WorldWideScience

Sample records for reveal reaction mechanism

  1. Attention: Reaction Time and Accuracy Reveal Different Mechanisms

    Science.gov (United States)

    Prinzmetal, William; McCool, Christin; Park, Samuel

    2005-01-01

    The authors propose that there are 2 different mechanisms whereby spatial cues capture attention. The voluntary mechanism is the strategic allocation of perceptual resources to the location most likely to contain the target. The involuntary mechanism is a reflexive orienting response that occurs even when the spatial cue does not indicate the…

  2. Revealing the reaction mechanisms of Li–O2 batteries using environmental transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Langli; Liu, Bin; Song, Shidong; Xu, Wu; Zhang, Ji-Guang; Wang, Chongmin

    2017-03-27

    The capacity, Coulombic efficiency, rate, and cyclability of a Li-O2 battery critically depend on the electrode reaction mechanism and the structure/morphology of the reaction product as well as their spatial and temporal evolution1-8, which are all further complicated by the choice of different electrolyte. For the case of aprotic cell, the discharge product, Li2O2, is formed through solution and surface mechanisms9,10, but little is known on the formation mechanism of the perplexing morphology of the reaction product11-15. For the case of Li-O2 battery using solid electrolyte, neither electrode reaction mechanism nor the nature of the reaction production is known. Herein, we reveal the full cycle reaction pathway for Li-O2 batteries and its correlation with the nature of the reaction product. Using an aberration-corrected environmental TEM under oxygen environment, we captured, for the first time, the morphology and phase evolution on the carbon nanotube (CNT) cathode of a working solid-state Li-O2 nano-battery16 and directly correlated these features with electrochemical reaction. We found that the oxygen reduction reaction on CNTs initially produces LiO2, which subsequently evolves to Li2O2 and O2 through disproportionation reaction. Surprisingly it is just the releasing of O2 that inflates the particles to a hollow structure with a Li2O outer surface layer and Li2O2 inner-shell, demonstrating that, in general, accommodation of the released O2 coupled with the Li+ ion diffusion and electron transport paths across both spatial and temporal scales critically governs the morphology of the discharging/charging product in Li-O2 system. We anticipate that the direct observation of Li-O2 reaction mechanisms and their correlation with the morphology of the reaction product set foundation for quantitative understanding/modeling of the electrochemical processes in the Li-O2 system, enabling rational design of both solid-state and aprotic Li-O2 batteries.

  3. Reaction mechanisms

    International Nuclear Information System (INIS)

    Nguyen Trong Anh

    1988-01-01

    The 1988 progress report of the Reaction Mechanisms laboratory (Polytechnic School, France), is presented. The research topics are: the valence bond methods, the radical chemistry, the modelling of the transition states by applying geometric constraints, the long range interactions (ion - molecule) in gaseous phase, the reaction sites in gaseous phase and the mass spectroscopy applications. The points of convergence between the investigations of the mass spectroscopy and the theoretical chemistry teams, as well as the purposes guiding the research programs, are discussed. The published papers, the conferences, the congress communications and the thesis, are also reported [fr

  4. Insights into reaction mechanisms in heterogeneous catalysis revealed by in situ NMR spectroscopy.

    Science.gov (United States)

    Blasco, Teresa

    2010-12-01

    This tutorial review intends to show the possibilities of in situ solid state NMR spectroscopy in the elucidation of reaction mechanisms and the nature of the active sites in heterogeneous catalysis. After a brief overview of the more usual experimental devices used for in situ solid state NMR spectroscopy measurements, some examples of applications taken from the recent literature will be presented. It will be shown that in situ NMR spectroscopy allows: (i) the identification of stable intermediates and transient species using indirect methods, (ii) to prove shape selectivity in zeolites, (iii) the study of reaction kinetics, and (iv) the determination of the nature and the role played by the active sites in a catalytic reaction. The approaches and methodology used to get this information will be illustrated here summarizing the most relevant contributions on the investigation of the mechanisms of a series of reactions of industrial interest: aromatization of alkanes on bifunctional catalysts, carbonylation reaction of methanol with carbon monoxide, ethylbenzene disproportionation, and the Beckmann rearrangement reaction. Special attention is paid to the research carried out on the role played by carbenium ions and alkoxy as intermediate species in the transformation of hydrocarbon molecules on solid acid catalysts.

  5. The enzymes of biotin dependent CO2 metabolism: What structures reveal about their reaction mechanisms

    Science.gov (United States)

    Waldrop, Grover L; Holden, Hazel M; Maurice, Martin St

    2012-01-01

    Biotin is the major cofactor involved in carbon dioxide metabolism. Indeed, biotin-dependent enzymes are ubiquitous in nature and are involved in a myriad of metabolic processes including fatty acid synthesis and gluconeogenesis. The cofactor, itself, is composed of a ureido ring, a tetrahydrothiophene ring, and a valeric acid side chain. It is the ureido ring that functions as the CO2 carrier. A complete understanding of biotin-dependent enzymes is critically important for translational research in light of the fact that some of these enzymes serve as targets for anti-obesity agents, antibiotics, and herbicides. Prior to 1990, however, there was a dearth of information regarding the molecular architectures of biotin-dependent enzymes. In recent years there has been an explosion in the number of three-dimensional structures reported for these proteins. Here we review our current understanding of the structures and functions of biotin-dependent enzymes. In addition, we provide a critical analysis of what these structures have and have not revealed about biotin-dependent catalysis. PMID:22969052

  6. Chemical kinetics and reaction mechanism

    International Nuclear Information System (INIS)

    Jung, Ou Sik; Park, Youn Yeol

    1996-12-01

    This book is about chemical kinetics and reaction mechanism. It consists of eleven chapters, which deal with reaction and reaction speed on reaction mechanism, simple reaction by rate expression, reversible reaction and simultaneous reaction, successive reaction, complicated reaction mechanism, assumption for reaction mechanism, transition state theory, successive reaction and oscillating reaction, reaction by solution, research method high except kinetics on reaction mechanism, high reaction of kinetics like pulsed radiolysis.

  7. Hadron reaction mechanisms

    International Nuclear Information System (INIS)

    Collins, P.D.B.; Martin, A.D.

    1982-01-01

    The mechanism of hadron scattering at high energies are reviewed in such a way as to combine the ideas of the parton model and quantum chromodynamics (QCD) with Regge theory and phenomenology. After a brief introduction to QCD and the basic features of hadron scattering data, scaling and the dimensional counting rules, the parton structure of hadrons, and the parton model for large momentum transfer processes, including scaling violations are discussed. Hadronic jets and the use of parton ideas in soft scattering processes are examined, attention being paid to Regge theory and its applications in exclusive and inclusive reactions, the relationship to parton exchange being stressed. The mechanisms of hadron production which build up cross sections, and hence the underlying Regge singularities, and the possible overlap of Regge and scaling regions are discussed. It is concluded that the key to understanding hadron reaction mechanisms seems to lie in the marriage of Regge theory with QCD. (author)

  8. Reaction mechanisms of metal complexes

    CERN Document Server

    Hay, R W

    2000-01-01

    This text provides a general background as a course module in the area of inorganic reaction mechanisms, suitable for advanced undergraduate and postgraduate study and/or research. The topic has important research applications in the metallurgical industry and is of interest in the science of biochemistry, biology, organic, inorganic and bioinorganic chemistry. In addition to coverage of substitution reactions in four-, five- and six-coordinate complexes, the book contains further chapters devoted to isomerization and racemization reactions, to the general field of redox reactions, and to the reactions of coordinated ligands. It is relevant in other fields such as organic, bioinorganic and biological chemistry, providing a bridge to organic reaction mechanisms. The book also contains a chapter on the kinetic background to the subject with many illustrative examples which should prove useful to those beginning research. Provides a general background as a course module in the area of inorganic reaction mechanis...

  9. Analysis of kinetic reaction mechanisms

    CERN Document Server

    Turányi, Tamás

    2014-01-01

    Chemical processes in many fields of science and technology, including combustion, atmospheric chemistry, environmental modelling, process engineering, and systems biology, can be described by detailed reaction mechanisms consisting of numerous reaction steps. This book describes methods for the analysis of reaction mechanisms that are applicable in all these fields. Topics addressed include: how sensitivity and uncertainty analyses allow the calculation of the overall uncertainty of simulation results and the identification of the most important input parameters, the ways in which mechanisms can be reduced without losing important kinetic and dynamic detail, and the application of reduced models for more accurate engineering optimizations. This monograph is invaluable for researchers and engineers dealing with detailed reaction mechanisms, but is also useful for graduate students of related courses in chemistry, mechanical engineering, energy and environmental science and biology.

  10. Language of Mechanisms: Exam Analysis Reveals Students' Strengths, Strategies, and Errors When Using the Electron-Pushing Formalism (Curved Arrows) in New Reactions

    Science.gov (United States)

    Flynn, Alison B.; Featherstone, Ryan B.

    2017-01-01

    This study investigated students' successes, strategies, and common errors in their answers to questions that involved the electron-pushing (curved arrow) formalism (EPF), part of organic chemistry's language. We analyzed students' answers to two question types on midterms and final exams: (1) draw the electron-pushing arrows of a reaction step,…

  11. Structure of the bacterial deacetylase LpxC bound to the nucleotide reaction product reveals mechanisms of oxyanion stabilization and proton transfer.

    Science.gov (United States)

    Clayton, Gina M; Klein, Daniel J; Rickert, Keith W; Patel, Sangita B; Kornienko, Maria; Zugay-Murphy, Joan; Reid, John C; Tummala, Srivanya; Sharma, Sujata; Singh, Sheo B; Miesel, Lynn; Lumb, Kevin J; Soisson, Stephen M

    2013-11-22

    The emergence of antibiotic-resistant strains of pathogenic bacteria is an increasing threat to global health that underscores an urgent need for an expanded antibacterial armamentarium. Gram-negative bacteria, such as Escherichia coli, have become increasingly important clinical pathogens with limited treatment options. This is due in part to their lipopolysaccharide (LPS) outer membrane components, which dually serve as endotoxins while also protecting Gram-negative bacteria from antibiotic entry. The LpxC enzyme catalyzes the committed step of LPS biosynthesis, making LpxC a promising target for new antibacterials. Here, we present the first structure of an LpxC enzyme in complex with the deacetylation reaction product, UDP-(3-O-(R-3-hydroxymyristoyl))-glucosamine. These studies provide valuable insight into recognition of substrates and products by LpxC and a platform for structure-guided drug discovery of broad spectrum Gram-negative antibiotics.

  12. Single-molecule fluorescence measurements reveal the reaction mechanisms of the core RISC, composed of human Argonaute 2 and a guide RNA.

    Science.gov (United States)

    Jo, Myung Hyun; Song, Ji-Joon; Hohng, Sungchul

    2015-12-01

    In eukaryotes, small RNAs play important roles in both gene regulation and resistance to viral infection. Argonaute proteins have been identified as a key component of the effector complexes of various RNA-silencing pathways, but the mechanistic roles of Argonaute proteins in these pathways are not clearly understood. To address this question, we performed single-molecule fluorescence experiments using an RNA-induced silencing complex (core-RISC) composed of a small RNA and human Argonaute 2. We found that target binding of core-RISC starts at the seed region of the guide RNA. After target binding, four distinct reactions followed: target cleavage, transient binding, stable binding, and Argonaute unloading. Target cleavage required extensive sequence complementarity and accelerated core-RISC dissociation for recycling. In contrast, the stable binding of core-RISC to target RNAs required seed-match only, suggesting a potential explanation for the seed-match rule of microRNA (miRNA) target selection.

  13. Reaction mechanisms in zeolite catalysis

    NARCIS (Netherlands)

    Rozanska, X.; Santen, van R.A.; Auerbach, S.C.; Carrado, K.A.; Dutta, P.D.

    2003-01-01

    A review; described are the most basic mechanistic reaction steps that are induced by zeolite catalysts. Details on the zeolitic properties that are relevant to mol. reactivity are also provided. The theor. methods and models at hand to allow the investigation of these reaction steps and that have

  14. Use of Isotopes for Studying Reaction Mechanisms

    Indian Academy of Sciences (India)

    of atoms during a chemical transformation. This strategy of determining reaction mechanisms is illustrated in the article with several examples. Introduction. When a reaction is carried out, the primary effort goes towards the identification of the product(s) of the reaction. A more time consuming endeavour, however, is the ...

  15. Morphing of the Dissipative Reaction Mechanism

    International Nuclear Information System (INIS)

    Schroeder, W.U.; Toke, J.; Gawlikowicz, W.; Houck, M.A.; Lu, J.; Pienkowski, L.

    2003-01-01

    Important trends in the evolution of heavy-ion reaction mechanisms with bombarding energy and impact parameter are reviewed. Essential features of dissipative reactions appear preserved at E/A = 50-62 MeV, such as dissipative orbiting and multi-nucleon exchange. The relaxation of the A/Z asymmetry with impact parameter is slow. Non-equilibrium emission of light particles and clusters is an important process accompanying the evolution of the mechanism. Evidence is presented for a new mechanism of statistical cluster emission from hot, metastable primary reaction products, driven by surface entropy. These results suggest a plausible reinterpretation of multi-fragmentation. (authors)

  16. Morphing of the Dissipative Reaction Mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Schroeder, W.U.; Toke, J.; Gawlikowicz, W.; Houck, M.A.; Lu, J.; Pienkowski, L. [Rochester Univ., Dept. of Chemistry, Rochester, NY (United States)

    2003-07-01

    Important trends in the evolution of heavy-ion reaction mechanisms with bombarding energy and impact parameter are reviewed. Essential features of dissipative reactions appear preserved at E/A = 50-62 MeV, such as dissipative orbiting and multi-nucleon exchange. The relaxation of the A/Z asymmetry with impact parameter is slow. Non-equilibrium emission of light particles and clusters is an important process accompanying the evolution of the mechanism. Evidence is presented for a new mechanism of statistical cluster emission from hot, metastable primary reaction products, driven by surface entropy. These results suggest a plausible reinterpretation of multi-fragmentation. (authors)

  17. Enhancement Mechanisms of Low Energy Nuclear Reactions

    OpenAIRE

    Gareev, F. A.; Zhidkova, I. E.

    2005-01-01

    The review of possible stimulation mechanisms of LENR (low energy nuclear reaction) is represented. We have concluded that transmutation of nuclei at low energies and excess heat are possible in the framework of the modern physical theory - the universal resonance synchronization principle [1] and based on its different enhancement mechanisms of reaction rates are responsible for these processes [2]. The excitation and ionization of atoms may play role as a trigger for LENR. Superlow energy o...

  18. Bimolecular reactions of carbenes: Proton transfer mechanism

    Science.gov (United States)

    Abu-Saleh, Abd Al-Aziz A.; Almatarneh, Mansour H.; Poirier, Raymond A.

    2018-04-01

    Here we report the bimolecular reaction of trifluoromethylhydroxycarbene conformers and the water-mediated mechanism of the 1,2-proton shift for the unimolecular trans-conformer by using quantum chemical calculations. The CCSD(T)/cc-pVTZ//MP2/cc-pVDZ potential-energy profile of the bimolecular reaction of cis- and trans-trifluoromethylhydroxycarbene, shows the lowest gas-phase barrier height of 13 kJ mol-1 compared to the recently reported value of 128 kJ mol-1 for the unimolecular reaction. We expect bimolecular reactions of carbene's stereoisomers will open a valuable field for new and useful synthetic strategies.

  19. Review of heavy ion reaction mechanisms

    International Nuclear Information System (INIS)

    Ngo, C.

    1986-04-01

    We review some of the many aspects of heavy-ion reaction mechanisms observed at bombarding energies smaller than approximately 50 MeV/u that is to say in what is called the low bombarding energy domain and the intermediate bombarding energy domain. We emphasize the results concerning the use of very heavy projectiles which has led to the observation of new mechanisms

  20. Explore the reaction mechanism of the Maillard reaction: a density functional theory study.

    Science.gov (United States)

    Ren, Ge-Rui; Zhao, Li-Jiang; Sun, Qiang; Xie, Hu-Jun; Lei, Qun-Fang; Fang, Wen-Jun

    2015-05-01

    The mechanism of Maillard reaction has been investigated by means of density functional theory calculations in the gaseous phase and aqueous solution. The Maillard reaction is a cascade of consecutive and parallel reaction. In the present model system study, glucose and glycine were taken as the initial reactants. On the basis of previous experimental results, the mechanisms of Maillard reaction have been proposed, and the possibility for the formation of different compounds have been evaluated through calculating the relative energy changes for different steps of reaction under different pH conditions. Our calculations reveal that the TS3 in Amadori rearrangement reaction is the rate-determining step of Maillard reaction with the activation barriers of about 66.7 and 68.8 kcal mol(-1) in the gaseous phase and aqueous solution, respectively. The calculation results are in good agreement with previous studies and could provide insights into the reaction mechanism of Maillard reaction, since experimental evaluation of the role of intermediates in the Maillard reaction is quite complicated.

  1. Mechanisms of inorganic and organometallic reactions

    CERN Document Server

    The purpose of this series is to provide a continuing critical review of the literature concerned with mechanistic aspects of inorganic and organo­ metallic reactions in solution, with coverage being complete in each volume. The papers discussed are selected on the basis of relevance to the elucidation of reaction mechanisms and many include results of a nonkinetic nature when useful mechanistic information can be deduced. The period of literature covered by this volume is July 1982 through December 1983, and in some instances papers not available for inclusion in the previous volume are also included. Numerical results are usually reported in the units used by the original authors, except where data from different papers are com­ pared and conversion to common units is necessary. As in previous volumes material included covers the major areas of redox processes, reactions of the nonmetallic elements, reaction of inert and labile metal complexes and the reactions of organometallic compounds. While m...

  2. Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

    Science.gov (United States)

    Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.

    2016-06-01

    Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

  3. Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization.

    Science.gov (United States)

    Khavrutskii, Ilja V; Smith, Jason B; Wallqvist, Anders

    2013-10-28

    Here, we apply the harmonic Fourier beads (HFB) path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical (QM) and hybrid QM∕molecular mechanical (QM∕MM) potential energy surfaces. To improve efficiency of the path optimization on such computationally demanding potentials, we combined HFB with conjugate gradient (CG) optimization. The combined CG-HFB method was used to study two biologically relevant reactions, namely, L- to D-alanine amino acid inversion and alcohol acylation by amides. The optimized paths revealed several unexpected reaction steps in the gas phase. For example, on the B3LYP∕6-31G(d,p) potential, we found that alanine inversion proceeded via previously unknown intermediates, 2-iminopropane-1,1-diol and 3-amino-3-methyloxiran-2-ol. The CG-HFB method accurately located transition states, aiding in the interpretation of complex reaction mechanisms. Thus, on the B3LYP∕6-31G(d,p) potential, the gas phase activation barriers for the inversion and acylation reactions were 50.5 and 39.9 kcal∕mol, respectively. These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins. We conclude that the combined CG-HFB method further advances QM and QM∕MM studies of reaction mechanisms.

  4. Elucidating reaction mechanisms on quantum computers

    Science.gov (United States)

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M.; Wecker, Dave; Troyer, Matthias

    2017-07-01

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

  5. Elucidating reaction mechanisms on quantum computers

    Science.gov (United States)

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M.; Wecker, Dave; Troyer, Matthias

    2017-01-01

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources. PMID:28674011

  6. Elucidating reaction mechanisms on quantum computers.

    Science.gov (United States)

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M; Wecker, Dave; Troyer, Matthias

    2017-07-18

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

  7. Reaction mechanism and reaction coordinates from the viewpoint of energy flow

    Energy Technology Data Exchange (ETDEWEB)

    Li, Wenjin; Ma, Ao, E-mail: aoma@uic.edu [Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607 (United States)

    2016-03-21

    Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C{sub 7eq} → C{sub 7ax} transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.

  8. Reaction mechanism and reaction coordinates from the viewpoint of energy flow

    International Nuclear Information System (INIS)

    Li, Wenjin; Ma, Ao

    2016-01-01

    Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C 7eq → C 7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.

  9. Reaction mechanisms in heavy ion fusion

    Directory of Open Access Journals (Sweden)

    Lubian J.

    2011-10-01

    Full Text Available We discuss the reaction mechanisms involved in heavy ion fusion. We begin with collisions of tightly bound systems, considering three energy regimes: energies above the Coulomb barrier, energies just below the barrier and deep sub-barrier energies. We show that channel coupling effects may influence the fusion process at above-barrier energies, increasing or reducing the cross section predicted by single barrier penetration model. Below the Coulomb barrier, it enhances the cross section, and this effect increases with the system’s size. It is argued that this behavior can be traced back to the increasing importance of Coulomb coupling with the charge of the collision partners. The sharp drop of the fusion cross section observed at deep sub-barrier energies is addressed and the theoretical approaches to this phenomenon are discussed. We then consider the reaction mechanisms involved in fusion reactions of weakly bound systems, paying particular attention to the calculations of complete and incomplete fusion available in the literature.

