 2, as we find for several physical examples, including electron-hole kinetics in graphene. When the standard kinetic equation breaks down, then one must develop a new singular wave kinetics. We discuss approaches from pioneering 1971 work of Newell & Aucoin on multi-scale perturbation theory for acoustic waves and field-theoretic methods based on exact Schwinger-Dyson integral equations for the wave dynamics.
Smit, de A.J.
2000-01-01
Detection of classical swine fever virus (CSFV) can be achieved by a range of assays of which the most commonly used are: immunohistochemical and virus culture techniques. New developments have enabled the detection of viral proteins by enzyme-linked immunosorbent assays (ELISAs) and the detection o
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.
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.
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...... 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....
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
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.
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.
Introduction to chemical kinetics
Soustelle, Michel
2013-01-01
This book is a progressive presentation of kinetics of the chemical reactions. It provides complete coverage of the domain of chemical kinetics, which is necessary for the various future users in the fields of Chemistry, Physical Chemistry, Materials Science, Chemical Engineering, Macromolecular Chemistry and Combustion. It will help them to understand the most sophisticated knowledge of their future job area. Over 15 chapters, this book present the fundamentals of chemical kinetics, its relations with reaction mechanisms and kinetic properties. Two chapters are then devoted to experimental re
Principles of chemical kinetics
House, James E
2007-01-01
James House's revised Principles of Chemical Kinetics provides a clear and logical description of chemical kinetics in a manner unlike any other book of its kind. Clearly written with detailed derivations, the text allows students to move rapidly from theoretical concepts of rates of reaction to concrete applications. Unlike other texts, House presents a balanced treatment of kinetic reactions in gas, solution, and solid states. The entire text has been revised and includes many new sections and an additional chapter on applications of kinetics. The topics covered include quantitative rela
Artificial Enzymes, "Chemzymes"
DEFF Research Database (Denmark)
Bjerre, Jeannette; Rousseau, Cyril Andre Raphaël; Pedersen, Lavinia Georgeta M;
2008-01-01
"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 chemzymes that catalyze conjugate additions, cycloadditions, and self-replicating processes. The focus will be mainly on cyclodextrin-based chemzymes since they have shown to be good candidate structures to base an enzyme model skeleton on. In addition hereto, other molecules that encompass binding......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...
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
Benefits from Tween during enzymic hydrolysis of corn stover
Energy Technology Data Exchange (ETDEWEB)
Kaar, W.E.; Holtzapple, M.T. [Texas A and M Univ., College Station, TX (United States). Dept. of Chemical Engineering
1998-08-20
Corn stover is a potential substrate for fermentation processes. Previous work with corn stover demonstrated that lime pretreatment rendered it digestible by cellulase; however, high sugar yields required very high enzyme loadings. Because cellulase is a significant cost in biomass conversion processes, the present study focused on improving the enzyme efficiency using Tween 20 and Tween 80; Tween 20 is slightly more effective than Tween 80. The recommended pretreatment conditions for the biomass remained unchanged regardless of whether Tween was added during the hydrolysis. The recommended Tween loading was 0.15 g Tween/g dry biomass. The critical relationship was the Tween loading on the biomass, not the Tween concentration in solution. The 72-h enzymic conversion of pretreated corn stover using 5 FPU cellulase/g dry biomass at 50 C with Tween 20 as part of the medium was 0.85 g/g for cellulose, 0.66 g/g for xylan, and 0.75 for total polysaccharide; addition of Tween improved the cellulose, xylan, and total polysaccharide conversions by 42, 40, and 42%, respectively. Kinetic analyses showed that Tween improved the enzymic absorption constants, which increased the effective hydrolysis rate compared to hydrolysis without Tween. Furthermore, Tween prevented thermal deactivation of the enzymes, which allows for the kinetic advantage of higher temperature hydrolysis. Ultimate digestion studies showed higher conversions for samples containing Tween, indicating a substrate effect. It appears that Tween improves corn stover hydrolysis through three effects: enzyme stabilizer, lignocellulose disrupter, and enzyme effector.