  10. Light ion reaction mechanisms and nuclear structure

    International Nuclear Information System (INIS)

    Robson, B.A.

    1986-01-01

    Of the many contributions to the subject 'Light ion reaction mechanism and nuclear structure', a few are selected and reviewed which highlight the present state of the field. Some contributions to the conference dealing with nuclear interactions are briefly outlined in the second section following an introductory section. Lane model calculations are compared with data for 9 Be and results are given showing angular distributions of the cross sections, the analyzing powers and the spin-rotation parameters for p - 40 Ca. Real central potential for d + 32 s resulting from the FB-analysis are compared with frozen density folding and delta-function folding. The third section deals with reaction mechanism. Data are cited which show near-side and far-side contributions to the calculated analyzing powers in the 116 Sn(d,p) 117 Sn (11.2 - ) transition. Calculations are compared with experimental A y and -(A yy + 2)/3. Also given are measurements of the cross sections and analyzing powers of the continuum energy spectra for the 58 Ni(p,p'x), along with relations between the analyzing powers and momentum transfer. The fourth section addresses nuclear structure. Cross sections and analyzing powers measured at 22 MeV for the reaction 208 Pb(p,t) 206 Pb(3 2 + ) are cited and considered. (Nogami, K.)

  11. Single Turnover at Molecular Polymerization Catalysts Reveals Spatiotemporally Resolved Reactions.

    Science.gov (United States)

    Easter, Quinn T; Blum, Suzanne A

    2017-10-23

    Multiple active individual molecular ruthenium catalysts have been pinpointed within growing polynorbornene, thereby revealing information on the reaction dynamics and location that is unavailable through traditional ensemble experiments. This is the first single-turnover imaging of a molecular catalyst by fluorescence microscopy and allows detection of individual monomer reactions at an industrially important molecular ruthenium ring-opening metathesis polymerization (ROMP) catalyst under synthetically relevant conditions (e.g. unmodified industrial catalyst, ambient pressure, condensed phase, ca. 0.03 m monomer). These results further establish the key fundamentals of this imaging technique for characterizing the reactivity and location of active molecular catalysts even when they are the minor components. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

    Science.gov (United States)

    Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús

    2015-01-01

    Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. The mechanism of the modified Ullmann reaction

    NARCIS (Netherlands)

    Sperotto, Elena; Klink, Gerard P.M. van; Koten, Gerard van; Vries, Johannes G. de

    2010-01-01

    The copper-mediated aromatic nucleophilic substitution reactions developed by Fritz Ullmann and Irma Goldberg required stoichiometric amounts of copper and very high reaction temperatures. Recently, it was found that addition of relatively cheap ligands (diamines, aminoalcohols, diketones, diols)

  14. On the mechanism of effective chemical reactions with turbulent mixing of reactants and finite rate of molecular reactions

    Energy Technology Data Exchange (ETDEWEB)

    Vorotilin, V. P., E-mail: VPVorotilin@yandex.ru [Russian Academy of Sciences, Institute of Applied Mechanics (Russian Federation)

    2017-01-15

    A generalization of the theory of chemical transformation processes under turbulent mixing of reactants and arbitrary values of the rate of molecular reactions is presented that was previously developed for the variant of an instantaneous reaction [13]. The use of the features of instantaneous reactions when considering the general case, namely, the introduction of the concept of effective reaction for the reactant volumes and writing a closing conservation equation for these volumes, became possible due to the partition of the whole amount of reactants into “active” and “passive” classes; the reactants of the first class are not mixed and react by the mechanism of instantaneous reactions, while the reactants of the second class approach each other only through molecular diffusion, and therefore their contribution to the reaction process can be neglected. The physical mechanism of reaction for the limit regime of an ideal mixing reactor (IMR) is revealed and described. Although formally the reaction rate in this regime depends on the concentration of passive fractions of the reactants, according to the theory presented, the true (hidden) mechanism of the reaction is associated only with the reaction of the active fractions of the reactants with vanishingly small concentration in the volume of the reactor. It is shown that the rate constant of fast chemical reactions can be evaluated when the mixing intensity of reactants is much less than that needed to reach the mixing conditions in an IMR.

  15. Insights into the mechanisms on chemical reactions: reaction paths for chemical reactions

    International Nuclear Information System (INIS)

    Dunning, T.H. Jr.; Rosen, E.; Eades, R.A.

    1987-01-01

    We report reaction paths for two prototypical chemical reactions: Li + HF, an electron transfer reaction, and OH + H 2 , an abstraction reaction. In the first reaction we consider the connection between the energetic terms in the reaction path Hamiltonian and the electronic changes which occur upon reaction. In the second reaction we consider the treatment of vibrational effects in chemical reactions in the reaction path formalism. 30 refs., 9 figs

  16. The Suzuki-Miyaura Cross-Coupling Reaction of Halogenated Aminopyrazoles: Method Development, Scope, and Mechanism of Dehalogenation Side Reaction.

    Science.gov (United States)

    Jedinák, Lukáš; Zátopková, Renáta; Zemánková, Hana; Šustková, Alena; Cankař, Petr

    2017-01-06

    The efficient Suzuki-Miyaura cross-coupling reaction of halogenated aminopyrazoles and their amides or ureas with a range of aryl, heteroaryl, and styryl boronic acids or esters has been developed. The method allowed incorporation of problematic substrates: aminopyrazoles bearing protected or unprotected pyrazole NH, as well as the free amino or N-amide group. Direct comparison of the chloro, bromo, and iodopyrazoles in the Suzuki-Miyaura reaction revealed that Br and Cl derivatives were superior to iodopyrazoles, as a result of reduced propensity to dehalogenation. Moreover, the mechanism and factors affecting the undesired dehalogenation side reaction were revealed.

  17. Reaction mechanism of dicofol removal by cellulase.

    Science.gov (United States)

    Wang, Ziyuan; Yang, Ting; Zhai, Zihan; Zhang, Boya; Zhang, Jianbo

    2015-10-01

    It remains unclear whether dicofol should be defined as a persistent organic pollutant. Its environmental persistence has gained attention. This study focused on its degradation by cellulase. Cellulase was separated using a gel chromatogram, and its degradation activity towards dicofol involved its endoglucanase activity. By analyzing the kinetic parameters of cellulase reacting with mixed substrates, it was shown that cellulase reacted on dicofol and carboxyl methyl cellulose through two different active centers. Thus, the degradation of dicofol was shown to be an oxidative process by cellulase. Next, by comparing the impacts of tert-butyl alcohol (a typical OH free-radical inhibitor) on the removal efficiencies of dicofol under both cellulase and Fenton reagent systems, it was shown that the removal of dicofol was initiated by OH free radicals produced by cellulase. Finally, 4,4'-dichloro-dibenzophenone and chloride were detected using gas chromatography mass spectrometry and ion chromatography analysis, which supported our hypothesis. The reaction mechanism was analyzed and involved an attack by OH free radicals at the orthocarbon of dicofol, resulting in the degradation product 4,4'-dichloro-dibenzophenone. Copyright © 2015. Published by Elsevier B.V.

  18. Report on research in progress in the reaction mechanism area

    International Nuclear Information System (INIS)

    Toledo, A.S. de; Canto, L.F.

    1982-01-01

    Research on reaction mechanisms which are being done by several groups in Brazil are reported. They are grouped in four types, namely, reactions induced by heavy and light ions, induced by electrons and finally by photons. (L.C.) [pt

  19. Report on research in progress in the reaction mechanism area

    Energy Technology Data Exchange (ETDEWEB)

    Toledo, A.S. de; Canto, L F [Sao Paulo Univ. (Brazil). Inst. de Fisica

    1982-09-01

    Research on reaction mechanisms which are being done by several groups in Brazil are reported. They are grouped in four types, namely, reactions induced by heavy and light ions, induced by electrons and finally by photons.

  20. Bell trajectories for revealing quantum control mechanisms

    International Nuclear Information System (INIS)

    Dennis, Eric; Rabitz, Herschel

    2003-01-01

    The dynamics induced while controlling quantum systems by optimally shaped laser pulses have often been difficult to understand in detail. A method is presented for quantifying the importance of specific sequences of quantum transitions involved in the control process. The method is based on a ''beable'' formulation of quantum mechanics due to John Bell that rigorously maps the quantum evolution onto an ensemble of stochastic trajectories over a classical state space. Detailed mechanism identification is illustrated with a model seven-level system. A general procedure is presented to extract mechanism information directly from closed-loop control experiments. Application to simulated experimental data for the model system proves robust with up to 25% noise

  1. Use of Isotopes for Studying Reaction Mechanisms

    Indian Academy of Sciences (India)

    In the first part of this series, we discussed how isotopes can be used as markers to determine the nature of intermediates in chemical reactions. The second part covered the effect of isotopes on equilibria and reactions, in processes where the bond to the isotopic a tom is broken. We showed with specific examples how.

  2. The three transglycosylation reactions catalyzed by cyclodextrin glycosyltransferase from Bacillus circulans (strain 251) proceed via different kinetic mechanisms

    NARCIS (Netherlands)

    Veen, Bart A. van der; Alebeek, Gert-Jan W.M. van; Uitdehaag, Joost C.M.; Dijkstra, Bauke W.; Dijkhuizen, Lubbert

    Cyclodextrin glycosyltransferase (CGTase) catalyzes three transglycosylation reactions via a double displacement mechanism involving a covalent enzyme-intermediate complex (substituted-enzyme intermediate). Characterization of the three transglycosylation reactions, however, revealed that they

  3. Dynamical barrier and isotope effects in the simplest substitution reaction via Walden inversion mechanism

    Science.gov (United States)

    Zhao, Zhiqiang; Zhang, Zhaojun; Liu, Shu; Zhang, Dong H.

    2017-02-01

    Reactions occurring at a carbon atom through the Walden inversion mechanism are one of the most important and useful classes of reactions in chemistry. Here we report an accurate theoretical study of the simplest reaction of that type: the H+CH4 substitution reaction and its isotope analogues. It is found that the reaction threshold versus collision energy is considerably higher than the barrier height. The reaction exhibits a strong normal secondary isotope effect on the cross-sections measured above the reaction threshold, and a small but reverse secondary kinetic isotope effect at room temperature. Detailed analysis reveals that the reaction proceeds along a path with a higher barrier height instead of the minimum-energy path because the umbrella angle of the non-reacting methyl group cannot change synchronously with the other reaction coordinates during the reaction due to insufficient energy transfer from the translational motion to the umbrella mode.

  4. Reaction mechanism of reductive decomposition of FGD gypsum with anthracite

    International Nuclear Information System (INIS)

    Zheng, Da; Lu, Hailin; Sun, Xiuyun; Liu, Xiaodong; Han, Weiqing; Wang, Lianjun

    2013-01-01

    Highlights: • The reaction mechanism was different if the molar ratio of C/CaSO 4 was different. • The yield of CaO rises with an increase in temperature. • The optimal ratio of C/CaSO 4 = 1.2:1. • The decomposition process is mainly apparent solid–solid reaction with liquid-phase involved. - Abstract: The process of decomposition reaction between flue gas desulfurization (FGD) gypsum and anthracite is complex, which depends on the reaction conditions and atmosphere. In this study, thermogravimetric analysis with Fourier transform infrared spectroscopy (TGA-FTIR), X-ray diffraction (XRD), scanning electron microscopy (SEM) and the experiment in a tubular reactor were used to characterize the decomposition reaction in a nitrogen atmosphere under different conditions. The reaction mechanism analysis showed that the decomposition reaction process and mechanism were different when the molar proportion of C/CaSO 4 was changed. The experiment results showed that appropriate increase in the C/CaSO 4 proportion and higher temperatures were suitable for the formation of the main production of CaO, which can help us to understand the solid state reaction mechanism better. Via kinetic analysis of the reaction between anthracite and FGD gypsum under the optimal molar ratio of C/CaSO 4 , the mechanism model of the reaction was confirmed and the decomposition process was a two-step reaction which was in accordance with apparent solid–solid reaction

  5. Recombination rate plasticity: revealing mechanisms by design

    Science.gov (United States)

    Sefick, Stephen; Rushton, Chase

    2017-01-01

    For over a century, scientists have known that meiotic recombination rates can vary considerably among individuals, and that environmental conditions can modify recombination rates relative to the background. A variety of external and intrinsic factors such as temperature, age, sex and starvation can elicit ‘plastic’ responses in recombination rate. The influence of recombination rate plasticity on genetic diversity of the next generation has interesting and important implications for how populations evolve. Further, many questions remain regarding the mechanisms and molecular processes that contribute to recombination rate plasticity. Here, we review 100 years of experimental work on recombination rate plasticity conducted in Drosophila melanogaster. We categorize this work into four major classes of experimental designs, which we describe via classic studies in D. melanogaster. Based on these studies, we highlight molecular mechanisms that are supported by experimental results and relate these findings to studies in other systems. We synthesize lessons learned from this model system into experimental guidelines for using recent advances in genotyping technologies, to study recombination rate plasticity in non-model organisms. Specifically, we recommend (1) using fine-scale genome-wide markers, (2) collecting time-course data, (3) including crossover distribution measurements, and (4) using mixed effects models to analyse results. To illustrate this approach, we present an application adhering to these guidelines from empirical work we conducted in Drosophila pseudoobscura. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’. PMID:29109222

  6. Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism.

    Science.gov (United States)

    Hamada, Yojiro; Kanematsu, Yusuke; Tachikawa, Masanori

    2016-10-11

    The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an S N 1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.

  7. Discriminative topological features reveal biological network mechanisms

    Directory of Open Access Journals (Sweden)

    Levovitz Chaya

    2004-11-01

    Full Text Available Abstract Background Recent genomic and bioinformatic advances have motivated the development of numerous network models intending to describe graphs of biological, technological, and sociological origin. In most cases the success of a model has been evaluated by how well it reproduces a few key features of the real-world data, such as degree distributions, mean geodesic lengths, and clustering coefficients. Often pairs of models can reproduce these features with indistinguishable fidelity despite being generated by vastly different mechanisms. In such cases, these few target features are insufficient to distinguish which of the different models best describes real world networks of interest; moreover, it is not clear a priori that any of the presently-existing algorithms for network generation offers a predictive description of the networks inspiring them. Results We present a method to assess systematically which of a set of proposed network generation algorithms gives the most accurate description of a given biological network. To derive discriminative classifiers, we construct a mapping from the set of all graphs to a high-dimensional (in principle infinite-dimensional "word space". This map defines an input space for classification schemes which allow us to state unambiguously which models are most descriptive of a given network of interest. Our training sets include networks generated from 17 models either drawn from the literature or introduced in this work. We show that different duplication-mutation schemes best describe the E. coli genetic network, the S. cerevisiae protein interaction network, and the C. elegans neuronal network, out of a set of network models including a linear preferential attachment model and a small-world model. Conclusions Our method is a first step towards systematizing network models and assessing their predictability, and we anticipate its usefulness for a number of communities.

  8. Integration of metabolome data with metabolic networks reveals reporter reactions

    DEFF Research Database (Denmark)

    Çakir, Tunahan; Patil, Kiran Raosaheb; Önsan, Zeynep Ilsen

    2006-01-01

    Interpreting quantitative metabolome data is a difficult task owing to the high connectivity in metabolic networks and inherent interdependency between enzymatic regulation, metabolite levels and fluxes. Here we present a hypothesis-driven algorithm for the integration of such data with metabolic...... network topology. The algorithm thus enables identification of reporter reactions, which are reactions where there are significant coordinated changes in the level of surrounding metabolites following environmental/genetic perturbations. Applicability of the algorithm is demonstrated by using data from...... is measured. By combining the results with transcriptome data, we further show that it is possible to infer whether the reactions are hierarchically or metabolically regulated. Hereby, the reported approach represents an attempt to map different layers of regulation within metabolic networks through...

  9. Decrypting Cryptochrome: Revealing the Molecular Identity of the Photoactivation Reaction

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Domratcheva, Tatiana; Shahi, Abdul Rehaman Moughal

    2012-01-01

    of cryptochrome must arise from the photoactivation reaction occurring in the protein: exposure to blue light results in electron transfer to a flavin pigment co-factor, leading to formation of an electron spin-entangled pair of radicals. Theoretical and experimental studies established long ago that such radical...... pairs, indeed, can act as a magnetic compass. The photo-reaction pathway in cryptochrome is not fully resolved yet. We employ ab initio quantum chemistry and classical all-atom MD simulations for Arabidopsis thaliana cryptochrome to determine how the radical pair is formed, becomes stabilized through...

  10. [Reaction mechanism studies of heavy ion induced nuclear reactions]: Annual progress report, October 1987

    International Nuclear Information System (INIS)

    Mignerey, A.C.

    1987-10-01

    The experiments which this group has been working on seek to define the reaction mechanisms responsible for complex fragment emission in heavy ion reactions. The reactions studied are La + La, La + Al, and La + Cu at 46.8 MeV/u; and Ne + Ag and Ne + Au reactions at 250 MeV/u. Another experimental program at the Oak Ridge Hollifield Heavy Ion Research Facility (HHIRF) is designed to measure the excitation energy division between reaction products in asymmetric deep inelastic reactions. A brief description is given of progress to date, the scientific goals of this experiment and the plastic phoswich detectors developed for this experiment

  11. Reaction mechanisms and staggering in S+Ni collisions

    International Nuclear Information System (INIS)

    D'Agostino, M.; Bruno, M.; Gulminelli, F.; Morelli, L.; Baiocco, G.; Bardelli, L.; Barlini, S.; Cannata, F.; Casini, G.; Geraci, E.; Gramegna, F.; Kravchuk, V.L.; Marchi, T.; Moroni, A.; Ordine, A.; Raduta, Ad.R.

    2011-01-01

    The reactions 32 S+ 58 Ni and 32 S+ 64 Ni are studied at 14.5 A MeV. After a selection of the collision mechanism, we show that important even-odd effects are present in the isotopic fragment distributions when the excitation energy is small. Close to the multifragmentation threshold this staggering appears hidden by the rapid variation of the production yields with the fragment size. Once this effect is accounted for, the staggering appears to be a universal feature of fragment production, slightly enhanced when the emission source is neutron poor. A closer look at the behavior of the production yields as a function of the neutron excess N-Z, reveals that odd-even effects cannot be explained by pairing effects in the nuclear masses alone, but depend in a more complex way on the de-excitation chain.

  12. Proton transfers in the Strecker reaction revealed by DFT calculations

    Directory of Open Access Journals (Sweden)

    Shinichi Yamabe

    2014-08-01

    Full Text Available The Strecker reaction of acetaldehyde, NH3, and HCN to afford alanine was studied by DFT calculations for the first time, which involves two reaction stages. In the first reaction stage, the aminonitrile was formed. The rate-determining step is the deprotonation of the NH3+ group in MeCH(OH-NH3+ to form 1-aminoethanol, which occurs with an activation energy barrier (ΔE≠ of 9.6 kcal/mol. The stereochemistry (R or S of the aminonitrile product is determined at the NH3 addition step to the carbonyl carbon of the aldehyde. While the addition of CN− to the carbon atom of the protonated imine 7 appears to scramble the stereochemistry, the water cluster above the imine plane reinforces the CN− to attack the imine group below the plane. The enforcement hinders the scrambling. In the second stage, the aminonitrile transforms to alanine, where an amide Me-CH(NH2-C(=O-NH2 is the key intermediate. The rate-determining step is the hydrolysis of the cyano group of N(amino-protonated aminonitrile which occurs with an ΔE≠ value of 34.7 kcal/mol. In the Strecker reaction, the proton transfer along the hydrogen bonds plays a crucial role.

  13. Mechanism of chimera formation during the Multiple Displacement Amplification reaction

    Directory of Open Access Journals (Sweden)

    Stockwell Timothy B

    2007-04-01

    Full Text Available Abstract Background Multiple Displacement Amplification (MDA is a method used for amplifying limiting DNA sources. The high molecular weight amplified DNA is ideal for DNA library construction. While this has enabled genomic sequencing from one or a few cells of unculturable microorganisms, the process is complicated by the tendency of MDA to generate chimeric DNA rearrangements in the amplified DNA. Determining the source of the DNA rearrangements would be an important step towards reducing or eliminating them. Results Here, we characterize the major types of chimeras formed by carrying out an MDA whole genome amplification from a single E. coli cell and sequencing by the 454 Life Sciences method. Analysis of 475 chimeras revealed the predominant reaction mechanisms that create the DNA rearrangements. The highly branched DNA synthesized in MDA can assume many alternative secondary structures. DNA strands extended on an initial template can be displaced becoming available to prime on a second template creating the chimeras. Evidence supports a model in which branch migration can displace 3'-ends freeing them to prime on the new templates. More than 85% of the resulting DNA rearrangements were inverted sequences with intervening deletions that the model predicts. Intramolecular rearrangements were favored, with displaced 3'-ends reannealing to single stranded 5'-strands contained within the same branched DNA molecule. In over 70% of the chimeric junctions, the 3' termini had initiated priming at complimentary sequences of 2–21 nucleotides (nts in the new templates. Conclusion Formation of chimeras is an important limitation to the MDA method, particularly for whole genome sequencing. Identification of the mechanism for chimera formation provides new insight into the MDA reaction and suggests methods to reduce chimeras. The 454 sequencing approach used here will provide a rapid method to assess the utility of reaction modifications.