Relaxation properties in classical diamagnetism
Carati, A.; Benfenati, F.; Galgani, L.
2011-06-01
It is an old result of Bohr that, according to classical statistical mechanics, at equilibrium a system of electrons in a static magnetic field presents no magnetization. Thus a magnetization can occur only in an out of equilibrium state, such as that produced through the Foucault currents when a magnetic field is switched on. It was suggested by Bohr that, after the establishment of such a nonequilibrium state, the system of electrons would quickly relax back to equilibrium. In the present paper, we study numerically the relaxation to equilibrium in a modified Bohr model, which is mathematically equivalent to a billiard with obstacles, immersed in a magnetic field that is adiabatically switched on. We show that it is not guaranteed that equilibrium is attained within the typical time scales of microscopic dynamics. Depending on the values of the parameters, one has a relaxation either to equilibrium or to a diamagnetic (presumably metastable) state. The analogy with the relaxation properties in the Fermi Pasta Ulam problem is also pointed out.
Classical universes are perfectly predictable!
Schmidt, Jan Hendrik
I argue that in a classical universe, all the events that ever happen are encoded in each of the universe's parts. This conflicts with a statement which is widely believed to lie at the basis of relativity theory: that the events in a space-time region R determine only the events in R's domain of dependence but not those in other space-time regions. I show how, from this understanding, a new prediction method (which I call the 'Smoothness Method') can be obtained which allows us to predict future events on the basis of local observational data. Like traditional prediction methods, this method makes use of so-called ' ceteris paribus clauses', i.e. assumptions about the unobserved parts of the universe. However, these assumptions are used in a way which enables us to predict the behaviour of open systems with arbitrary accuracy, regardless of the influence of their environment-which has not been achieved by traditional methods. In a sequel to this paper (Schmidt, 1998), I will prove the Uniqueness and Predictability Theorems on which the Smoothness Method is based, and comment in more detail on its mathematical properties.
Pembrolizumab in classical Hodgkin's lymphoma.
Maly, Joseph; Alinari, Lapo
2016-09-01
Pembrolizumab is a humanized monoclonal antibody directed against programmed cell death protein 1 (PD-1), a key immune-inhibitory molecule expressed on T cells and implicated in CD4+ T-cell exhaustion and tumor immune-escape mechanisms. Classical Hodgkin's lymphoma (cHL) is a unique B-cell malignancy in the sense that malignant Reed-Sternberg (RS) cells represent a small percentage of cells within an extensive immune cell infiltrate. PD-1 ligands are upregulated on RS cells as a consequence of both chromosome 9p24.1 amplification and Epstein-Barr virus infection and by interacting with PD-1 promote an immune-suppressive effect. By augmenting antitumor immune response, pembrolizumab and nivolumab, another monoclonal antibody against PD-1, have shown significant activity in patients with relapsed/refractory cHL as well as an acceptable toxicity profile with immune-related adverse events that are generally manageable. In this review, we explore the rationale for targeting PD-1 in cHL, review the clinical trial results supporting the use of checkpoint inhibitors in this disease, and present future directions for investigation in which this approach may be used.
Rebrightening Phenomenon in Classical Novae
Kato, Taichi; Maehara, Hiroyuki; Kiyota, Seiichiro
2009-01-01
Two classical novae V1493 Aql and V2362 Cyg were known to exhibit unprecedented large-amplitude rebrightening during the late stage of their evolution. We analyzed common properties in these two light curves. We show that these unusual light curves are very well expressed by a combination of power-law decline, omnipresent in fast novae, and exponential brightening. We propose a schematic interpretation of the properties common to these rebrightenings can be a consequence of a shock resulting from a secondary ejection and its breakout in the optically thick nova winds. This interpretation has an advantage in explaining the rapid fading following the rebrightening and the subsequent evolution of the light curve. The exponential rise might reflect emerging light from the shock front, analogous to a radiative precursor in a supernova shock breakout. The consequence of such a shock in the nova wind potentially explains many kinds of unusual phenomena in novae including early-stage variations and potentially dust f...