  14. KINETICS AND MECHANISM OF REACTION OF ACIDIC ...

    African Journals Online (AJOL)

    The kinetics and mechanism of the oxidation of two phenoxazine dyes namely Nile blue (7-amino-3-diethylamino-8,9-benzo phenoxazine chloride, NB+) and Meldola\\'s blue (3- dimethylamino-8,9-benzo phenoxazine chloride, MB+) with acidic chlorite and hypochlorous acid have been investigated using a UV-visible and a ...

  15. Nuclear excitations and reaction mechanisms. Progress report

    International Nuclear Information System (INIS)

    Fallieros, S.; Levin, F.S.

    1986-01-01

    Theoretical research is being conducted on the following topics: photon scattering, gauge invariance and the extension of Siefert's Theorem; retardation effects in photonuclear absorption and the Cabibbo Radicati Sum Rule; isovector transition densities, currents and response functions; the electric polarizability, the magnetic susceptibility and the distribution of oscillator strengths in some elementary systems; relativistic models and processes; properties of skyrmions; multiquark compound bags and the charge form factor of the A = 3 nuclei; nuclear reaction theory; three-particle scattering theory; deuteron-nucleus model calculations; asymptotia in three-particle scattering systems; and time-dependent approach to few-nucleon collisions. Progress in each of these areas is reviewed briefly. A list of invited talks and of publications for the fiscal year 1986 is included. 27 refs

  16. Control of Maillard Reactions in Foods: Strategies and Chemical Mechanisms.

    Science.gov (United States)

    Lund, Marianne N; Ray, Colin A

    2017-06-14

    Maillard reactions lead to changes in food color, organoleptic properties, protein functionality, and protein digestibility. Numerous different strategies for controlling Maillard reactions in foods have been attempted during the past decades. In this paper, recent advances in strategies for controlling the Maillard reaction and subsequent downstream reaction products in food systems are critically reviewed. The underlying mechanisms at play are presented, strengths and weaknesses of each strategy are discussed, and reasonable reaction mechanisms are proposed to reinforce the evaluations. The review includes strategies involving addition of functional ingredients, such as plant polyphenols and vitamins, as well as enzymes. The resulting trapping or modification of Maillard targets, reactive intermediates, and advanced glycation endproducts (AGEs) are presented with their potential unwanted side effects. Finally, recent advances in processing for control of Maillard reactions are discussed.

  17. Kinetic mechanism for modeling of electrochemical reactions.

    Science.gov (United States)

    Cervenka, Petr; Hrdlička, Jiří; Přibyl, Michal; Snita, Dalimil

    2012-04-01

    We propose a kinetic mechanism of electrochemical interactions. We assume fast formation and recombination of electron donors D- and acceptors A+ on electrode surfaces. These mediators are continuously formed in the electrode matter by thermal fluctuations. The mediators D- and A+, chemically equivalent to the electrode metal, enter electrochemical interactions on the electrode surfaces. Electrochemical dynamics and current-voltage characteristics of a selected electrochemical system are studied. Our results are in good qualitative agreement with those given by the classical Butler-Volmer kinetics. The proposed model can be used to study fast electrochemical processes in microsystems and nanosystems that are often out of the thermal equilibrium. Moreover, the kinetic mechanism operates only with the surface concentrations of chemical reactants and local electric potentials, which facilitates the study of electrochemical systems with indefinable bulk.

  18. Sugarcane bagasse gasification: Global reaction mechanism of syngas evolution

    International Nuclear Information System (INIS)

    Ahmed, I.I.; Gupta, A.K.

    2012-01-01

    Highlights: ► Gasification of sugarcane bagasse has been investigated using a semi batch reactor. ► Global reaction mechanism combining pyrolysis and gasification reactions is presented. ► High flow rates of syngas supported fragmentation and secondary reactions. ► CO flow rate increased at higher heating rates at the expense of CO 2 production. ► At high temperatures merger between pyrolysis and char gasification occurs. -- Abstract: Steam gasification of sugarcane bagasse has been investigated. A semi batch reactor with a fixed amount of sugarcane bagasse sample placed in steady flow of high temperature steam at atmospheric pressure has been used. The gasification of bagasse was examined at reactor and steam temperatures of 800, 900 and 1000 °C. The evolution of syngas flow rate and chemical composition has been monitored. The evolution of chemical composition and total flow rate of the syngas has been used to formulate a global reaction mechanism. The mechanism combines pyrolysis reaction mechanisms from the literature and steam gasification/reforming reactions. Steam gasification steps include steam–hydrocarbons reforming, char gasification and water gas shift reactions. Evidence of fragmentation, secondary ring opening reactions and tertiary reactions resulting in formation of gaseous hydrocarbons is supported by higher flow rates of syngas and hydrogen at high heating rates and high reactor temperatures. Increase in carbon monoxide flow rate at the expense of carbon dioxide flow rate with the increase in reactor temperature has been observed. This increase in the ratio of CO/CO 2 flow rate confirms the production of CO and CO 2 from the competing reaction routes. At 1000 °C gasification a total merging between the pyrolysis step and the char gasification step has been observed. This is attributed to acceleration of char gasification reactions and acceleration of steam–hydrocarbons reforming reactions. These hydrocarbons are the precursors to

  19. Electric reaction arising in bone subjected to mechanical loadings

    Science.gov (United States)

    Murasawa, Go; Cho, Hideo; Ogawa, Kazuma

    2006-03-01

    The aim of present study is the investigation of the electric reaction arising in bone subjected to mechanical loadings. Firstly, specimen was fabricated from femur of cow, and ultrasonic propagation in bone was measured by ultrasonic technique. Secondary, 4-point bending test was conducted up to fracture, and electric reaction arising in bone was measured during loading. Thirdly, cyclic 4-point bending test was conducted to investigate the effect of applied displacement speed on electric reaction.

  20. Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations.

    Science.gov (United States)

    Moreira, Cátia; Ramos, Maria J; Fernandes, Pedro Alexandrino

    2016-06-27

    This paper is devoted to the understanding of the reaction mechanism of mycobacterium tuberculosis glutamine synthetase (mtGS) with atomic detail, using computational quantum mechanics/molecular mechanics (QM/MM) methods at the ONIOM M06-D3/6-311++G(2d,2p):ff99SB//B3LYP/6-31G(d):ff99SB level of theory. The complete reaction undergoes a three-step mechanism: the spontaneous transfer of phosphate from ATP to glutamate upon ammonium binding (ammonium quickly loses a proton to Asp54), the attack of ammonia on phosphorylated glutamate (yielding protonated glutamine), and the deprotonation of glutamine by the leaving phosphate. This exothermic reaction has an activation free energy of 21.5 kcal mol(-1) , which is consistent with that described for Escherichia coli glutamine synthetase (15-17 kcal mol(-1) ). The participating active site residues have been identified and their role and energy contributions clarified. This study provides an insightful atomic description of the biosynthetic reaction that takes place in this enzyme, opening doors for more accurate studies for developing new anti-tuberculosis therapies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Pump-shaped dump optimal control reveals the nuclear reaction pathway of isomerization of a photoexcited cyanine dye.

    Science.gov (United States)

    Dietzek, Benjamin; Brüggemann, Ben; Pascher, Torbjörn; Yartsev, Arkady

    2007-10-31

    Using optimal control as a spectroscopic tool we decipher the details of the molecular dynamics of the essential multidimensional excited-state photoisomerization - a fundamental chemical reaction of key importance in biology. Two distinct nuclear motions are identified in addition to the overall bond-twisting motion: Initially, the reaction is dominated by motion perpendicular to the torsion coordinate. At later times, a second optically active vibration drives the system along the reaction path to the bottom of the excited-state potential. The time scales of the wavepacket motion on a different part of the excited-state potential are detailed by pump-shaped dump optimal control. This technique offers new means to control a chemical reaction far from the Franck-Condon point of absorption and to map details of excited-state reaction pathways revealing unique insights into the underlying reaction mechanism.

  2. Thermodynamic chemical energy transfer mechanisms of non-equilibrium, quasi-equilibrium, and equilibrium chemical reactions

    International Nuclear Information System (INIS)

    Roh, Heui-Seol

    2015-01-01

    Chemical energy transfer mechanisms at finite temperature are explored by a chemical energy transfer theory which is capable of investigating various chemical mechanisms of non-equilibrium, quasi-equilibrium, and equilibrium. Gibbs energy fluxes are obtained as a function of chemical potential, time, and displacement. Diffusion, convection, internal convection, and internal equilibrium chemical energy fluxes are demonstrated. The theory reveals that there are chemical energy flux gaps and broken discrete symmetries at the activation chemical potential, time, and displacement. The statistical, thermodynamic theory is the unification of diffusion and internal convection chemical reactions which reduces to the non-equilibrium generalization beyond the quasi-equilibrium theories of migration and diffusion processes. The relationship between kinetic theories of chemical and electrochemical reactions is also explored. The theory is applied to explore non-equilibrium chemical reactions as an illustration. Three variable separation constants indicate particle number constants and play key roles in describing the distinct chemical reaction mechanisms. The kinetics of chemical energy transfer accounts for the four control mechanisms of chemical reactions such as activation, concentration, transition, and film chemical reactions. - Highlights: • Chemical energy transfer theory is proposed for non-, quasi-, and equilibrium. • Gibbs energy fluxes are expressed by chemical potential, time, and displacement. • Relationship between chemical and electrochemical reactions is discussed. • Theory is applied to explore nonequilibrium energy transfer in chemical reactions. • Kinetics of non-equilibrium chemical reactions shows the four control mechanisms

  3. Reactions of a stable dialkylsilylene and their mechanisms

    Indian Academy of Sciences (India)

    Stable silylene; mechanisms; photoreaction; addition; insertion; DFT. 1. ... Some of these reactions provide useful ... Although much attention has been ... sis, structure, and spectroscopic properties of 1 that .... Because silylenes are usually in the singlet ground state ..... selective 1,2-/1,4-addition reactions of dialkylsilylenes.

  4. Mechanism of the CO2-Ca(OH)2 reaction

    International Nuclear Information System (INIS)

    Chew, V.S.; Cheh, C.H.; Glass, R.W.

    1983-01-01

    Recent studies clearly showed the importance of moisture in achieving high Ca(OH) 2 absorbent utilization for removing CO 2 from gas streams at ambient temperatures. However, the role of moisture and the mechanism of the reaction was not well understood. This paper summarizes the results of a study of the mechanism of the CO 2 -Ca(OH) 2 reaction with emphasis on the role of moisture. The reaction between Ca(OH) 2 and CO 2 in moist N 2 was found to be first order with respect to the reactants with a rate constant of about 100 min -1 . At high humidities, the rate of reaction was chemically controlled, but at low humidities, the reaction rate was limited by the diffusion through the carbonate layer formed by the reaction. Calculations showed that capillary condensation could have occurred only in about 2% of the pore volume and was unlikely to have affected the reaction rate significantly by allowing the reaction to occur in the liquid phase. It was, therefore, concluded that the main role of moisture was to improve the Ca(OH) 2 utilization by lowering the resistance to diffusion through the carbonate layer

  5. The Electronic Flux in Chemical Reactions. Insights on the Mechanism of the Maillard Reaction

    Science.gov (United States)

    Flores, Patricio; Gutiérrez-Oliva, Soledad; Herrera, Bárbara; Silva, Eduardo; Toro-Labbé, Alejandro

    2007-11-01

    The electronic transfer that occurs during a chemical process is analysed in term of a new concept, the electronic flux, that allows characterizing the regions along the reaction coordinate where electron transfer is actually taking place. The electron flux is quantified through the variation of the electronic chemical potential with respect to the reaction coordinate and is used, together with the reaction force, to shed light on reaction mechanism of the Schiff base formation in the Maillard reaction. By partitioning the reaction coordinate in regions in which different process might be taking place, electronic reordering associated to polarization and transfer has been identified and found to be localized at specific transition state regions where most bond forming and breaking occur.

  6. Reaction mechanisms of ruthenium tetroxide mediated oxidations of organic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Froehaug, Astrid Elisabeth

    1995-12-31

    This thesis reports a study of the mechanism of ruthenium tetroxide mediated oxidations of saturated hydrocarbons, ethers, alkenes and alcohols. Several methods were used. The RuO{sub 4}-mediated oxidations of adamantane and cis-decalin were studied in CCl{sub 4}-CH{sub 3}CN-H{sub 2}O and in acetone-water. The rate of reaction was found to be moderately influenced by the polarity of the solvent. Solvent properties other than the polarity were also found to influence the reaction rates. From the oxidations of adamantane and adamantane-1,3,5,7-d{sub 4} two primary kinetic deuterium isotope effects were found. These were comparable with the deuterium isotope effects found for the analogous oxidations of cis-decalin and cis-decalin-d{sub 18}. The results seem to exclude both a one step hydride abstraction reaction mechanism and a one step concerted mechanism, as well as a scheme where two such mechanisms compete. The observations may be explained by a two step reaction mechanism consisting of a pre-equilibrium with formation of a substrate-RuO{sub 4} complex followed by a concerted rate determining reaction. The RuO{sub 4}-mediated oxidation of ethers was of kinetic second order with a small enthalpy of activation and a large negative entropy of activation. Oxidation of cyclopropylmethyl methyl ether gave methyl cyclopropanecarboxylate, no rearranged products were observed. On RuO{sub 4} oxidations in CCl{sub 4} with NaIO{sub 4} as stoichiometric oxidant, no chlorinated products were observed. Several observations not in agreement with a hydride or a hydrogen abstraction mechanism may be explained by assuming that the reaction proceeds by either a concerted reaction or by a reversible oxidative addition of the ether to RuO{sub 4} followed by a slow concerted step. 228 refs., 9 figs., 27 tabs.

  7. Reaction mechanisms in cellulose pyrolysis: a literature review

    Energy Technology Data Exchange (ETDEWEB)

    Molton, P.M.; Demmitt, T.F.

    1977-08-01

    A bibliographic review of 195 references is presented outlining the history of the research into the mechanisms of cellulose pyrolysis. Topics discussed are: initial product identification, mechanism of initial formation of levoglucosan, from cellulose and from related compounds, decomposition of cellulose to other compounds, formation of aromatics, pyrolysis of levoglucosan, crosslinking of cellulose, pyrolytic reactions of cellulose derivatives, and the effects of inorganic salts on the pyrolysis mechanism. (JSR)

  8. Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins

    Energy Technology Data Exchange (ETDEWEB)

    Garrison, W.M.

    1985-01-01

    The purpose of this review is to bring together and to correlate the wide variety of experimental studies that provide information on the reaction products and reaction mechanisms involved in the radiolysis of peptides, polypeptides and proteins (including chromosomal proteins) in both aqueous and solid-state systems. The comparative radiation chemistry of these systems is developed in terms of specific reactions of the peptide main-chain and the aliphatic, aromatic-unsaturated and sulfur-containing side-chains. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis and ESR spectroscopy is included. 147 refs.

  9. Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins

    International Nuclear Information System (INIS)

    Garrison, W.M.

    1985-01-01

    The purpose of this review is to bring together and to correlate the wide variety of experimental studies that provide information on the reaction products and reaction mechanisms involved in the radiolysis of peptides, polypeptides and proteins (including chromosomal proteins) in both aqueous and solid-state systems. The comparative radiation chemistry of these systems is developed in terms of specific reactions of the peptide main-chain and the aliphatic, aromatic-unsaturated and sulfur-containing side-chains. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis and ESR spectroscopy is included. 147 refs

  10. Reaction mechanisms for on-surface synthesis of covalent nanostructures

    International Nuclear Information System (INIS)

    Björk, J

    2016-01-01

    In recent years, on-surface synthesis has become an increasingly popular strategy to form covalent nanostructures. The approach has great prospects for facilitating the manufacture of a range of fascinating materials with atomic precision. However, the on-surface reactions are enigmatic to control, currently restricting its bright perspectives and there is a great need to explore how the reactions are governed. The objective of this topical review is to summarize theoretical work that has focused on comprehending on-surface synthesis protocols through studies of reaction mechanisms. (topical review)

  11. Cyclodextrin-Catalyzed Organic Synthesis: Reactions, Mechanisms, and Applications

    Directory of Open Access Journals (Sweden)

    Chang Cai Bai

    2017-09-01

    Full Text Available Cyclodextrins are well-known macrocyclic oligosaccharides that consist of α-(1,4 linked glucose units and have been widely used as artificial enzymes, chiral separators, chemical sensors, and drug excipients, owing to their hydrophobic and chiral interiors. Due to their remarkable inclusion capabilities with small organic molecules, more recent interests focus on organic reactions catalyzed by cyclodextrins. This contribution outlines the current progress in cyclodextrin-catalyzed organic reactions. Particular emphases are given to the organic reaction mechanisms and their applications. In the end, the future directions of research in this field are proposed.

  12. The dynamics of the Hg + Br2 reaction: elucidation of the reaction mechanism for the Br exchange reaction.

    Science.gov (United States)

    Jambrina, P G; Menéndez, M; Aoiz, F J

    2017-06-28

    In spite of its importance in the Hg atmospheric chemistry, the dynamics of the Hg + Br 2 → HgBr + Br reaction is poorly understood. In this article, we have carried out a comprehensive study of the reaction mechanism of this reaction by means of quasiclassical trajectories (QCTs) on an existing ab initio potential energy surface (PES). The reaction has a non trivial dynamics, as a consequence of its large endothermicity, the presence of a deep potential well, and the competition between the Br exchange and the collision induced dissociation processes. Our calculations demonstrate that insertion is only relevant at energies just above the reaction threshold and that, at energies above 2.3 eV, HgBr formation typically takes place via a sort of frustrated dissociation. In order to compare directly with the results obtained in extensive cross molecular beam experiments for the homologous reaction with I 2 , angular distributions in the laboratory frame for Hg + Br 2 have been simulated under similar experimental conditions. The lack of agreement at the highest energies considered suggests that either the two reactions have substantially different mechanisms or that calculations on a single PES cannot account for the dynamics at those energies.

  13. Understanding organometallic reaction mechanisms and catalysis experimental and computational tools computational and experimental tools

    CERN Document Server

    Ananikov, Valentin P

    2014-01-01

    Exploring and highlighting the new horizons in the studies of reaction mechanisms that open joint application of experimental studies and theoretical calculations is the goal of this book. The latest insights and developments in the mechanistic studies of organometallic reactions and catalytic processes are presented and reviewed. The book adopts a unique approach, exemplifying how to use experiments, spectroscopy measurements, and computational methods to reveal reaction pathways and molecular structures of catalysts, rather than concentrating solely on one discipline. The result is a deeper

  14. Kinetics and Mechanisms of Calcite Reactions with Saline Waters

    Energy Technology Data Exchange (ETDEWEB)

    Gorman, Brian P [Colorado School of Mines, Golden, CO (United States)

    2015-09-02

    Project Description: The general objective of the proposed research is to determine the kinetics and mechanisms of calcite reactions with saline waters over a wide range of saline water composition, pCO2, and modest ranges in T and P. This will be accomplished by studying both reaction rates and solubility from changes in solution chemistry, and making nanoscale observations of calcite precipitate surface morphology and composition at the micro-to-nano-scale to provide an understanding of controlling reaction mechanisms and pathways. The specific objectives necessary to reach the general objective are: a) determination of how pCO2, Ca2+, ionic strength and “foreign” ions influence reaction rates; and b) investigate the influence of these parameters on apparent kinetic solubility from dissolution and precipitation reactions. This information will clearly be central to the construction of reliable reaction-transport models to predict reservoir and formation response to increased CO2 in saline waters. This program was initially collaborative with John Morse at Texas A&M, however his passing shortly after the beginning of this program resulted in abbreviated research time and effort. Summary of Results: Early studies using electron microscopy and spectroscopy indicated that carbonate precipitation from natural seawater (NSW) conditions onto aragonite substrates was mediated by a surface amorphous calcium carbonate layer. It was hypothesized that this ACC layer (observed after < 5days reaction time) was responsible for the abnormal reaction kinetics and also served as a metastable seed layer for growth of epitaxial aragonite. Further studies of the ACC formation mechanism indicated a strong dependence on the Mg concentration in solution. Subsequent studies at shorter times (10 hrs) on calcite substrates and in a wide range of supersaturation conditions did not indicate any ACC layer. Instead, an epitaxial layer by layer

  15. Prediction of Tetraoxygen Reaction Mechanism with Sulfur Atom on the Singlet Potential Energy Surface

    Directory of Open Access Journals (Sweden)

    Ashraf Khademzadeh

    2014-01-01

    Full Text Available The mechanism of S+O4 (D2h reaction has been investigated at the B3LYP/6-311+G(3df and CCSD levels on the singlet potential energy surface. One stable complex has been found for the S+O4 (D2h reaction, IN1, on the singlet potential energy surface. For the title reaction, we obtained four kinds of products at the B3LYP level, which have enough thermodynamic stability. The results reveal that the product P3 is spontaneous and exothermic with −188.042 and −179.147 kcal/mol in Gibbs free energy and enthalpy of reaction, respectively. Because P1 adduct is produced after passing two low energy level transition states, kinetically, it is the most favorable adduct in the 1S+1O4 (D2h atmospheric reactions.

  16. Alcali-silica reactions: Mechanisms for crack formations

    DEFF Research Database (Denmark)

    Goltermann, Per

    2006-01-01

    Alkali-silica reactions (ASR) are found all over the world and cause a large number of damage, which have lead to different sets of requirements in the different countries for the aggregates, the cements and the admixtures. One of the reasons for the damage and the different requirements is that ......Alkali-silica reactions (ASR) are found all over the world and cause a large number of damage, which have lead to different sets of requirements in the different countries for the aggregates, the cements and the admixtures. One of the reasons for the damage and the different requirements...... is that the mechanical behavior of the ASR has not been fully investigated, although the chemical aspects of ASR have been dealt with in depth. This paper presents a unified, mechanical explanation of the ASR damage mechanism, covering the relevant aspects of the diffusion model; the stress-variations in the aggregate...

  17. Structure and Reaction Mechanism of Pyrrolysine Synthase (PylD)

    KAUST Repository

    Quitterer, Felix; Beck, Philipp; Bacher, Adelbert; Groll, Michael

    2013-01-01

    The final step in the biosynthesis of the 22nd genetically encoded amino acid, pyrrolysine, is catalyzed by PylD, a structurally and mechanistically unique dehydrogenase. This catalyzed reaction includes an induced-fit mechanism achieved by major structural rearrangements of the N-terminal helix upon substrate binding. Different steps of the reaction trajectory are visualized by complex structures of PylD with substrate and product. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Structure and Reaction Mechanism of Pyrrolysine Synthase (PylD)

    KAUST Repository

    Quitterer, Felix

    2013-05-29

    The final step in the biosynthesis of the 22nd genetically encoded amino acid, pyrrolysine, is catalyzed by PylD, a structurally and mechanistically unique dehydrogenase. This catalyzed reaction includes an induced-fit mechanism achieved by major structural rearrangements of the N-terminal helix upon substrate binding. Different steps of the reaction trajectory are visualized by complex structures of PylD with substrate and product. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Reaction mechanisms of CO2 activation and catalytic reduction

    International Nuclear Information System (INIS)

    Wolff, Niklas von

    2016-01-01

    The use of CO 2 as a C1 chemical feedstock for the fine chemical industry is interesting both economically and ecologically, as CO 2 is non-toxic, abundant and cheap. Nevertheless, transformations of CO 2 into value-added products is hampered by its high thermodynamic stability and its inertness toward reduction. In order to design new catalysts able to overcome this kinetic challenge, a profound understanding of the reaction mechanisms at play in CO 2 reduction is needed. Using novel N/Si+ frustrated Lewis pairs (FLPs), the influence of CO 2 adducts and different hydro-borane reducing agents on the reaction mechanism in the catalytic hydroboration of CO 2 were investigated, both by DFT calculations and experiments. In a second step, the reaction mechanism of a novel reaction for the creation of C-C bonds from CO 2 and pyridyl-silanes (C 5 H 4 N-SiMe 3 ) was analyzed by DFT calculations. It was shown that CO 2 plays a double role in this transformation, acting both as a catalyst and a C1-building block. The fine understanding of this transformation then led to the development of a novel approach for the synthesis of sulfones and sulfonamides. Starting from SO 2 and aromatic silanes/amine silanes, these products were obtained in a single step under metal-free conditions. Noteworthy, sulfones and sulfonamides are common motifs in organic chemistry and found in a variety of highly important drugs. Finally, this concept was extended to aromatic halides as coupling partners, and it was thus shown for the first time that a sulfonylative Hiyama reaction is a possible approach to the synthesis of sulfones. (author) [fr

  20. High resolution studies of pion-nucleus reaction mechanism

    International Nuclear Information System (INIS)

    Morris, C.L.

    1983-01-01

    Pion inelastic scattering is generally well described as a first order process using the DWIA. This is especially true for a large body of inelastic scattering data to low-lying collective states which is well-described by form factors obtained in (e,e') and the DWIA. Some data for which this model does not work are presented. Higher order reaction mechanisms have been invoked to explain some of these data. However, no model of these second order processes gives a satisfactory explanation of the entire data set. Experimentally, more data for pion-induced transitions to low-spin unnatural-parity states which have been studied by other probes would be useful in sorting out the reaction mechanisms responsible for the anomalous cross sections observed for the 1 + states in 12 C. Theoretically, a consistent evaluation of possible second-order diagrams in inelastic scattering, such as is being attempted for DCX 22 , would be useful

  1. Reaction mechanism in high energy heavy-ion collisions

    International Nuclear Information System (INIS)

    Tanihata, Isao.

    1982-04-01

    The reaction mechanism in high energy heavy-ion collision is discussed. The discussion is mainly based on the experimental data. Empirical equations have been given for the total cross-sections of nucleus-nucleus reactions and the reaction cross-sections. These cross-sections are well described by the geometrical size of the colliding nuclei. The cross-sections are also understood by microscopic calculation. The charged particle multiplicity gives additional information about the geometrical aspect of heavy ion collision. The data suggested that the total energy, independent of projectile size, is most important for determining the multiplicity. The inclusive proton spectrum in a heavy ion collision showed two distinct regions. The one is the fragment region, and the other the participant region. The spectral shapes of inclusive pion spectra are reasonably well explained by the Coulomb interaction of pions with nuclear fragments. The high energy heavy ion reaction occurs in the overlap region of the projectile and target. This has been tested by measuring the number of participants for various reactions. The space and the time structure of the collision are also discussed in this paper as well as the dynamical aspects of the collision. (Kato, T.)

  2. Transglycosylation reactions, a main mechanism of phenolics incorporation in coffee melanoidins: Inhibition by Maillard reaction.

    Science.gov (United States)

    Moreira, Ana S P; Nunes, Fernando M; Simões, Cristiana; Maciel, Elisabete; Domingues, Pedro; Domingues, M Rosário M; Coimbra, Manuel A

    2017-07-15

    Under roasting conditions, polysaccharides depolymerize and also are able to polymerize, forming new polymers through non-enzymatic transglycosylation reactions (TGRs). TGRs can also occur between carbohydrates and aglycones, such as the phenolic compounds present in daily consumed foods like coffee. In this study, glycosidically-linked phenolic compounds were quantified in coffee melanoidins, the polymeric nitrogenous brown-colored compounds formed during roasting, defined as end-products of Maillard reaction. One third of the phenolics present were in glycosidically-linked form. In addition, the roasting of solid-state mixtures mimicking coffee beans composition allowed the conclusion that proteins play a regulatory role in TGRs extension and, consequently, modulate melanoidins composition. Overall, the results obtained showed that TGRs are a main mechanism of phenolics incorporation in melanoidins and are inhibited by amino groups through Maillard reaction. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Reaction Mechanisms of Magnesium Potassium Phosphate Cement and its Application

    Science.gov (United States)

    Qiao, Fei

    Magnesium potassium phosphate cement (MKPC) is a kind of cementitious binder in which the chemical bond is formed via a heterogeneous acid-base reaction between dead burned magnesia powder and potassium phosphate solution at room temperature. Small amount of boron compounds can be incorporated in the cement as a setting retarder. The final reaction product of MgO-KH2PO4-H 2O ternary system is identified as magnesium potassium phosphate hexahydrate, MgKPO4·6H2O. However, the mechanisms and procedures through which this crystalline product is formed and the conditions under which the crystallization process would be influenced are not yet clear. Understanding of the reaction mechanism of the system is helpful for developing new methodologies to control the rapid reaction process and furthermore, to adjust the phase assemblage of the binder, and to enhance the macroscopic properties. This study is mainly focused on the examination of the reaction mechanism of MKPC. In addition, the formulation optimization, microstructure characterization and field application in rapid repair are also systematically studied. The chemical reactions between magnesia and potassium dihydrogen phosphate are essentially an acid-base reaction with strong heat release, the pH and temperature variation throughout the reaction process could provide useful information to disclose the different stages in the reaction. However, it would be very difficult to conduct such tests on the cement paste due to the limited water content and fast setting. In the current research, the reaction mechanism of MKPC is investigated on the diluted MKPC system through monitoring the pH and temperature development, identification of the solid phase formed, and measurement of the ionic concentration of the solution. The reaction process can be explained as follows: when magnesia and potassium phosphate powder are mixed with water, phosphate is readily dissolved, which is instantly followed by the dissociation of

  4. Photocatalytic degradation of paracetamol: intermediates and total reaction mechanism.

    Science.gov (United States)

    Moctezuma, Edgar; Leyva, Elisa; Aguilar, Claudia A; Luna, Raúl A; Montalvo, Carlos

    2012-12-01

    The advanced oxidation of paracetamol (PAM) promoted by TiO(2)/UV system in aqueous medium was investigated. Monitoring this reaction by HPLC and TOC, it was demonstrated that while oxidation of paracetamol is quite efficient under these conditions, its mineralization is not complete. HPLC indicated the formation of hydroquinone, benzoquinone, p-aminophenol and p-nitrophenol in the reaction mixtures. Further evidence of p-nitrophenol formation was obtained following the reaction by UV-vis spectroscopy. Continuous monitoring by IR spectroscopy demonstrated the breaking of the aromatic amide present in PAM and subsequent formation of several aromatic intermediate compounds such as p-aminophenol and p-nitrophenol. These aromatic compounds were eventually converted into trans-unsaturated carboxylic acids. Based on these experimental results, an alternative deacylation mechanism for the photocatalytic oxidation of paracetamol is proposed. Our studies also demonstrated IR spectroscopy to be a useful technique to investigate oxidative mechanisms of pharmaceutical compounds. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Doorway states in nuclear reactions as a manifestation of the 'super-radiant' mechanism

    International Nuclear Information System (INIS)

    Auerbach, N.; Zelevinsky, V.

    2007-01-01

    A mechanism is considered for generating doorway states and intermediate structure in low-energy nuclear reactions as a result of collectivization of widths of unstable intrinsic states coupled to common decay channels. At the limit of strong continuum coupling, the segregation of broad ('super-radiating') and narrow ('trapped') states occurs revealing the separation of direct and compound processes. We discuss the conditions for the appearance of intermediate structure in this process and doorways related to certain decay channels

  6. High-energy nuclear reaction mechanisms - fission, fragmentation and spallation

    International Nuclear Information System (INIS)

    Kaufman, S.B.

    1987-01-01

    Measurements of the correlations in kinetic energy, mass, charge, and angle of coincident fragments formed in high-energy nuclear reactions have helped to characterize the processes of fission, fragmentation and spallation. For example, fission or fission-like two-body breakup mechanisms result in a strong angular correlation between two heavy fragments; in addition, the momentum transfer in the reaction can be deduced from the correlation. Another example is the multiplicity of light charged particles associated with a given heavy fragment, which is a measure of the violence of the collision, thus distinguishing between central and peripheral collisions. A summary of what has been learned about these processes from such studies will be given, along with some suggestions for further experiments

  7. Reaction mechanisms for enhancing carbon dioxide mineral sequestration

    Science.gov (United States)

    Jarvis, Karalee Ann

    Increasing global temperature resulting from the increased release of carbon dioxide into the atmosphere is one of the greatest problems facing society. Nevertheless, coal plants remain the largest source of electrical energy and carbon dioxide gas. For this reason, researchers are searching for methods to reduce carbon dioxide emissions into the atmosphere from the combustion of coal. Mineral sequestration of carbon dioxide reacted in electrolyte solutions at 185°C and 2200 psi with olivine (magnesium silicate) has been shown to produce environmentally benign carbonates. However, to make this method feasible for industrial applications, the reaction rate needs to be increased. Two methods were employed to increase the rate of mineral sequestration: reactant composition and concentration were altered independently in various runs. The products were analyzed with complete combustion for total carbon content. Crystalline phases in the product were analyzed with Debye-Scherrer X-ray powder diffraction. To understand the reaction mechanism, single crystals of San Carlos Olivine were reacted in two solutions: (0.64 M NaHCO3/1 M NaCl) and (5.5 M KHCO3) and analyzed with scanning electron microscopy (SEM), transmission electron microscopy (TEM), electron energy loss spectroscopy (EELS), and fluctuation electron microscopy (FEM) to study the surface morphology, atomic crystalline structure, composition and amorphous structure. From solution chemistry studies, it was found that increasing the activity of the bicarbonate ion increased the conversion rate of carbon dioxide to magnesite. The fastest conversion, 60% conversion in one hour, occurred in a solution of 5.5 M KHCO3. The reaction product particles, magnesium carbonate, significantly increased in both number density and size on the coupon when the bicarbonate ion activity was increased. During some experiments reaction vessel corrosion also altered the mineral sequestration mechanism. Nickel ions from vessel

  8. A discrete model to study reaction-diffusion-mechanics systems.

    Science.gov (United States)

    Weise, Louis D; Nash, Martyn P; Panfilov, Alexander V

    2011-01-01

    This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.

  9. New Mechanism of Low Energy Nuclear Reactions Using Superlow

    Science.gov (United States)

    Gareev, F. A.; Zhidkova, I. E.

    2006-03-01

    We proposed a new mechanism of LENR (low energy nuclear reactions) cooperative processes in the whole system - nuclei+atoms+condensed matter can occur at smaller threshold than the corresponding ones assoiciated with free constituents. The cooperative processes can be induced and enhanced by (``superlow energy'') external fields. The excess heat is the emission of internal energy, and transmutations from LENR are the result of redistribution of the internal energy of the whole system. A review of possible stimulation mechanisms of LENR is presented. We have concluded that transmutation of nuclei at low energies and excess heat are possible in the framework of the known fundamental physical laws: The universal resonance synchronization principle, and based on it, different enhancement mechanisms of reaction rates are responsible for these processes. The excitation and ionization of atoms may play the role of a trigger for LENR. F.A. Gareev, I.E. Zhidkova, E-print arXiv Nucl-th/0511092 v1 30 Nov 2005. F.A. Gareev, In: FPB-98, Novosibirsk, June 1998, p.92; F.A.Gareev, G.F. Gareeva, in: Novosibirsk, July 2000, p.161. F.A. Gareev, I.E. Zhidkova and Yu.L. Ratis, Preprint JINR P4-2004-68, Dubna, 2004. F.A. Gareev, I.E. Zhidkova, E-print arXiv Nucl-th/0505021 9 May 2005.

  10. A discrete model to study reaction-diffusion-mechanics systems.

    Directory of Open Access Journals (Sweden)

    Louis D Weise

    Full Text Available This article introduces a discrete reaction-diffusion-mechanics (dRDM model to study the effects of deformation on reaction-diffusion (RD processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material. Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.

  11. Geometric Mechanics Reveals Optimal Complex Terrestrial Undulation Patterns

    Science.gov (United States)

    Gong, Chaohui; Astley, Henry; Schiebel, Perrin; Dai, Jin; Travers, Matthew; Goldman, Daniel; Choset, Howie; CMU Team; GT Team

    Geometric mechanics offers useful tools for intuitively analyzing biological and robotic locomotion. However, utility of these tools were previously restricted to systems that have only two internal degrees of freedom and in uniform media. We show kinematics of complex locomotors that make intermittent contacts with substrates can be approximated as a linear combination of two shape bases, and can be represented using two variables. Therefore, the tools of geometric mechanics can be used to analyze motions of locomotors with many degrees of freedom. To demonstrate the proposed technique, we present studies on two different types of snake gaits which utilize combinations of waves in the horizontal and vertical planes: sidewinding (in the sidewinder rattlesnake C. cerastes) and lateral undulation (in the desert specialist snake C. occipitalis). C. cerastes moves by generating posteriorly traveling body waves in the horizontal and vertical directions, with a relative phase offset equal to +/-π/2 while C. occipitalismaintains a π/2 offset of a frequency doubled vertical wave. Geometric analysis reveals these coordination patterns enable optimal movement in the two different styles of undulatory terrestrial locomotion. More broadly, these examples demonstrate the utility of geometric mechanics in analyzing realistic biological and robotic locomotion.

  12. Reaction mechanism and spectroscopy of transfer reactions induced by heavy ions

    International Nuclear Information System (INIS)

    Lemaire, M.-C.

    1977-01-01

    The specific features displayed by data on heavy ion elastic and inelastic angular distributions are discussed, and their physical origin is pointed out from semi-classical calculations in counterpart ambiguities in the phenomenological description of the optical potential appear. Two nucleon transfer reactions induced by heavy ions successfully point out important contributions of a two-step process where the transfer is proceeding via target and residual nucleus inelastic excitation. At incident energies not too high above the Coulomb barrier, such process produces clear shape changes between different final state angular distributions. At higher incident energy, the angular distributions are forward peaked and display oscillations for both mechanisms. As for four-nucleon transfer reactions, the existing data suggest that the nucleons are well transferred into a Os relative

  13. Radiation-protective drugs and their reaction mechanisms

    International Nuclear Information System (INIS)

    Livesey, J.C.; Reed, D.J.; Adamson, L.F.

    1985-01-01

    The objective of this book is to provide the reader with a concise review of radioprotective drugs and their reaction mechanisms. The first chapter reviews the effect of radiation on biological systems at the atomic, molecular, and subcellular levels. The second chapter discusses endogenous factors that influence radioresistance. Chapter 3 presents the main theme of the book, chemical radioprotection and its mechanisms, and examines the basis of natural radioprotection and how it may be affected by exogenous chemicals. Chapter 4, the Therapy of Radiation Damage, is a very brief general discussion that only touches on some of the experimental approaches to therapy. Chapter 5 contains recommendations for future research. The two appendices list research in progress in the United States and some radioprotective compounds of possible investigational interest. Also included is a brief discussion of structure-activity relationships

  14. Mechanisms of polyphosphate glucokinase and polyphosphate kinase reactions

    International Nuclear Information System (INIS)

    Pepin, C.A.; Robinson, N.A.; Wood, H.G.

    1986-01-01

    Polyphosphate glucokinase [poly(P)GK] catalyzes the following reaction: poly(P)/sub n/ + glucose → poly(P)/sub n-1/ + G-6-P. With long chain poly(P) [n=750 to 400] the mechanism appeared to be processive, in which there is phosphorylation of glucose without release of intermediate sizes of the poly(P) until the chain is about 100, thereafter there were intermediate sizes formed apparently by a non-processive process. Poly(P) kinase catalyzes the following reaction: ATP + poly(P)/sub n/ ↔ ADP + poly(P)/sub n + 1/. Using short chain 32 [P] poly(P) as a primer and non-radioactive ATP, long chain poly(P) is formed processively. The resulting chain has a short length labeled with 32 [P] contributed by the primer on one end and the remainder is made up of unlabeled (P) from the ATP. The authors have used this 32 [P] poly(P) as a substrate with poly(P)GK. If the mechanism of the poly(P)GK were initially processive, there would be a 50% chance the phosphate would be utilized from the unlabeled end and 50% of the 32 [P] would remain in the shortened chain. However, all the 32 [P] was lost when 20% of the poly(P) was converted to G-6-P. In contrast, with poly(P) kinase, the % of poly(P) utilized was equivalent to the % of 32 [P] converted to ATP, which is consistent with a strictly processive mechanism. Even though the mechanism of poly(P)GK appeared to be processive with long chains, the on and off rate of poly(P) from the enzyme is such that there is random removal of (P) from both ends of the poly(P) chain

  15. The chemistry of the carbothermal synthesis of β-SiC : reaction mechanism, reaction rate and grain growth

    NARCIS (Netherlands)

    van Dijen, F.K.; Metselaar, R.

    1991-01-01

    Evidence is given that in the present case the reaction mechanism of ß-SiC formation from silica and carbon is a direct solid-state reaction in which silica migrates over the silicon carbide surface to the carbon. A high value (440 kJ/mol) of activation energy is obtained for this reaction. This

  16. Kinetics and mechanisms of reactions involving small aromatic reactive intermediates

    Energy Technology Data Exchange (ETDEWEB)

    Lin, M.C. [Emory Univ., Atlanta, GA (United States)

    1993-12-01

    Small aromatic radicals such as C{sub 6}H{sub 5}, C{sub 6}H{sub 5}O and C{sub 6}H{sub 4} are key prototype species of their homologs. C{sub 6}H{sub 5} and its oxidation product, C{sub 6}H{sub 5}O are believed to be important intermediates which play a pivotal role in hydrocarbon combustion, particularly with regard to soot formation. Despite their fundamental importance, experimental data on the reaction mechanisms and reactivities of these species are very limited. For C{sub 6}H{sub 5}, most kinetic data except its reactions with NO and NO{sub 2}, were obtained by relative rate measurements. For C{sub 6}H{sub 5}O, the authors have earlier measured its fragmentation reaction producing C{sub 5}H{sub 5} + CO in shock waves. For C{sub 6}H{sub 4}, the only rate constant measured in the gas phase is its recombination rate at room temperature. The authors have proposed to investigate systematically the kinetics and mechanisms of this important class of molecules using two parallel laser diagnostic techniques--laser resonance absorption (LRA) and resonance enhanced multiphoton ionization mass spectrometry (REMPI/MS). In the past two years, study has been focused on the development of a new multipass adsorption technique--the {open_quotes}cavity-ring-down{close_quotes} technique for kinetic applications. The preliminary results of this study appear to be quite good and the sensitivity of the technique is at least comparable to that of the laser-induced fluorescence method.