Classical topology and quantum states
Indian Academy of Sciences (India)
A P Balachandran
2001-02-01
Any two inﬁnite-dimensional (separable) Hilbert spaces are unitarily isomorphic. The sets of all their self-adjoint operators are also therefore unitarily equivalent. Thus if all self-adjoint operators can be observed, and if there is no further major axiom in quantum physics than those formulated for example in Dirac’s ‘quantum mechanics’, then a quantum physicist would not be able to tell a torus from a hole in the ground. We argue that there are indeed such axioms involving observables with smooth time evolution: they contain commutative subalgebras from which the spatial slice of spacetime with its topology (and with further reﬁnements of the axiom, its - and ∞ - structures) can be reconstructed using Gel’fand–Naimark theory and its extensions. Classical topology is an attribute of only certain quantum observables for these axioms, the spatial slice emergent from quantum physics getting progressively less differentiable with increasingly higher excitations of energy and eventually altogether ceasing to exist. After formulating these axioms, we apply them to show the possibility of topology change and to discuss quantized fuzzy topologies. Fundamental issues concerning the role of time in quantum physics are also addressed.
Beyond Vmax and Km: How details of enzyme function influence geochemical cycles
Steen, A. D.
2015-12-01
Enzymes catalyze the vast majority of chemical reactions relevant to geomicrobiology. Studies of the activities of enzymes in environmental systems often report Vmax (the maximum possible rate of reaction; often proportional to the concentration of enzymes in the system) and sometimes Km (a measure of the affinity between enzymes and their substrates). However, enzyme studies - particularly those related to enzymes involved in organic carbon oxidation - are often limited to only those parameters, and a relatively limited and mixed set of enzymes. Here I will discuss some novel methods to assay and characterize the specific sets of enzymes that may be important to the carbon cycle in aquatic environments. First, kinetic experiments revealed the collective properties of the complex mixtures of extracellular peptidases that occur where microbial communities are diverse. Crystal structures combined with biochemical characterization of specific enzymes can yield more detailed information about key steps in organic carbon transformations. These new techniques have the potential to provide mechanistic grounding to geomicrobiological models.
Structural analysis of enzymes used for bioindustry and bioremediation.
Tanokura, Masaru; Miyakawa, Takuya; Guan, Lijun; Hou, Feng
2015-01-01
Microbial enzymes have been widely applied in the large-scale, bioindustrial manufacture of food products and pharmaceuticals due to their high substrate specificity and stereoselectivity, and their effectiveness under mild conditions with low environmental burden. At the same time, bioremedial techniques using microbial enzymes have been developed to solve the problem of industrial waste, particularly with respect to persistent chemicals and toxic substances. And finally, structural studies of these enzymes have revealed the mechanistic basis of enzymatic reactions, including the stereoselectivity and binding specificity of substrates and cofactors. The obtained structural insights are useful not only to deepen our understanding of enzymes with potential bioindustrial and/or bioremedial application, but also for the functional improvement of enzymes through rational protein engineering. This review shows the structural bases for various types of enzymatic reactions, including the substrate specificity accompanying cofactor-controlled and kinetic mechanisms.
How many enzyme molecules are needed for discrimination oriented applications?
Gorecki, Jerzy; Gorecka, Joanna N; Nowakowski, Bogdan; Ueno, Hiroshi; Yoshikawa, Kenichi
2016-07-27
Chemical reactions establish a molecular mechanism for information processing in living organisms. Here we consider a simple enzymatic reaction model that can be used to discriminate parameters characterizing periodic reagent inflow. Numerical simulations based on the kinetic equations show that there exist a range of inflow frequencies and amplitudes in which the time evolution of the system is very sensitive to small changes in the values of these parameters. However, the kinetic equations are derived for the thermodynamic limit, whereas in a real biological medium, like a cell, the number of enzyme molecules is an integer and finite. We use stochastic simulations to estimate discriminator reliability as a function of the number of enzyme molecules involved. For systems with 10 000 molecules the functionality predicted by kinetic equations is confirmed. If the number of molecules is decreased to 100, discrimination becomes unreliable. PMID:27405538
Locking classical correlation in quantum states
Di Vincenzo, D P; Leung, D; Smolin, J A; Terhal, B M; Vincenzo, David Di; Horodecki, Michal; Leung, Debbie; Smolin, John; Terhal, Barbara
2003-01-01
We show that there exist bipartite quantum states which contain large hidden classical correlation that can be unlocked by a disproportionately small amount of classical communication. In particular, there are $(2n+1)$-qubit states for which a one bit message doubles the optimal classical mutual information between measurement results on the subsystems, from $n/2$ bits to $n$ bits. States exhibiting this behavior need not be entangled. We study the range of states exhibiting this phenomenon and bound its magnitude.