  17. Opto-acoustic microscopy reveals adhesion mechanics of single cells

    Science.gov (United States)

    Abi Ghanem, Maroun; Dehoux, Thomas; Liu, Liwang; Le Saux, Guillaume; Plawinski, Laurent; Durrieu, Marie-Christine; Audoin, Bertrand

    2018-01-01

    Laser-generated GHz-ultrasonic-based technologies have shown the ability to image single cell adhesion and stiffness simultaneously. Using this new modality, we here demonstrate quantitative indicators to investigate contact mechanics and adhesion processes of the cell. We cultured human cells on a rigid substrate, and we used an inverted pulsed opto-acoustic microscope to generate acoustic pulses containing frequencies up to 100 GHz in the substrate. We map the reflection of the acoustic pulses at the cell-substrate interface to obtain images of the acoustic impedance of the cell, Zc, as well as of the stiffness of the interface, K, with 1 μm lateral resolution. Our results show that the standard deviation ΔZc reveals differences between different cell types arising from the multiplicity of local conformations within the nucleus. From the distribution of K-values within the nuclear region, we extract a mean interfacial stiffness, Km, that quantifies the average contact force in areas of the cell displaying weak bonding. By analogy with classical contact mechanics, we also define the ratio of the real to nominal contact areas, Sr/St. We show that Km can be interpreted as a quantitative indicator of passive contact at metal-cell interfaces, while Sr/St is sensitive to active adhesive processes in the nuclear region. The ability to separate the contributions of passive and active adhesion processes should allow gaining insight into cell-substrate interactions, with important applications in tissue engineering.

  18. Integrative modelling reveals mechanisms linking productivity and plant species richness.

    Science.gov (United States)

    Grace, James B; Anderson, T Michael; Seabloom, Eric W; Borer, Elizabeth T; Adler, Peter B; Harpole, W Stanley; Hautier, Yann; Hillebrand, Helmut; Lind, Eric M; Pärtel, Meelis; Bakker, Jonathan D; Buckley, Yvonne M; Crawley, Michael J; Damschen, Ellen I; Davies, Kendi F; Fay, Philip A; Firn, Jennifer; Gruner, Daniel S; Hector, Andy; Knops, Johannes M H; MacDougall, Andrew S; Melbourne, Brett A; Morgan, John W; Orrock, John L; Prober, Suzanne M; Smith, Melinda D

    2016-01-21

    How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.

  19. Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics.

    Science.gov (United States)

    Hudson, Nathan E; Ding, Feng; Bucay, Igal; O'Brien, E Timothy; Gorkun, Oleg V; Superfine, Richard; Lord, Susan T; Dokholyan, Nikolay V; Falvo, Michael R

    2013-06-18

    Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin's elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin's mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  20. Submillisecond Elastic Recoil Reveals Molecular Origins of Fibrin Fiber Mechanics

    Science.gov (United States)

    Hudson, Nathan E.; Ding, Feng; Bucay, Igal; O’Brien, E. Timothy; Gorkun, Oleg V.; Superfine, Richard; Lord, Susan T.; Dokholyan, Nikolay V.; Falvo, Michael R.

    2013-01-01

    Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin’s elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin’s mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers. PMID:23790375

  1. Investigation of organometallic reaction mechanisms with one and two dimensional vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Cahoon, James Francis [Univ. of California, Berkeley, CA (United States)

    2008-12-01

    One and two dimensional time-resolved vibrational spectroscopy has been used to investigate the elementary reactions of several prototypical organometallic complexes in room temperature solution. The electron transfer and ligand substitution reactions of photogenerated 17-electron organometallic radicals CpW(CO)3 and CpFe(CO)2 have been examined with one dimensional spectroscopy on the picosecond through microsecond time-scales, revealing the importance of caging effects and odd-electron intermediates in these reactions. Similarly, an investigation of the photophysics of the simple Fischer carbene complex Cr(CO)5[CMe(OMe)] showed that this class of molecule undergoes an unusual molecular rearrangement on the picosecond time-scale, briefly forming a metal-ketene complex. Although time-resolved spectroscopy has long been used for these types of photoinitiated reactions, the advent of two dimensional vibrational spectroscopy (2D-IR) opens the possibility to examine the ultrafast dynamics of molecules under thermal equilibrium conditions. Using this method, the picosecond fluxional rearrangements of the model metal carbonyl Fe(CO)5 have been examined, revealing the mechanism, time-scale, and transition state of the fluxional reaction. The success of this experiment demonstrates that 2D-IR is a powerful technique to examine the thermally-driven, ultrafast rearrangements of organometallic molecules in solution.

  2. On the knock-out mechanism for the 12C(P,α)9B reaction

    International Nuclear Information System (INIS)

    Hassan, M.Y.M.; Ismail, E.H.; Rabie, A.

    1978-01-01

    The mechanism of the reaction 12 C(P,α) 9 B is studied using zero range distorted wave Born approximation. The knock out mechanism is assumed to represent this reaction both in the forward and backward angles. (orig.) [de

  3. Mechanism of the Glycosidic Bond Cleavage of Mismatched Thymine in Human Thymine DNA Glycosylase Revealed by Classical Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Calculations.

    Science.gov (United States)

    Kanaan, Natalia; Crehuet, Ramon; Imhof, Petra

    2015-09-24

    Base excision of mismatched or damaged nucleotides catalyzed by glycosylase enzymes is the first step of the base excision repair system, a machinery preserving the integrity of DNA. Thymine DNA glycosylase recognizes and removes mismatched thymine by cleaving the C1'-N1 bond between the base and the sugar ring. Our quantum mechanical/molecular mechanical calculations of this reaction in human thymine DNA glycosylase reveal a requirement for a positive charge in the active site to facilitate C1'-N1 bond scission: protonation of His151 significantly lowers the free energy barrier for C1'-N1 bond dissociation compared to the situation with neutral His151. Shuttling a proton from His151 to the thymine base further reduces the activation free energy for glycosidic bond cleavage. Classical molecular dynamics simulations of the H151A mutant suggest that the mutation to the smaller, neutral, residue increases the water accessibility of the thymine base, rendering direct proton transfer from the bulk feasible. Quantum mechanical/molecular mechanical calculations of the glycosidic bond cleavage reaction in the H151A mutant show that the activation free energy is slightly lower than in the wild-type enzyme, explaining the experimentally observed higher reaction rates in this mutant.

  4. Optimized reaction mechanism rate rules for ignition of normal alkanes

    KAUST Repository

    Cai, Liming

    2016-08-11

    The increasing demand for cleaner combustion and reduced greenhouse gas emissions motivates research on the combustion of hydrocarbon fuels and their surrogates. Accurate detailed chemical kinetic models are an important prerequisite for high fidelity reacting flow simulations capable of improving combustor design and operation. The development of such models for many new fuel components and/or surrogate molecules is greatly facilitated by the application of reaction classes and rate rules. Accurate and versatile rate rules are desirable to improve the predictive accuracy of kinetic models. A major contribution in the literature is the recent work by Bugler et al. (2015), which has significantly improved rate rules and thermochemical parameters used in kinetic modeling of alkanes. In the present study, it is demonstrated that rate rules can be used and consistently optimized for a set of normal alkanes including n-heptane, n-octane, n-nonane, n-decane, and n-undecane, thereby improving the predictive accuracy for all the considered fuels. A Bayesian framework is applied in the calibration of the rate rules. The optimized rate rules are subsequently applied to generate a mechanism for n-dodecane, which was not part of the training set for the optimized rate rules. The developed mechanism shows accurate predictions compared with published well-validated mechanisms for a wide range of conditions.

  5. Opto-acoustic microscopy reveals adhesion mechanics of single cells.

    Science.gov (United States)

    Abi Ghanem, Maroun; Dehoux, Thomas; Liu, Liwang; Le Saux, Guillaume; Plawinski, Laurent; Durrieu, Marie-Christine; Audoin, Bertrand

    2018-01-01

    Laser-generated GHz-ultrasonic-based technologies have shown the ability to image single cell adhesion and stiffness simultaneously. Using this new modality, we here demonstrate quantitative indicators to investigate contact mechanics and adhesion processes of the cell. We cultured human cells on a rigid substrate, and we used an inverted pulsed opto-acoustic microscope to generate acoustic pulses containing frequencies up to 100 GHz in the substrate. We map the reflection of the acoustic pulses at the cell-substrate interface to obtain images of the acoustic impedance of the cell, Z c , as well as of the stiffness of the interface, K, with 1 μm lateral resolution. Our results show that the standard deviation ΔZ c reveals differences between different cell types arising from the multiplicity of local conformations within the nucleus. From the distribution of K-values within the nuclear region, we extract a mean interfacial stiffness, K m , that quantifies the average contact force in areas of the cell displaying weak bonding. By analogy with classical contact mechanics, we also define the ratio of the real to nominal contact areas, S r /S t . We show that K m can be interpreted as a quantitative indicator of passive contact at metal-cell interfaces, while S r /S t is sensitive to active adhesive processes in the nuclear region. The ability to separate the contributions of passive and active adhesion processes should allow gaining insight into cell-substrate interactions, with important applications in tissue engineering.

  6. Tc1-mediated contact sensitivity reaction, its mechanism and regulation

    Directory of Open Access Journals (Sweden)

    Magdalena Zemelka-Wiącek

    2014-07-01

    Full Text Available The contact hypersensitivity reaction (CHS to haptens is a classic example of cell-mediated immune response. In the effector phase, two stages can be distinguished: an early component, that appears only 2 hours after subsequent contact with the hapten, and the late component that develops approximately 24 hours later which is mediated by TCRαβ+ cells. The effector lymphocytes may be CD4+ T helper 1 (Th1 cells or CD8+ T cytotoxic 1 (Tc1 cells, which depends on the employed hapten and/or mice strain. NKT lymphocytes play the crucial role in the CHS initiation, by supporting B1 cells in the antigen-specific IgM antibodies production. The development of an early component is essential for the recruitment of T effector (Teff cells to the side of hapten deposition and for the complete expansion of inflammatory reaction. The CHS reaction is under T regulatory (Treg cells control, both in the induction phase as well as in the effector phase. A new view of a negative regulation of the Tc1 mediated CHS response is based on the suppression induced by epicutaneous (EC application of protein antigen. The DNP-BSA skin application, on a gauze patch, leads to a state of immunosuppression. This maneuver results in rising the population of Treg cells with TCRαβ+CD4+CD25+Foxp3+ phenotype. The mechanism of suppression requires direct contact between Treg cells and Teff cells and the participation of CTLA-4 molecule is also necessary. The described method of evoking immune tolerance via EC immunization may contribute to elaborate a new method of allergic contact dermatitis therapy. This is because of its effectiveness, ease of induction and non-invasive protein antigen application.

  7. Low Energy Electrons as Probing Tool for Astrochemical Reaction Mechanisms

    Science.gov (United States)

    Hendrik Bredehöft, Jan; Swiderek, Petra; Hamann, Thorben

    The complexity of molecules found in space varies widely. On one end of the scale of molecular complexity is the hydrogen molecule H2 . Its formation from H atoms is if not understood than at least thoroughly investigated[1]. On the other side of said spectrum the precursors to biopolymers can be found, such as amino acids[2,3], sugars[4], lipids, cofactors[5], etc, and the kerogen-like organic polymer material in carbonaceous meteorites called "black stuff" [6]. These have also received broad attention in the last decades. Sitting in the middle between these two extremes are simple molecules that are observed by radio astronomy throughout the Universe. These are molecules like methane (CH4 ), methanol (CH3 OH), formaldehyde (CH2 O), hydrogen cyanide (HCN), and many many others. So far more than 40 such species have been identified.[7] They are often used in laboratory experiments to create larger complex molecules on the surface of simulated interstellar dust grains.[2,8] The mechanisms of formation of these observed starting materials for prebiotic chemistry is however not always clear. Also the exact mechanisms of formation of larger molecules in photochemical experiments are largely unclear. This is mostly due to the very complex chemistry going on which involves many different radicals and ions. The creation of radicals and ions can be studied in detail in laboratory simulations. They can be created in a setup mimicking interstellar grain chemistry using slow electrons. There is no free electron radiation in space. What can be found though is a lot of radiation of different sorts. There is electromagnetic radiation (UV light, X-Rays, rays, etc.) and there is particulate radiation as well in the form of high energy ions. This radiation can provide energy that drives chemical reactions in the ice mantles of interstellar dust grains. And while the multitude of different kinds of radiation might be a little confusing, they all have one thing in common: Upon

  8. Revisiting the Kinetics and Mechanism of Bromate-Bromide Reaction

    Directory of Open Access Journals (Sweden)

    Côrtes Carlos Eduardo S.

    2001-01-01

    Full Text Available The bromate-bromide reaction was investigated in an acidity range not studied yet. The reaction was followed at the Br2/Br3- isosbestic point (lambda = 446 nm. It was observed a first-order behavior for bromate and bromide ions and a second-order behavior for H+ ion that results in the rate law nu = k[BrO3-][Br- ][H+]². This rate law suggests a mechanism involving two successive protonation of bromate followed by the interaction of the intermediate species H2BrO3+ with bromide. These results disagree with the obtained by other authors who observed a second-order behavior for the bromide and first-order for H+, and have proposed intermediate species like H2Br2O3 and HBr2O3-. The second-order for [H+] observed in the range 0.005 <= [H+] <= 2.77 mol L-1 sets down that the pKa of bromic acid, HBrO3, must be lower than -0.5 (T = 25 °C, different from all other values for this pKa proposed in the literature.

  9. BlenX-based compositional modeling of complex reaction mechanisms

    Directory of Open Access Journals (Sweden)

    Judit Zámborszky

    2010-02-01

    Full Text Available Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of BlenX compositionality.

  10. The Physical Mechanism of Frictional Aging Revealed by Nanoindentation Creep

    Science.gov (United States)

    Thom, C.; Carpick, R. W.; Goldsby, D. L.

    2017-12-01

    A classical observation from rock friction experiments is that friction increases linearly with the logarithm of the time of stationary contact, a phenomenon sometimes referred to as aging. Aging is most often attributed to an increase in the real area of contact due to asperity creep. However, recent atomic force microscopy (AFM) experiments and molecular dynamics simulations suggest that time-dependent siloxane (Si—O—Si) bonding gives rise to aging in silica-silica contacts in the absence of plastic deformation. Determining whether an increase in contact `quantity' (due to creep), contact `quality' (due to chemical bonding), or another unknown mechanism causes aging is a challenging experimental task, despite its importance for developing a physical basis for rate and state friction laws. An intriguing observation is that aging is absent in friction experiments on quartz rocks and gouge at humidities water on asperity creep (via hydrolytic weakening) or on the adhesive strength of contacts. To discern between these possibilities, we have conducted nanoindentation experiments on single crystals of quartz to measure their indentation hardness and creep behavior at humidities of 2% to 50%, and in vacuum. Samples were loaded at 1000 mN/s to a peak load of 15, 40, or 400 mN, which was then held constant for 10 s. After the peak load is reached, the tip sinks into the material with time due to creep of the indentation contact. Our experiments reveal that there is no effect of varying humidity on either indentation hardness or indentation creep behavior over the full range of humidities investigated. If asperity creep were the dominant mechanism of frictional aging for quartz in the experiments cited above, then significant increases in hardness and decreases in the growth rate of indentation contacts at low humidities is expected, in stark contrast with our nanoindentation data. Our experiments indicate that asperity creep cannot be the cause of aging in quartz

  11. Comparative analysis reveals the underlying mechanism of vertebrate seasonal reproduction.

    Science.gov (United States)

    Ikegami, Keisuke; Yoshimura, Takashi

    2016-02-01

    Animals utilize photoperiodic changes as a calendar to regulate seasonal reproduction. Birds have highly sophisticated photoperiodic mechanisms and functional genomics analysis in quail uncovered the signal transduction pathway regulating avian seasonal reproduction. Birds detect light with deep brain photoreceptors. Long day (LD) stimulus induces secretion of thyroid-stimulating hormone (TSH) from the pars tuberalis (PT) of the pituitary gland. PT-derived TSH locally activates thyroid hormone (TH) in the hypothalamus, which induces gonadotropin-releasing hormone (GnRH) and hence gonadotropin secretion. However, during winter, low temperatures increase serum TH for adaptive thermogenesis, which accelerates germ cell apoptosis by activating the genes involved in metamorphosis. Therefore, TH has a dual role in the regulation of seasonal reproduction. Studies using TSH receptor knockout mice confirmed the involvement of PT-derived TSH in mammalian seasonal reproduction. In addition, studies in mice revealed that the tissue-specific glycosylation of TSH diversifies its function in the circulation to avoid crosstalk. In contrast to birds and mammals, one of the molecular machineries necessary for the seasonal reproduction of fish are localized in the saccus vasculosus from the photoreceptor to the neuroendocrine output. Thus, comparative analysis is a powerful tool to uncover the universality and diversity of fundamental properties in various organisms. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. An efficient quantum mechanical method for radical pair recombination reactions.

    Science.gov (United States)

    Lewis, Alan M; Fay, Thomas P; Manolopoulos, David E

    2016-12-28

    The standard quantum mechanical expressions for the singlet and triplet survival probabilities and product yields of a radical pair recombination reaction involve a trace over the states in a combined electronic and nuclear spin Hilbert space. If this trace is evaluated deterministically, by performing a separate time-dependent wavepacket calculation for each initial state in the Hilbert space, the computational effort scales as O(Z 2 log⁡Z), where Z is the total number of nuclear spin states. Here we show that the trace can also be evaluated stochastically, by exploiting the properties of spin coherent states. This results in a computational effort of O(MZlog⁡Z), where M is the number of Monte Carlo samples needed for convergence. Example calculations on a strongly coupled radical pair with Z>10 6 show that the singlet yield can be converged to graphical accuracy using just M=200 samples, resulting in a speed up by a factor of >5000 over a standard deterministic calculation. We expect that this factor will greatly facilitate future quantum mechanical simulations of a wide variety of radical pairs of interest in chemistry and biology.

  13. Reaction trajectory revealed by a joint analysis of protein data bank.

    Science.gov (United States)

    Ren, Zhong

    2013-01-01

    Structural motions along a reaction pathway hold the secret about how a biological macromolecule functions. If each static structure were considered as a snapshot of the protein molecule in action, a large collection of structures would constitute a multidimensional conformational space of an enormous size. Here I present a joint analysis of hundreds of known structures of human hemoglobin in the Protein Data Bank. By applying singular value decomposition to distance matrices of these structures, I demonstrate that this large collection of structural snapshots, derived under a wide range of experimental conditions, arrange orderly along a reaction pathway. The structural motions along this extensive trajectory, including several helical transformations, arrive at a reverse engineered mechanism of the cooperative machinery (Ren, companion article), and shed light on pathological properties of the abnormal homotetrameric hemoglobins from α-thalassemia. This method of meta-analysis provides a general approach to structural dynamics based on static protein structures in this post genomics era.

  14. Reaction trajectory revealed by a joint analysis of protein data bank.

    Directory of Open Access Journals (Sweden)

    Zhong Ren

    Full Text Available Structural motions along a reaction pathway hold the secret about how a biological macromolecule functions. If each static structure were considered as a snapshot of the protein molecule in action, a large collection of structures would constitute a multidimensional conformational space of an enormous size. Here I present a joint analysis of hundreds of known structures of human hemoglobin in the Protein Data Bank. By applying singular value decomposition to distance matrices of these structures, I demonstrate that this large collection of structural snapshots, derived under a wide range of experimental conditions, arrange orderly along a reaction pathway. The structural motions along this extensive trajectory, including several helical transformations, arrive at a reverse engineered mechanism of the cooperative machinery (Ren, companion article, and shed light on pathological properties of the abnormal homotetrameric hemoglobins from α-thalassemia. This method of meta-analysis provides a general approach to structural dynamics based on static protein structures in this post genomics era.

  15. Mechano-chemical synthesis of strontium britholites: Reaction mechanism

    International Nuclear Information System (INIS)

    Gmati, N.; Boughzala, K.; Bouzouita, K.; Abdellaoui, M.