A Drosophila melanogaster model of classic galactosemia
Kushner, Rebekah F.; Ryan, Emily L.; Sefton, Jennifer M. I.; Rebecca D Sanders; Lucioni, Patricia Jumbo; Kenneth H Moberg; Fridovich-Keil, Judith L.
2010-01-01
Classic galactosemia is a potentially lethal disorder that results from profound impairment of galactose-1-phosphate uridylyltransferase (GALT). Despite decades of research, the underlying pathophysiology of classic galactosemia remains unclear, in part owing to the lack of an appropriate animal model. Here, we report the establishment of a Drosophila melanogaster model of classic galactosemia; this is the first whole-animal genetic model to mimic aspects of the patient phenotype. Analogous t...
Classical Underpinnings of Gravitationally Induced Quantum Interference
Mannheim, P D
1996-01-01
We show that the gravitational modification of the phase of a neutron beam (the COW experiment) has a classical origin, being due to the time delay which classical particles experience in traversing a background gravitational field. Similarly, we show that classical light waves also undergo a phase shift in traversing a gravitational field. We show that the COW experiment respects the equivalence principle even in the presence of quantum mechanics.
Delayed Choice Between Purely Classical States
Jason A. C. Gallas
2006-01-01
It is argued that Wheeler's insightful idea of delayed choice experiments may be explored at a classical level, arising naturally from number-theoretical conjugacies always necessarily present in the equations of motion. For simple and representative systems, we illustrate how to cast the equations of motion in a form encoding all classical states simultaneously through a ``state parameter''. By suitably selecting the parameter one may project the system into any desired classical state.
The relation between classical and quantum electrodynamics
Mario Bacelar Valente
2012-01-01
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 ex...
On the Temperature Dependence of Enzyme-Catalyzed Rates.
Arcus, Vickery L; Prentice, Erica J; Hobbs, Joanne K; Mulholland, Adrian J; Van der Kamp, Marc W; Pudney, Christopher R; Parker, Emily J; Schipper, Louis A
2016-03-29
One of the critical variables that determine the rate of any reaction is temperature. For biological systems, the effects of temperature are convoluted with myriad (and often opposing) contributions from enzyme catalysis, protein stability, and temperature-dependent regulation, for example. We have coined the phrase "macromolecular rate theory (MMRT)" to describe the temperature dependence of enzyme-catalyzed rates independent of stability or regulatory processes. Central to MMRT is the observation that enzyme-catalyzed reactions occur with significant values of ΔCp(‡) that are in general negative. That is, the heat capacity (Cp) for the enzyme-substrate complex is generally larger than the Cp for the enzyme-transition state complex. Consistent with a classical description of enzyme catalysis, a negative value for ΔCp(‡) is the result of the enzyme binding relatively weakly to the substrate and very tightly to the transition state. This observation of negative ΔCp(‡) has important implications for the temperature dependence of enzyme-catalyzed rates. Here, we lay out the fundamentals of MMRT. We present a number of hypotheses that arise directly from MMRT including a theoretical justification for the large size of enzymes and the basis for their optimum temperatures. We rationalize the behavior of psychrophilic enzymes and describe a "psychrophilic trap" which places limits on the evolution of enzymes in low temperature environments. One of the defining characteristics of biology is catalysis of chemical reactions by enzymes, and enzymes drive much of metabolism. Therefore, we also expect to see characteristics of MMRT at the level of cells, whole organisms, and even ecosystems.