    2011-01-01

    The britholites have gained a great interest thanks to their potential applications as matrices for the confinement of the byproducts in the nuclear industry such as minor actinides and long-lived fission products. However, the preparation of britholites requires high temperatures, above 1200 C. In this work, we strive to prepare these kinds of compounds by a mechano-chemical synthesis at room temperature from the starting materials SrF 2 , SrCO 3 , Sr 2 P 2 O 7 , La 2 O 3 and SiO 2 using a planetary ball mill. The obtained results showed that the prepared products were carbonated apatites and the corresponding powders contained some unreacted silica and lanthana. To obtain pure britholites, a heat-treatment at 1100 C was required. The mechanism involved in the different steps of the reaction is discussed in this paper. The obtained results suggest that the use of raw materials containing no carbonate is expected to directly lead to pure britholites by appropriate milling at room temperature. (authors)

  16. The reaction mechanism of the (3HE,T) reaction and applications to nuclear structure

    NARCIS (Netherlands)

    1986-01-01

    In this thesis we present a study on the reaction meachanism of the (3He,t) reaction at 70-80 MeV bombarding energy and on structures of the residual nuclei excited in this reaction: 24-Al, 26-Al, 28-P, 32-Cl, 40-Sc, 42-Sc and 58-Cu... Zie: Summary

  17. Revealing the Interface Structure and Bonding Mechanism of Coupling Agent Treated WPC

    Directory of Open Access Journals (Sweden)

    Jiuping Rao

    2018-03-01

    Full Text Available This paper presents the interfacial optimisation of wood plastic composites (WPC based on recycled wood flour and polyethylene by employing maleated and silane coupling agents. The effect of the incorporation of the coupling agents on the variation of chemical structure of the composites were investigated by Attenuated total reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR and Solid state 13C Nuclear Magnetic Resonance spectroscopy (NMR analyses. The results revealed the chemical reactions that occurred between the coupling agents and raw materials, which thus contributed to the enhancement of compatibility and interfacial adhesion between the constituents of WPC. NMR results also indicated that there existed the transformation of crystalline cellulose to an amorphous state during the coupling agent treatments, reflecting the inferior resonance of crystalline carbohydrates. Fluorescence Microscope (FM and Scanning Electron Microscope (SEM analyses showed the improvements of wood particle dispersion and wettability, compatibility of the constituents, and resin penetration, and impregnation of the composites after the coupling agent treatments. The optimised interface of the composites was attributed to interdiffusion, electrostatic adhesion, chemical reactions, and mechanical interlocking bonding mechanisms.

  18. Theoretical Study of Sodium-Water Surface Reaction Mechanism

    Science.gov (United States)

    Kikuchi, Shin; Kurihara, Akikazu; Ohshima, Hiroyuki; Hashimoto, Kenro

    Computational study of the sodium-water reaction at the gas (water) - liquid (sodium) interface has been carried out using the ab initio (first-principle) method. A possible reaction channel has been identified for the stepwise OH bond dissociations of a single water molecule. The energetics including the binding energy of a water molecule on the sodium surface, the activation energies of the bond cleavages, and the reaction energies, have been evaluated, and the rate constants of the first and second OH bond-breakings have been compared. It was found that the estimated rate constant of the former was much larger than the latter. The results are the basis for constructing the chemical reaction model used in a multi-dimensional sodium-water reaction code, SERAPHIM, being developed by Japan Atomic Energy Agency (JAEA) toward the safety assessment of the steam generator (SG) in a sodium-cooled fast reactor (SFR).

  19. Theoretical study of sodium-water surface reaction mechanism

    International Nuclear Information System (INIS)

    Kikuchi, Shin; Kurihara, Akikazu; Ohshima, Hiroyuki; Hashimoto, Kenro

    2012-01-01

    Computational study of the sodium-water reaction at the gas (water) - liquid (sodium) interface has been carried out using the ab initio (first-principle) method. A possible reaction channel has been identified for the stepwise OH bond dissociations of a single water molecule. The energetics including the binding energy of a water molecule on the sodium surface, the activation energies of the bond cleavages, and the reaction energies, have been evaluated, and the rate constants of the first and second OH bond-breakings have been compared. It was found that the estimated rate constant of the former was much larger than the latter. The results are the basis for constructing the chemical reaction model used in a multi-dimensional sodium-water reaction code, SERAPHIM, being developed by Japan Atomic Energy Agency (JAEA) toward the safety assessment of the steam generator (SG) in a sodium-cooled fast reactor (SFR). (author)

  20. New mechanism of spiral wave initiation in a reaction-diffusion-mechanics system.

    Directory of Open Access Journals (Sweden)

    Louis D Weise

    Full Text Available Spiral wave initiation in the heart muscle is a mechanism for the onset of dangerous cardiac arrhythmias. A standard protocol for spiral wave initiation is the application of a stimulus in the refractory tail of a propagating excitation wave, a region that we call the "classical vulnerable zone." Previous studies of vulnerability to spiral wave initiation did not take the influence of deformation into account, which has been shown to have a substantial effect on the excitation process of cardiomyocytes via the mechano-electrical feedback phenomenon. In this work we study the effect of deformation on the vulnerability of excitable media in a discrete reaction-diffusion-mechanics (dRDM model. The dRDM model combines FitzHugh-Nagumo type equations for cardiac excitation with a discrete mechanical description of a finite-elastic isotropic material (Seth material to model cardiac excitation-contraction coupling and stretch activated depolarizing current. We show that deformation alters the "classical," and forms a new vulnerable zone at longer coupling intervals. This mechanically caused vulnerable zone results in a new mechanism of spiral wave initiation, where unidirectional conduction block and rotation directions of the consequently initiated spiral waves are opposite compared to the mechanism of spiral wave initiation due to the "classical vulnerable zone." We show that this new mechanism of spiral wave initiation can naturally occur in situations that involve wave fronts with curvature, and discuss its relation to supernormal excitability of cardiac tissue. The concept of mechanically induced vulnerability may lead to a better understanding about the onset of dangerous heart arrhythmias via mechano-electrical feedback.

  1. New mechanism of spiral wave initiation in a reaction-diffusion-mechanics system.

    Science.gov (United States)

    Weise, Louis D; Panfilov, Alexander V

    2011-01-01

    Spiral wave initiation in the heart muscle is a mechanism for the onset of dangerous cardiac arrhythmias. A standard protocol for spiral wave initiation is the application of a stimulus in the refractory tail of a propagating excitation wave, a region that we call the "classical vulnerable zone." Previous studies of vulnerability to spiral wave initiation did not take the influence of deformation into account, which has been shown to have a substantial effect on the excitation process of cardiomyocytes via the mechano-electrical feedback phenomenon. In this work we study the effect of deformation on the vulnerability of excitable media in a discrete reaction-diffusion-mechanics (dRDM) model. The dRDM model combines FitzHugh-Nagumo type equations for cardiac excitation with a discrete mechanical description of a finite-elastic isotropic material (Seth material) to model cardiac excitation-contraction coupling and stretch activated depolarizing current. We show that deformation alters the "classical," and forms a new vulnerable zone at longer coupling intervals. This mechanically caused vulnerable zone results in a new mechanism of spiral wave initiation, where unidirectional conduction block and rotation directions of the consequently initiated spiral waves are opposite compared to the mechanism of spiral wave initiation due to the "classical vulnerable zone." We show that this new mechanism of spiral wave initiation can naturally occur in situations that involve wave fronts with curvature, and discuss its relation to supernormal excitability of cardiac tissue. The concept of mechanically induced vulnerability may lead to a better understanding about the onset of dangerous heart arrhythmias via mechano-electrical feedback.

  2. Pre-equilibrium nuclear reactions: An introduction to classical and quantum-mechanical models

    International Nuclear Information System (INIS)

    Koning, A.J.; Akkermans, J.M.

    1999-01-01

    In studies of light-ion induced nuclear reactions one distinguishes three different mechanisms: direct, compound and pre-equilibrium nuclear reactions. These reaction processes can be subdivided according to time scales or, equivalently, the number of intranuclear collisions taking place before emission. Furthermore, each mechanism preferably excites certain parts of the nuclear level spectrum and is characterized by different types of angular distributions. This presentation includes description of the classical, exciton model, semi-classical models, with some selected results, and quantum mechanical models. A survey of classical versus quantum-mechanical pre-equilibrium reaction theory is presented including practical applications

  3. "Gear mechanism" of bariatric interventions revealed by untargeted metabolomics.

    Science.gov (United States)

    Samczuk, Paulina; Luba, Magdalena; Godzien, Joanna; Mastrangelo, Annalaura; Hady, Hady Razak; Dadan, Jacek; Barbas, Coral; Gorska, Maria; Kretowski, Adam; Ciborowski, Michal

    2018-03-20

    Mechanisms responsible for metabolic gains after bariatric surgery are not entirely clear. The purpose of this study was evaluation of metabolic changes after laparoscopic Roux-en-Y gastric bypass or laparoscopic sleeve gastrectomy in semi-annual follow up. The study participants were selected from obese patients with T2DM who underwent one of the mentioned bariatric procedures. Serum metabolic fingerprinting by use of liquid and gas chromatography with mass spectrometry detection was performed on samples obtained from studied patients before, one, and six months post-surgery. Performed analyses resulted in 49 significant and identified metabolites. Comparison of the two described procedures has allowed to detect metabolites linked with numerous pathways, processes and diseases. Based on the metabolites detected and pathways affected, we propose a "gear mechanism" showing molecular changes evoked by both bariatric procedures. Critical evaluation of clinical data and obtained metabolomics results enables us to conclude that both procedures are very similar in terms of general clinical outcome, but they strongly differ from each other in molecular mechanisms leading to the final effect. For the first time general metabolic effect of bariatric procedures is described. New hypotheses concerning molecular mechanisms induced by bariatric surgeries and new gut microbiota modulations are presented. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. Transcriptome profiling reveals regulatory mechanisms underlying Corolla Senescence in Petunia

    Science.gov (United States)

    Genetic regulatory mechanisms that govern petal natural senescence in petunia is complicated and unclear. To identify key genes and pathways that regulate the process, we initiated a transcriptome analysis in petunia petals at four developmental time points, including petal opening without anthesis ...

  5. Reaction mechanisms for the synthesis of the heaviest elements from heavy ion reactions

    International Nuclear Information System (INIS)

    Gaeggeler, H.W.

    1988-10-01

    This review paper concerns fusion reactions with light heavy-ions, cold fusion, transfer reactions using light heavy-ions or heavy ions. In two appendices, methods for the separation and detection of nuclides in the domain of heaviest elements are described and a comment on the discovery of the element 104 is given. 51 figs., 10 tabs., 335 refs

  6. Optimized reaction mechanism rate rules for ignition of normal alkanes

    KAUST Repository

    Cai, Liming; Pitsch, Heinz; Mohamed, Samah; Raman, Venkat; Bugler, John; Curran, Henry; Sarathy, Mani

    2016-01-01

    fidelity reacting flow simulations capable of improving combustor design and operation. The development of such models for many new fuel components and/or surrogate molecules is greatly facilitated by the application of reaction classes and rate rules

  7. Mechanisms in adverse reactions to food. The sinuses

    DEFF Research Database (Denmark)

    Høst, A

    1995-01-01

    Food allergy is an extremely rare cause of chronic sinusitis. Mucosal inflammation in chronic sinusitis is rarely caused by allergic reactions to foods but rather viral infections in the upper respiratory tract.......Food allergy is an extremely rare cause of chronic sinusitis. Mucosal inflammation in chronic sinusitis is rarely caused by allergic reactions to foods but rather viral infections in the upper respiratory tract....

  8. Mechanism of tellurium isomers excitation in (γ, n) reactions

    International Nuclear Information System (INIS)

    Mazur, V.M.; Symochko, D.M.; Bigan, Z.M.; Poltorzhytska, T.V.; Derechkey, P.S.

    2012-01-01

    Isomeric yield ratios for the 119 Te, 121 Te, 123 Te, 127 Te, 129 Te nuclei were obtained in (γ, n) reactions with bremsstrahlung end point energies ranging 10 - 22 MeV with δE = 0.5 MeV step. Experimental isomeric ratios were used to calculate the cross-sections of (γ, n) m reactions, that were further compared with TALYS-1.4 calculations

  9. Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions.

    Science.gov (United States)

    Acevedo, Orlando; Jorgensen, William L

    2010-01-19

    Application of combined quantum and molecular mechanical (QM/MM) methods focuses on predicting activation barriers and the structures of stationary points for organic and enzymatic reactions. Characterization of the factors that stabilize transition structures in solution and in enzyme active sites provides a basis for design and optimization of catalysts. Continued technological advances allowed for expansion from prototypical cases to mechanistic studies featuring detailed enzyme and condensed-phase environments with full integration of the QM calculations and configurational sampling. This required improved algorithms featuring fast QM methods, advances in computing changes in free energies including free-energy perturbation (FEP) calculations, and enhanced configurational sampling. In particular, the present Account highlights development of the PDDG/PM3 semi-empirical QM method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo (MC) simulations, and a polynomial quadrature method for efficient modeling of proton-transfer reactions. The utility of this QM/MM/MC/FEP methodology is illustrated for a variety of organic reactions including substitution, decarboxylation, elimination, and pericyclic reactions. A comparison to experimental kinetic results on medium effects has verified the accuracy of the QM/MM approach in the full range of solvents from hydrocarbons to water to ionic liquids. Corresponding results from ab initio and density functional theory (DFT) methods with continuum-based treatments of solvation reveal deficiencies, particularly for protic solvents. Also summarized in this Account are three specific QM/MM applications to biomolecular systems: (1) a recent study that clarified the mechanism for the reaction of 2-pyrone derivatives catalyzed by macrophomate synthase as a tandem Michael-aldol sequence rather than a Diels-Alder reaction, (2) elucidation of the mechanism of action of fatty

  10. Possibilities and scope of the double isotope effect method in the elucidation of mechanisms of enzyme catalyzed reactions

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, H L; Medina, R [Technische Univ. Muenchen, Freising (Germany, F.R.). Lehrstuhl fuer Allgemeine Chemie und Biochemie

    1991-01-01

    Kinetic isotope effects on enzyme catalyzed reactions are indicative for the first irreversible in a sequence of individual steps. Hints on the relative velocities of other steps can only be obtained from the partitioning factor R and its dependence on external reaction conditions. In general, the experimental data needed are obtained from isotope abundance measurements in a defined position of the substrate or product as a function of turnover. This method does not reveal events dealing with neighbour atoms or preceding the main isotope sensitive step. In the method presented here, the analytical measurement is extended to the second atom involved in a bond fission of formation (Double Isotope Effect Method). It is shown that the additional results obtained support the identification of the main isotopically sensitive step and its relative contribution to the overall reaction rate, the identification of other kinetically significant steps and the differentiation between stepwise and concerted reaction mechanisms. The method and its advantages are demonstrated on reactions comprising C-N-bond splitting (urease and arginase reaction), C-C-bound fission (reactions catalyzed by pyruvate-dehydrogenase, pyruvate-formiate-lyase and lactate-oxidase), C-O-bound formation (ribulose-bisphosphate-oxygenase reaction), and N-O-bond fission (nitrate- and nitrite-reductase reactions). (orig.).

  11. A reaction mechanism for gasoline surrogate fuels for large polycyclic aromatic hydrocarbons

    KAUST Repository

    Raj, Abhijeet; Charry Prada, Iran David; Amer, Ahmad Amer; Chung, Suk-Ho

    2012-01-01

    This work aims to develop a reaction mechanism for gasoline surrogate fuels (n-heptane, iso-octane and toluene) with an emphasis on the formation of large polycyclic aromatic hydrocarbons (PAHs). Starting from an existing base mechanism for gasoline

  12. Calcium transport mechanism in molting crayfish revealed by microanalysis

    International Nuclear Information System (INIS)

    Mizuhira, V.; Ueno, M.

    1983-01-01

    Crayfish provide a good model in which to study the transport mechanism of Ca ions. During the molting stage, decalcified Ca ions are transferred into the blood and accumulate in the gastrolith epithelium, after which a gastrolith is formed on the surface of the epithelium. The gastrolith is dissolved in the stomach after molting, and the Ca is reabsorbed and redistributed throughout the newly formed exoskeleton. We studied the mechanism of Ca transport by cytochemical precipitation of Ca ions and by electron microanalysis, including X-ray microanalysis (EDX) and electron energy-loss spectroscopy (EELS), with a computer. In EDX analysis, the fine precipitates of K-antimonate in the gastrolith mitochondria clearly defined Ca with antimony; we also observed a large amount of Ca-oxalate in the mitochondria, and Ca-K X-ray pulses were clearly defined. Ca-K X-rays were also detected from fresh freeze-substituted mitochondria. Finally, we succeeded in taking a Ca-L EELS image from the mitochondria of fresh freeze-substituted thin sections. Only a very small amount of Ca was detected from the cell membrane and other organelles. Ca-adenosine triphosphatase (ATPase) and Mg-ATPase activity was also very clearly demonstrated in the mitochondria. These enzymes may play an important role in Ca metabolism

  13. Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism.

    Science.gov (United States)

    Schuijers, Jurian; Manteiga, John Colonnese; Weintraub, Abraham Selby; Day, Daniel Sindt; Zamudio, Alicia Viridiana; Hnisz, Denes; Lee, Tong Ihn; Young, Richard Allen

    2018-04-10

    Transcriptional dysregulation of the MYC oncogene is among the most frequent events in aggressive tumor cells, and this is generally accomplished by acquisition of a super-enhancer somewhere within the 2.8 Mb TAD where MYC resides. We find that these diverse cancer-specific super-enhancers, differing in size and location, interact with the MYC gene through a common and conserved CTCF binding site located 2 kb upstream of the MYC promoter. Genetic perturbation of this enhancer-docking site in tumor cells reduces CTCF binding, super-enhancer interaction, MYC gene expression, and cell proliferation. CTCF binding is highly sensitive to DNA methylation, and this enhancer-docking site, which is hypomethylated in diverse cancers, can be inactivated through epigenetic editing with dCas9-DNMT. Similar enhancer-docking sites occur at other genes, including genes with prominent roles in multiple cancers, suggesting a mechanism by which tumor cell oncogenes can generally hijack enhancers. These results provide insights into mechanisms that allow a single target gene to be regulated by diverse enhancer elements in different cell types. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  14. Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism

    Directory of Open Access Journals (Sweden)

    Jurian Schuijers

    2018-04-01

    Full Text Available Summary: Transcriptional dysregulation of the MYC oncogene is among the most frequent events in aggressive tumor cells, and this is generally accomplished by acquisition of a super-enhancer somewhere within the 2.8 Mb TAD where MYC resides. We find that these diverse cancer-specific super-enhancers, differing in size and location, interact with the MYC gene through a common and conserved CTCF binding site located 2 kb upstream of the MYC promoter. Genetic perturbation of this enhancer-docking site in tumor cells reduces CTCF binding, super-enhancer interaction, MYC gene expression, and cell proliferation. CTCF binding is highly sensitive to DNA methylation, and this enhancer-docking site, which is hypomethylated in diverse cancers, can be inactivated through epigenetic editing with dCas9-DNMT. Similar enhancer-docking sites occur at other genes, including genes with prominent roles in multiple cancers, suggesting a mechanism by which tumor cell oncogenes can generally hijack enhancers. These results provide insights into mechanisms that allow a single target gene to be regulated by diverse enhancer elements in different cell types. : Schuijers et al. show that a conserved CTCF site at the promoter of the MYC oncogene plays an important role in enhancer-promoter looping with tumor-specific super-enhancers. Perturbation of this site provides a potential therapeutic vulnerability. Keywords: gene regulation, super-enhancers, chromosome structure, enhancer docking

  15. Reaction mechanism of sterol hydroxylation by steroid C25 dehydrogenase - Homology model, reactivity and isoenzymatic diversity.

    Science.gov (United States)

    Rugor, Agnieszka; Wójcik-Augustyn, Anna; Niedzialkowska, Ewa; Mordalski, Stefan; Staroń, Jakub; Bojarski, Andrzej; Szaleniec, Maciej

    2017-08-01

    Steroid C25 dehydrogenase (S25DH) is a molybdenum-containing oxidoreductase isolated from the anaerobic Sterolibacterium denitrificans Chol-1S. S25DH is classified as 'EBDH-like' enzyme (EBDH, ethylbenzene dehydrogenase) and catalyzes the introduction of an OH group to the C25 atom of a sterol aliphatic side-chain. Due to its regioselectivity, S25DH is proposed as a catalyst in production of pharmaceuticals: calcifediol or 25-hydroxycholesterol. The aim of presented research was to obtain structural model of catalytic subunit α and investigate the reaction mechanism of the O 2 -independent tertiary carbon atom activation. Based on homology modeling and theoretical calculations, a S25DH α subunit model was for the first time characterized and compared to other S25DH-like isoforms. The molecular dynamics simulations of the enzyme-substrate complexes revealed two stable binding modes of a substrate, which are stabilized predominantly by van der Waals forces in the hydrophobic substrate channel. However, H-bond interactions involving polar residues with C3=O/C3-OH in the steroid ring appear to be responsible for positioning the substrate. These results may explain the experimental kinetic results which showed that 3-ketosterols are hydroxylated 5-10-fold faster than 3-hydroxysterols. The reaction mechanism was studied using QM:MM and QM-only cluster models. The postulated mechanism involves homolytic CH cleavage by the MoO ligand, giving rise to a radical intermediate with product obtained in an OH rebound process. The hypothesis was supported by kinetic isotopic effect (KIE) experiments involving 25,26,26,26-[ 2 H]-cholesterol (4.5) and the theoretically predicted intrinsic KIE (7.0-7.2). Finally, we have demonstrated that the recombinant S25DH-like isoform catalyzes the same reaction as S25DH. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Reaction mechanism of CO oxidation on Cu2O(111): A density functional study

    Science.gov (United States)

    Sun, Bao-Zhen; Chen, Wen-Kai; Xu, Yi-Jun

    2010-10-01

    The possible reaction mechanisms for CO oxidation on the perfect Cu2O(111) surface have been investigated by performing periodic density functional theoretical calculations. We find that Cu2O(111) is able to facilitate the CO oxidation with different mechanisms. Four possible mechanisms are explored (denoted as MER1, MER2, MLH1, and MLH2, respectively): MER1 is CO(gas)+O2(ads)-->CO2(gas) MER2 is CO(gas)+O2(ads)-->CO3(ads)-->O(ads)+CO2(gas) MLH1 refers to CO(ads)+O2(ads)-->O(ads)+CO2(ads) and MLH2 refers to CO(ads)+O2(ads)-->OOCO(ads)-->O(ads)+CO2(ads). Our transition state calculations clearly reveal that MER1 and MLH2 are both viable; but MER1 mechanism preferentially operates, in which only a moderate energy barrier (60.22 kJ/mol) needs to be overcome. When CO oxidation takes place along MER2 path, it is facile for CO3 formation, but is difficult for its decomposition, thereby CO3 species can stably exist on Cu2O(111). Of course, the reaction of CO with lattice O of Cu2O(111) is also considered. However, the calculated barrier is 600.00 kJ/mol, which is too large to make the path feasible. So, we believe that on Cu2O(111), CO reacts with adsorbed O, rather than lattice O, to form CO2. This is different from the usual Mars-van Krevene mechanism. The present results enrich our understanding of the catalytic oxidation of CO by copper-based and metal-oxide catalysts.

  17. Recent developments in semiclassical mechanics: eigenvalues and reaction rate constants

    International Nuclear Information System (INIS)

    Miller, W.H.

    1976-04-01

    A semiclassical treatment of eigenvalues for a multidimensional non-separable potential function and of the rate constant for a chemical reaction with an activation barrier is presented. Both phenomena are seen to be described by essentially the same semiclassical formalism, which is based on a construction of the total Hamiltonian in terms of the complete set of ''good'' action variables (or adiabatic invariants) associated with the minimum in the potential energy surface for the eigenvalue case, or the saddle point in the potential energy surface for the case of chemical reaction

  18. On the mechanism of photocatalytic reactions with eosin Y

    Directory of Open Access Journals (Sweden)

    Michal Majek

    2014-04-01

    Full Text Available A combined spectroscopic, synthetic, and apparative study has allowed a more detailed mechanistic rationalization of several recently reported eosin Y-catalyzed aromatic substitutions at arenediazonium salts. The operation of rapid acid–base equilibria, direct photolysis pathways, and radical chain reactions has been discussed on the basis of pH, solvent polarity, lamp type, absorption properties, and quantum yields. Determination of the latter proved to be an especially valuable tool for the distinction between radical chain and photocatalytic reactions.

  19. Knowing beans: Human mirror mechanisms revealed through motor adaptation

    Directory of Open Access Journals (Sweden)

    Arthur M Glenberg

    2010-11-01

    Full Text Available Human mirror mechanisms (MMs respond during both performed and observed action and appear to underlie action goal recognition. We introduce a behavioral procedure for discovering and clarifying functional MM properties: Blindfolded participants repeatedly move beans either toward or away from themselves to induce motor adaptation. Then, the bias for perceiving direction of ambiguous visual movement in depth is measured. Bias is affected by a number of beans moved, b movement direction, and c similarity of the visual stimulus to the hand used to move beans. This cross-modal adaptation pattern supports both the validity of human MMs and functionality of our testing instrument. We also discuss related work that extends the motor adaptation paradigm to investigate contributions of MMs to speech perception and language comprehension.

  20. Visualization of reaction mechanism by CG based on quantum ...

    African Journals Online (AJOL)

    In this work, the change in the molecular configuration in fundamental chemical reactions such as, F + HCl ¨ HF + Cl, I + H2¨ HI + H, OH- + CH3Cl ¨ CH3OH + Cl-, and esterification of acetic acid and ethyl alcohol were visualized by the quantum chemical calculation MOPAC with PM5 Hamiltonian. The CG teaching material ...

  1. Tris(Cyclopentadienyl)Uranium-t-Butyl: Synthesis, reactions, and mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Weydert, M.

    1993-04-01

    Compounds (RC[sub 5]H[sub 4])[sub 3]U(t-Bu) were prepared for R = H, Me, Et. Their decomposition products in aromatic solvents are consistent with a radical decomposition pathway induced by solvent-assisted U-C bond homolysis. NMR was used to study the reactions of (RC[sub 5]H[sub 4])[sub 3]UCl with t-BuLi (R = t-Bu, Me[sub 3]Si). Reactions of (MeC[sub 5]H[sub 4])[sub 3]U(t-Bu) with Lewis bases and fluorocarbons were studied. Analogous reaction chemistry between (RC[sub 5]H[sub 4])[sub 3]ThX systems and t-BuLi was also studied, and reactivity differences between U and Th are discussed. Synthesis of sterically crowded (RC[sub 5]H[sub 4])[sub 4]U compounds is next considered. Reaction of the trivalent (RC[sub 5]H[sub 4])[sub 3]U with (RC[sub 5]H[sub 4])[sub 2]Hg results in formation of (RC[sub 5]H[sub 4])[sub 4]U. Steric congestion, cyclopentadienyl ligand exchange, and electron transfer are discussed. (DLC)

  2. Tris(Cyclopentadienyl)Uranium-t-Butyl: Synthesis, reactions, and mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Weydert, Marc [Univ. of California, Berkeley, CA (United States)

    1993-04-01

    Compounds (RC5H4)3U(t-Bu) were prepared for R = H, Me, Et. Their decomposition products in aromatic solvents are consistent with a radical decomposition pathway induced by solvent-assisted U-C bond homolysis. NMR was used to study the reactions of (RC5H4)3UCl with t-BuLi (R = t-Bu, Me3Si). Reactions of (MeC5H4)3U(t-Bu) with Lewis bases and fluorocarbons were studied. Analogous reaction chemistry between (RC5H4)3ThX systems and t-BuLi was also studied, and reactivity differences between U and Th are discussed. Synthesis of sterically crowded (RC5H4)4U compounds is next considered. Reaction of the trivalent (RC5H4)3U with (RC5H4)2Hg results in formation of (RC5H4)4U. Steric congestion, cyclopentadienyl ligand exchange, and electron transfer are discussed. (DLC)

  3. Reaction mechanism of O-acylhydroxamate with cysteine proteases

    Indian Academy of Sciences (India)

    WINTEC

    more stable than the reactant and hence the reaction enthalpy is found to be exothermic. ... healing, fertilization, cell differentiation and growth, ... to lower the side effects of drug administration. Since ... tozoa and plants. ... give turnover products or could produce a stable ad- ...... be due to the hydrolysis with water molecule.

  4. Iron Contamination Mechanism and Reaction Performance Research on FCC Catalyst

    Directory of Open Access Journals (Sweden)

    Zhaoyong Liu

    2015-01-01

    Full Text Available FCC (Fluid Catalytic Cracking catalyst iron poisoning would not only influence units’ product slate; when the poisoning is serious, it could also jeopardize FCC catalysts’ fluidization in reaction-regeneration system and further cause bad influences on units’ stable operation. Under catalytic cracking reaction conditions, large amount of iron nanonodules is formed on the seriously iron contaminated catalyst due to exothermic reaction. These nodules intensify the attrition between catalyst particles and generate plenty of fines which severely influence units’ smooth running. A dense layer could be formed on the catalysts’ surface after iron contamination and the dense layer stops reactants to diffuse to inner structures of catalyst. This causes extremely negative effects on catalyst’s heavy oil conversion ability and could greatly cut down gasoline yield while increasing yields of dry gas, coke, and slurry largely. Research shows that catalyst’s reaction performance would be severely deteriorated when iron content in E-cat (equilibrium catalyst exceeds 8000 μg/g.

  5. Mechanisms in adverse reactions to food. The ear

    DEFF Research Database (Denmark)

    Høst, A

    1995-01-01

    Otitis media with effusion is rarely caused by allergy to food. Allergic inflammation in the nasal mucosa, mainly due to IgE-mediated reactions to foods, may cause eustachian tube dysfunction and subsequent otitis media with effusion. Inflammatory mediators from the nasal mucosa transported via...

  6. Coupling Effect between Mechanical Loading and Chemical Reactions

    Czech Academy of Sciences Publication Activity Database

    Klika, Václav; Maršík, František

    2009-01-01

    Roč. 113, č. 44 (2009), s. 14689-14697 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GA106/08/0557 Institutional research plan: CEZ:AV0Z20760514 Keywords : coupling * dynamic loading * reaction kinetics Subject RIV: FI - Traumatology, Orthopedics Impact factor: 3.471, year: 2009

  7. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation.

    Science.gov (United States)

    Sun, Jian; Zhang, Qing; Schlick, Tamar

    2005-06-07

    Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agreement with hydrodynamic measurements and suggest that the array adopts highly irregular 3D zig-zag conformations at high (physiological) salt concentrations and transitions into the extended "beads-on-a-string" conformation at low salt. Energy analyses indicate that the repulsion among linker DNA leads to this extended form, whereas internucleosome attraction drives the folding at high salt. The balance between these two contributions determines the salt-dependent condensation. Importantly, the internucleosome and linker DNA-nucleosome attractions require histone tails; we find that the H3 tails, in particular, are crucial for stabilizing the moderately folded fiber at physiological monovalent salt.

  8. Unified connected theory of few-body reaction mechanisms in N-body scattering theory

    Science.gov (United States)

    Polyzou, W. N.; Redish, E. F.

    1978-01-01

    A unified treatment of different reaction mechanisms in nonrelativistic N-body scattering is presented. The theory is based on connected kernel integral equations that are expected to become compact for reasonable constraints on the potentials. The operators T/sub +-//sup ab/(A) are approximate transition operators that describe the scattering proceeding through an arbitrary reaction mechanism A. These operators are uniquely determined by a connected kernel equation and satisfy an optical theorem consistent with the choice of reaction mechanism. Connected kernel equations relating T/sub +-//sup ab/(A) to the full T/sub +-//sup ab/ allow correction of the approximate solutions for any ignored process to any order. This theory gives a unified treatment of all few-body reaction mechanisms with the same dynamic simplicity of a model calculation, but can include complicated reaction mechanisms involving overlapping configurations where it is difficult to formulate models.

  9. Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity.

    Directory of Open Access Journals (Sweden)

    Andrey Alexeyenko

    2010-05-01

    Full Text Available In order to generate hypotheses regarding the mechanisms by which 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin causes toxicity, we analyzed global gene expression changes in developing zebrafish embryos exposed to this potent toxicant in the context of a dynamic gene network. For this purpose, we also computationally inferred a zebrafish (Danio rerio interactome based on orthologs and interaction data from other eukaryotes.Using novel computational tools to analyze this interactome, we distinguished between dioxin-dependent and dioxin-independent interactions between proteins, and tracked the temporal propagation of dioxin-dependent transcriptional changes from a few genes that were altered initially, to large groups of biologically coherent genes at later times. The most notable processes altered at later developmental stages were calcium and iron metabolism, embryonic morphogenesis including neuronal and retinal development, a variety of mitochondria-related functions, and generalized stress response (not including induction of antioxidant genes. Within the interactome, many of these responses were connected to cytochrome P4501A (cyp1a as well as other genes that were dioxin-regulated one day after exposure. This suggests that cyp1a may play a key role initiating the toxic dysregulation of those processes, rather than serving simply as a passive marker of dioxin exposure, as suggested by earlier research.Thus, a powerful microarray experiment coupled with a flexible interactome and multi-pronged interactome tools (which are now made publicly available for microarray analysis and related work suggest the hypothesis that dioxin, best known in fish as a potent cardioteratogen, has many other targets. Many of these types of toxicity have been observed in mammalian species and are potentially caused by alterations to cyp1a.

  10. A DFT study on the mechanisms for the cycloaddition reactions between 1-aza-2-azoniaallene cations and acetylenes.

    Science.gov (United States)

    Wang, Jing-mei; Li, Zhi-ming; Wang, Quan-rui; Tao, Feng-gang

    2013-01-01

    The mechanisms of cycloaddition reactions between 1-aza-2-azoniaallene cations 1 and acetylenes 2 have been investigated using the global electrophilicity and nucleophilicity of the corresponding reactants as global reactivity indexes defined within the conceptual density functional theory. The reactivity and regioselectivity of these reactions were predicted by analysis of the energies, geometries, and electronic nature of the transition state structures. The theoretical results revealed that the reaction features a tandem process: an ionic 1,3-dipolar cycloaddition to produce the cycloadducts 3 H-pyrazolium salts 3 followed by a [1,2]-shift affording the thermodynamically more stable adducts 4 or 5. The mechanism of the cycloaddition reactions can be described as an asynchronous concerted pathway with reverse electron demand. The model reaction has also been investigated at the QCISD/6-31++G(d,p) and CCSD(T)/6-31++G(d,p)//B3LYP/6-31++G(d,p) levels as well as by the DFT. The polarizable continuum model, at the B3LYP/6-31++G(d,p) level of theory, was used to study solvent effects on all the studied reactions. In solvent dichloromethane, all the initial cycloadducts 3 were obtained via direct ionic process as the result of the solvent effect. The consecutive [1,2]-shift reaction, in which intermediates 3 are rearranged to the five-membered heterocycles 4/5, is proved to be a kinetically controlled reaction, and the regioselectivity can be modulated by varying the migrant. The LOL function and RDG function based on localized electron analysis were used to analysis the covalent bond and noncovalent interactions in order to unravel the mechanism of the title reactions.

  11. Oxidative Dehydrogenation on Nanocarbon: Insights into the Reaction Mechanism and Kinetics via in Situ Experimental Methods.

    Science.gov (United States)

    Qi, Wei; Yan, Pengqiang; Su, Dang Sheng

    2018-03-20

    Sustainable and environmentally benign catalytic processes are vital for the future to supply the world population with clean energy and industrial products. The replacement of conventional metal or metal oxide catalysts with earth abundant and renewable nonmetallic materials has attracted considerable research interests in the field of catalysis and material science. The stable and efficient catalytic performance of nanocarbon materials was discovered at the end of last century, and these materials are considered as potential alternatives for conventional metal-based catalysts. With its rapid development in the past 20 years, the research field of carbon catalysis has been experiencing a smooth transition from the discovery of novel nanocarbon materials or related new reaction systems to the atomistic-level mechanistic understanding on the catalytic process and the subsequent rational design of the practical catalytic reaction systems. In this Account, we summarize the recent progress in the kinetic and mechanistic studies on nanocarbon catalyzed alkane oxidative dehydrogenation (ODH) reactions. The paper attempts to extract general concepts and basic regularities for carbon catalytic process directing us on the way for rational design of novel efficient metal-free catalysts. The nature of the active sites for ODH reactions has been revealed through microcalorimetric analysis, ambient pressure X-ray photoelectron spectroscopy (XPS) measurement, and in situ chemical titration strategies. The detailed kinetic analysis and in situ catalyst structure characterization suggests that carbon catalyzed ODH reactions involve the redox cycles of the ketonic carbonyl-hydroxyl pairs, and the key physicochemical parameters (activation energy, reaction order, and rate/equilibrium constants, etc.) of the carbon catalytic systems are proposed and compared with conventional transition metal oxide catalysts. The proposal of the intrinsic catalytic activity (TOF) provides the

  12. Multilevel Quantum Mechanics Theories and Molecular Mechanics Calculations of the Cl- + CH3I Reaction in Water.

    Science.gov (United States)

    Liu, Peng; Li, Chen; Wang, Dunyou

    2017-10-19

    The Cl - + CH 3 I → CH 3 Cl + I - reaction in water was studied using combined multilevel quantum mechanism theories and molecular mechanics with an explicit water solvent model. The study shows a significant influence of aqueous solution on the structures of the stationary points along the reaction pathway. A detailed, atomic-level evolution of the reaction mechanism shows a concerted one-bond-broken and one-bond-formed mechanism, as well as a synchronized charge-transfer process. The potentials of mean force calculated with the CCSD(T) and DFT treatments of the solute produce a free activation barrier at 24.5 and 19.0 kcal/mol, respectively, which agrees with the experimental one at 22.0 kcal/mol. The solvent effects have also been quantitatively analyzed: in total, the solvent effects raise the activation energy by 20.2 kcal/mol, which shows a significant impact on this reaction in water.

  13. Nuclear reaction mechanisms. Progress report, June 1976--July 1977

    Energy Technology Data Exchange (ETDEWEB)

    Blann, M.

    1977-01-01

    Research under the subject contract is on heavy ion induced reactions, both on experimental measurement and theoretical interpretation. Measurements have included determination of elastic scattering, evaporation residue, fission, quasi elastic and deep inelastic scattering cross sections. From these data we have extracted information on fusion barrier heights and radii, nucleus-nucleus potentials and fission parameterizations at high angular momenta. We have started investigating influence of excitation energies on inverse cross sections and of precompound decay in heavy ion reactions, and have investigated multidimensional potential energy surfaces for heavy ion collisions. Work which has been published is listed in the Publications Section; work not yet published and/or in progress is discussed herein.

  14. Nuclear reaction mechanisms. Progress report, June 1976--July 1977

    International Nuclear Information System (INIS)

    Blann, M.

    1977-01-01

    Research under the subject contract is on heavy ion induced reactions, both on experimental measurement and theoretical interpretation. Measurements have included determination of elastic scattering, evaporation residue, fission, quasi elastic and deep inelastic scattering cross sections. From these data we have extracted information on fusion barrier heights and radii, nucleus-nucleus potentials and fission parameterizations at high angular momenta. We have started investigating influence of excitation energies on inverse cross sections and of precompound decay in heavy ion reactions, and have investigated multidimensional potential energy surfaces for heavy ion collisions. Work which has been published is listed in the Publications Section; work not yet published and/or in progress is discussed herein

  15. Illustration of reaction mechanism in polyatomic systems via computer movies

    International Nuclear Information System (INIS)

    Raff, L.M.

    1974-01-01

    The CD 4 + T* systems is suited for classroom illustration of reaction dynamics. Questions about the system can be illustrated by reducing selected many-body trajectories to a 16 mm color movie that represents the six-body motion in projected coordinates. Such a movie has been produced for this system. The production procedure used is reported, and a detailed description of the contents of the movie is given. (U.S.)

  16. On the mechanism of photocatalytic reactions with eosin Y

    OpenAIRE

    Majek, Michal; Filace, Fabiana; von Wangelin, Axel Jacobi

    2014-01-01

    Summary A combined spectroscopic, synthetic, and apparative study has allowed a more detailed mechanistic rationalization of several recently reported eosin Y-catalyzed aromatic substitutions at arenediazonium salts. The operation of rapid acid–base equilibria, direct photolysis pathways, and radical chain reactions has been discussed on the basis of pH, solvent polarity, lamp type, absorption properties, and quantum yields. Determination of the latter proved to be an especially valuable tool...

  17. Chlorination of tramadol: Reaction kinetics, mechanism and genotoxicity evaluation.

    Science.gov (United States)

    Cheng, Hanyang; Song, Dean; Chang, Yangyang; Liu, Huijuan; Qu, Jiuhui

    2015-12-01

    Tramadol (TRA) is one of the most detected analgesics in environmental matrices, and it is of high significance to study the reactivity of TRA during chlorination considering its potential toxicity to the environment. The chlorine/TRA reaction is first order with respect to the TRA concentration, and a combination of first-order and second-order with respect to chlorine concentration. The pH dependence of the observed rate constants (kobs) showed that the TRA oxidation reactivity increased with increasing pH. kobs can be quantitatively described by considering all active species including Cl2, Cl2O and HOCl, and the individual rate constants of HOCl/TRA(0), HOCl/TRAH(+), Cl2/TRA and Cl2O/TRA reactions were calculated to be (2.61±0.29)×10(3)M(-1)s(-1), 14.73±4.17M(-1)s(-1), (3.93±0.34)×10(5)M(-1)s(-1) and (5.66±1.83)×10(6)M(-1)s(-1), respectively. Eleven degradation products were detected with UPLC-Q-TOF-MS, and the corresponding structures of eight products found under various pH conditions were proposed. The amine group was proposed to be the initial attack site under alkaline pH conditions, where reaction of the deprotonated amine group with HOCl is favorable. Under acidic and neutral pH conditions, however, two possible reaction pathways were proposed. One is an electrophilic substitution on the aromatic ring, and another is an electrophilic substitution on the nitrogen, leading to an N-chlorinated intermediate, which can be further oxidized. Finally, the SOS/umu test showed that the genotoxicity of TRA chlorination products increased with increasing dosage of chlorine, which was mostly attributed to the formation of some chlorine substitution products. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Novel error propagation approach for reducing H2S/O2 reaction mechanism

    International Nuclear Information System (INIS)

    Selim, H.; Gupta, A.K.; Sassi, M.

    2012-01-01

    A reduction strategy of hydrogen sulfide/oxygen reaction mechanism is conducted to simplify the detailed mechanism. Direct relation graph and error propagation methodology (DRGEP) has been used. A novel approach of direct elementary reaction error (DERE) has been developed in this study. The developed approach allowed for further reduction of the reaction mechanism. The reduced mechanism has been compared with the detailed mechanism under different conditions to emphasize its validity. The results obtained from the resulting reduced mechanism showed good agreement with that from the detailed mechanism. However, some discrepancies have been found for some species. Hydrogen and oxygen mole fractions showed the largest discrepancy of all combustion products. The reduced mechanism was also found to be capable of tracking the changes that occur in chemical kinetics through the change in reaction conditions. A comparison on the ignition delay time obtained from the reduced mechanism and previous experimental data showed good agreement. The reduced mechanism was used to track changes in mechanistic pathways of Claus reactions with the reaction progress.

  19. Development of a robust and compact kerosene–diesel reaction mechanism for diesel engines

    International Nuclear Information System (INIS)

    Tay, Kun Lin; Yang, Wenming; Mohan, Balaji; An, Hui; Zhou, Dezhi; Yu, Wenbin

    2016-01-01

    Highlights: • An approach is used to develop a robust kerosene–diesel reaction mechanism. • Ignition delay of the kerosene sub-mechanism is well validated with experiments. • The kerosene sub-mechanism reproduces the flame lift-off lengths of Jet-A reasonably well. • The kerosene sub-mechanism performs reasonably well under engine conditions. - Abstract: The use of kerosene fuels in internal combustion engines is getting more widespread. The North Atlantic Treaty Organization military is pushing for the use of a single fuel on the battlefield in order to reduce logistical issues. Moreover, in some countries, fuel adulteration is a serious matter where kerosene is blended with diesel and used in diesel engines. So far, most investigations done regarding the use of kerosene fuels in diesel engines are experimental and there is negligible simulation work done in this area possibly because of the lack of a robust and compact kerosene reaction mechanism. This work focuses on the development of a small but reliable kerosene–diesel reaction mechanism, suitable to be used for diesel engine simulations. The new kerosene–diesel reaction mechanism consists only of 48 species and 152 reactions. Furthermore, the kerosene sub-mechanism in this new mechanism is well validated for its ignition delay times and has proven to replicate kerosene combustion well in a constant volume combustion chamber and an optical engine. Overall, this new kerosene–diesel reaction mechanism is proven to be robust and practical for diesel engine simulations.

  20. On the reaction of the nitroso group with olefins. Mechanisms of ene reactions

    International Nuclear Information System (INIS)

    Seymour, C.A.; Greene, F.D.

    1982-01-01

    Intra- and intermolecular isotope effects point to a two-step process for the reaction of pentafluoronitrosobenzene with tetramethylethylene to afford the ene product, rate-determining formation of an intermediate (for which the arizidine N-oxide is suggested) followed by C-H (or C-D) cleavage to the ene product

  1. Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics

    NARCIS (Netherlands)

    De Wispelaere, K.; Ensing, B.; Ghysels, A.; Meijer, E.J.; van Van Speybroeck, V.

    2015-01-01

    The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first

  2. Eletromagnetic radiation and the mechanical reactions arising from it

    CERN Document Server

    Schott, G A

    1912-01-01

    Fundamental equations of the electron theory ; transformation of the potentials ; other types of solution ; physical interpretation of the solutions obtained ; illustrative examples ; remarks on the solutions obtained and on the methods of calculating the potentials in general ; periodic motions ; on the distant field due to a moving charge ; pseudo-periodic and aperiodic motions ; on the field near the orbit of a moving charge or group ; the mechanical forces acting on electric charges in motion ; the motion of groups of electric charges ; on the Doppler effect ; on the disturbed motion of a ring of electrons ; on the field close to a point charge in motion ; the mechanical force exterted by an electron on itself ; the mechanical explanation of the electron ; the mechanics of the Lorentz electron ; problems illustrative of the motion of the Lorentz electron.

  3. Multi-nucleon transfer: a probe to investigate the reaction mechanism around the barrier

    International Nuclear Information System (INIS)

    Mandal, Samit K.

    2014-01-01

    The investigation of multi-nucleon transfer mechanism offers valuable information on the pairing interactions that enhance the transfer of nucleon pairs across heavy ions involved in the reaction. These reactions are also a useful tool to study exotic nuclei far from the stability line, which can be explored with the new generation radioactive beam facility. In this talk, multi-nucleon transfer reaction mechanisms between heavy ions and their effect on the reaction dynamics around the coulomb barrier energies have been discussed. Experimental results will be presented with a semi classical description of multi nucleon transfer reaction calculation. One and two nucleon transfer cross sections reproduced using a quantum mechanical coupled channel calculations will also be discussed. A feasibility of investigation of multi-nucleon transfer mechanism to explore the pairing correlation at moderate spin states with radioactive beams will be discussed. (author)

  4. Role of hydrogen bonds in the reaction mechanism of chalcone isomerase.

    Science.gov (United States)

    Jez, Joseph M; Bowman, Marianne E; Noel, Joseph P

    2002-04-23

    In flavonoid, isoflavonoid, and anthocyanin biosynthesis, chalcone isomerase (CHI) catalyzes the intramolecular cyclization of chalcones into (S)-flavanones with a second-order rate constant that approaches the diffusion-controlled limit. The three-dimensional structures of alfalfa CHI complexed with different flavanones indicate that two sets of hydrogen bonds may possess critical roles in catalysis. The first set of interactions includes two conserved amino acids (Thr48 and Tyr106) that mediate a hydrogen bond network with two active site water molecules. The second set of hydrogen bonds occurs between the flavanone 7-hydroxyl group and two active site residues (Asn113 and Thr190). Comparison of the steady-state kinetic parameters of wild-type and mutant CHIs demonstrates that efficient cyclization of various chalcones into their respective flavanones requires both sets of contacts. For example, the T48A, T48S, Y106F, N113A, and T190A mutants exhibit 1550-, 3-, 30-, 7-, and 6-fold reductions in k(cat) and 2-3-fold changes in K(m) with 4,2',4'-trihydroxychalcone as a substrate. Kinetic comparisons of the pH-dependence of the reactions catalyzed by wild-type and mutant enzymes indicate that the active site hydrogen bonds contributed by these four residues do not significantly alter the pK(a) of the intramolecular cyclization reaction. Determinations of solvent kinetic isotope and solvent viscosity effects for wild-type and mutant enzymes reveal a change from a diffusion-controlled reaction to one limited by chemistry in the T48A and Y106F mutants. The X-ray crystal structures of the T48A and Y106F mutants support the assertion that the observed kinetic effects result from the loss of key hydrogen bonds at the CHI active site. Our results are consistent with a reaction mechanism for CHI in which Thr48 polarizes the ketone of the substrate and Tyr106 stabilizes a key catalytic water molecule. Hydrogen bonds contributed by Asn113 and Thr190 provide additional

  5. A mathematical analysis of Prx2-STAT3 disulfide exchange rate constants for a bimolecular reaction mechanism.

    Science.gov (United States)

    Langford, Troy F; Deen, William M; Sikes, Hadley D

    2018-03-22

    Appreciation of peroxiredoxins as the major regulators of H 2 O 2 concentrations in human cells has led to a new understanding of redox signaling. In addition to their status as the primary reducers of H 2 O 2 to water, the oxidized peroxiredoxin byproduct of this reaction has recently been shown capable of participation in H 2 O 2 -mediated signaling pathways through disulfide exchange reactions with the transcription factor STAT3. The dynamics of peroxidase-transcription factor disulfide exchange reactions have not yet been considered in detail with respect to how these reactions fit into the larger network of competing reactions in human cells. In this study, we used a kinetic model of oxidation and reduction reactions related to H 2 O 2 metabolism in the cytosol of human cells to study the dynamics of peroxiredoxin-2 mediated oxidation of the redox-regulated transcription factor STAT3. In combination with previously reported experimental data, the model was used to estimate the rate coefficient of a biomolecular reaction between Prx2 and STAT3 for two sets of assumptions that constitute lower and upper bound cases. Using these estimates, we calculated the relative rates of the reaction of oxidized peroxiredoxin-2 and STAT3 and other competing reactions in the cytosol. These calculations revealed that peroxiredoxin-2-mediated oxidation of STAT3 likely occurs at a much slower rate than competing reactions in the cytosol. This analysis suggests the existence of more complex mechanisms, potentially involving currently unknown protein-protein recognition partners, which facilitate disulfide exchange reactions between peroxiredoxin-2 and STAT3. Copyright © 2018 Elsevier Inc. All rights reserved.

  6. Mechanism to preserve phrenic nerve function during photosensitization reaction: drug uptake and photosensitization reaction effect on electric propagation

    Science.gov (United States)

    Takahashi, Haruka; Hamada, Risa; Ogawa, Emiyu; Arai, Tsunenori

    2018-02-01

    To study a mechanism of phrenic nerve preservation phenomena during a photosensitization reaction, we investigated an uptake of talaporfin sodium and photosensitization reaction effect on an electric propagation. Right phrenic nerve was completely preserved after superior vena cava isolations using the photosensitization reaction in canine animal experiments, in spite of adjacent myocardium was electrically blocked. We predicted that low drug uptake and/or low photosensitization reaction effect on the nerve might be a mechanism of that phenomena. To investigate uptake to various nerve tissue, a healthy extracted crayfish ventral nerve cord and an extracted porcine phrenic nerve were immersed in 20 μg/ml talaporfin sodium solution for 0-240 min. The mean talaporfin sodium fluorescence brightness increased depending on the immersion time. This brightness saturated around the immersion time of 120 min. We found that talaporfin sodium uptake inside the perineurium which directly related to the electric propagation function was lower than that of outside in the porcine phrenic nerve. To investigate photosensitization reaction effect on electric propagation, the crayfish nerve was immersed into the same solution for 15 min and irradiated by a 663 nm laser light with 120 mW/cm2. Since we found the action potential disappeared when the irradiation time was 25-65 s, we consider that the crayfish nerve does not tolerant to the photosensitization reaction on electric propagation function at atmospheric pressure. From these results, we think that the low uptake of talaporfin sodium inside the perineurium and low oxygen partial pressure of nerve might be the possible mechanism to preserve phrenic nerve in vivo.

  7. Derivation of the reduced reaction mechanisms of ozone depletion events in the Arctic spring by using concentration sensitivity analysis and principal component analysis

    Directory of Open Access Journals (Sweden)

    L. Cao

    2016-12-01

    Full Text Available The ozone depletion events (ODEs in the springtime Arctic have been investigated since the 1980s. It is found that the depletion of ozone is highly associated with an auto-catalytic reaction cycle, which involves mostly the bromine-containing compounds. Moreover, bromide stored in various substrates in the Arctic such as the underlying surface covered by ice and snow can be also activated by the absorbed HOBr. Subsequently, this leads to an explosive increase of the bromine amount in the troposphere, which is called the “bromine explosion mechanism”. In the present study, a reaction scheme representing the chemistry of ozone depletion and halogen release is processed with two different mechanism reduction approaches, namely, the concentration sensitivity analysis and the principal component analysis. In the concentration sensitivity analysis, the interdependence of the mixing ratios of ozone and principal bromine species on the rate of each reaction in the ODE mechanism is identified. Furthermore, the most influential reactions in different time periods of ODEs are also revealed. By removing 11 reactions with the maximum absolute values of sensitivities lower than 10 %, a reduced reaction mechanism of ODEs is derived. The onsets of each time period of ODEs in simulations using the original reaction mechanism and the reduced reaction mechanism are identical while the maximum deviation of the mixing ratio of principal bromine species between different mechanisms is found to be less than 1 %. By performing the principal component analysis on an array of the sensitivity matrices, the dependence of a particular species concentration on a combination of the reaction rates in the mechanism is revealed. Redundant reactions are indicated by principal components corresponding to small eigenvalues and insignificant elements in principal components with large eigenvalues. Through this investigation, aside from the 11 reactions identified as

  8. Phenomenological description of selected elementary chemical reaction mechanisms: An information-theoretic study

    International Nuclear Information System (INIS)

    Esquivel, R.O.; Flores-Gallegos, N.; Iuga, C.; Carrera, E.M.; Angulo, J.C.; Antolin, J.

    2010-01-01

    The information-theoretic description of the course of two elementary chemical reactions allows a phenomenological description of the chemical course of the hydrogenic abstraction and the S N 2 identity reactions by use of Shannon entropic measures in position and momentum spaces. The analyses reveal their synchronous/asynchronous mechanistic behavior.

  9. Investigation of the kinetics and mechanism of the glycerol chlorination reaction using gas chromatography–mass spectrometry

    Directory of Open Access Journals (Sweden)

    JUN WANG

    2010-01-01

    Full Text Available As a primary by-product in biodiesel production, glycerol can be used to prepare an important fine chemical, epichlorohydrin, by the glycerol chlorination reaction. Although this process has been applied in industrial production, unfortunately, less attention has been paid to the analysis and separation of the compounds in the glycerol chlorination products. In this study, a convenient and accurate method to determine the products in glycerol chlorination reaction was established and based on the results the kinetic mechanism of the reaction was investigated. The structure of main products, including 1,3--dichloropropan-2-ol, 2,3-dichloropropan-1-ol, 3-chloro-1,2-propanediol, 2-chloro-1,3-propanediol and glycerol was ascertained by gas chromatography–mass spectrometry and the isomers of the products were distinguished. Apidic acid was considered as the best catalyst because of its excellent catalytic effect and high boiling point. The mechanism of the glycerol chlorination reaction was proposed and a new kinetic model was developed. Kinetic equations of the process in the experimental range were obtained by data fitting and the activation energies of each tandem reaction were 30.7, 41.8, 29.4 and 49.5 kJ mol-1, respectively. This study revealed the process and mechanism of the kinetics and provides the theoretical basis for engineering problems.

  10. Heterogeneity of ductular reactions in adult rat and human liver revealed by novel expression of deleted in malignant brain tumor 1

    DEFF Research Database (Denmark)

    Bisgaard, H.C.; Holmskov, U.; Santoni-Rugiu, E.

    2002-01-01

    The regenerative capacity of mammalian adult liver reflects the ability of a number of cell populations within the hepatic lineage to take action. Limited information is available regarding factors and mechanisms that determine the specific lineage level at which liver cells contribute to liver......), were specifically associated with the emergence of ductular (oval) cell populations in injured liver. Subsequent cloning and characterization of the rat DMBT1 homologue revealed a highly inducible expression in ductular reactions composed of transit-amplifying ductular (oval) cells, but not in ductular...... reactions after ligation of the common bile duct. In human liver diseases, DMBT1 was expressed in ductular reactions after infection with hepatitis B and acetaminophen intoxication, but not in primary biliary cirrhosis, primary sclerosing cholangitis, and obstruction of the large bile duct. The expression...

  11. Nuclear and hadronic reaction mechanisms producing spin asymmetry

    Indian Academy of Sciences (India)

    We briefly review concept of the quark recombination (QRC) model and a general success of the model. To solve the existing problem, so called anomalous spin observables, in the high energy hyperon spin phenomena, we propose a mechanism; the primarily produced quarks, which are predominantly and quarks, ...

  12. Reaction kinetics and mechanism of magnetic field effects in cryptochrome

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Schulten, Klaus

    2012-01-01

    Creatures as varied as mammals, fish, insects, reptiles, and birds have an intriguing sixth sense that allows them to orient themselves in the Earth's magnetic field. Despite decades of study, the physical basis of this magnetic sense remains elusive. A likely mechanism is furnished by magnetically...

  13. Nuclear and hadronic reaction mechanisms producing spin asymmetry

    Indian Academy of Sciences (India)

    naka

    are predominantly u and d quarks, act as the leading partons to form the hyperons. Extension of the quark recombination concept with this mechanism is successful in providing a good account of the anomalous spin observables. Another kind of anomaly, the non-zero analysing power and spin depolarization in the A ...

  14. What Protein Charging (and Supercharging) Reveal about the Mechanism of Electrospray Ionization

    Science.gov (United States)

    Ogorzalek Loo, Rachel R.; Lakshmanan, Rajeswari; Loo, Joseph A.

    2014-10-01

    Understanding the charging mechanism of electrospray ionization is central to overcoming shortcomings such as ion suppression or limited dynamic range, and explaining phenomena such as supercharging. Towards that end, we explore what accumulated observations reveal about the mechanism of electrospray. We introduce the idea of an intermediate region for electrospray ionization (and other ionization methods) to account for the facts that solution charge state distributions (CSDs) do not correlate with those observed by ESI-MS (the latter bear more charge) and that gas phase reactions can reduce, but not increase, the extent of charging. This region incorporates properties (e.g., basicities) intermediate between solution and gas phase. Assuming that droplet species polarize within the high electric field leads to equations describing ion emission resembling those from the equilibrium partitioning model. The equations predict many trends successfully, including CSD shifts to higher m/z for concentrated analytes and shifts to lower m/z for sprays employing smaller emitter opening diameters. From this view, a single mechanism can be formulated to explain how reagents that promote analyte charging ("supercharging") such as m-NBA, sulfolane, and 3-nitrobenzonitrile increase analyte charge from "denaturing" and "native" solvent systems. It is suggested that additives' Brønsted basicities are inversely correlated to their ability to shift CSDs to lower m/z in positive ESI, as are Brønsted acidities for negative ESI. Because supercharging agents reduce an analyte's solution ionization, excess spray charge is bestowed on evaporating ions carrying fewer opposing charges. Brønsted basicity (or acidity) determines how much ESI charge is lost to the agent (unavailable to evaporating analyte).

  15. Ambiguities in the reaction mechanism for (e,e'N)

    International Nuclear Information System (INIS)

    Forest, T. de Jr.

    1984-01-01

    The primary motivation for performing quasi-elastic (e,e'N) experiments revolves around the plane wave impulse approximation (PWIA) description of this reaction. Since the PWIA is an approximation, corrections are necessary in practice in order to extract the desired nuclear structure. Unless one understands the physics behind these corrections this introduces ambiguities. In fact the PWIA itself is an ambiguous prescription since a 'free' off-shell cross section is not a well-defined concept. It is these ambiguities which are discussed in this talk. Most of the paper is devoted to the ambiguities associated with the electromagnetic interaction. The author concentrates on four topics: (1) the interaction of the electron with the nucleus in general; (2) ambiguities in the application of the impulse approximation; (3) the sigma-omega model; and (4) the Coulomb sum rule. (Auth.)

  16. Analysis of reaction products formed in the gas phase reaction of E,E-2,4-hexadienal with atmospheric oxidants: Reaction mechanisms and atmospheric implications

    Science.gov (United States)

    Colmenar, I.; Martin, P.; Cabañas, B.; Salgado, S.; Martinez, E.

    2018-03-01

    An analysis of reaction products for the reaction of E,E-2,4-hexadienal with chlorine atoms (Cl) and OH and NO3 radicals has been carried out at the first time with the aim of obtaining a better understanding of the tropospheric reactivity of α,β-unsaturated carbonyl compounds. Fourier Transform Infrared (FTIR) spectroscopy and Gas Chromatography-Mass Spectrometry with a Time of Flight detector (GC-TOFMS) were used to carry out the qualitative and/or quantitative analyses. Reaction products in gas and particulate phase were observed from the reactions of E,E-2,4- hexadienal with all oxidants. E/Z-Butenedial and maleic anhydride were the main products identified in gas phase. E-butenedial calculated molar yield ranging from 4 to 10%. A significant amount of multifunctional compounds (chloro and hydroxy carbonyls) was identified. These compounds could be formed in particulate phase explaining the ∼90% of unaccounted carbon in gas phase. The reaction with Cl atoms in the presence of NOx with a long reaction time gave Peroxy Acetyl Nitrate (PAN) as an additional product, which is known for being an important specie in the generation of the photochemical smog. Nitrated compounds were the major organic products from the reaction with the NO3 radical. Based on the identified products, the reaction mechanisms have been proposed. In these mechanisms a double bond addition of the atmospheric oxidant at C4/C5 of E,E-2,4-hexadienal is the first step for tropospheric degradation.

  17. Insights into the Reaction Mechanism of Aromatic Ring Cleavage by Homogentisate Dioxygenase: A Quantum Mechanical/Molecular Mechanical Study.

    Science.gov (United States)

    Qi, Yue; Lu, Jiarui; Lai, Wenzhen

    2016-05-26

    To elucidate the reaction mechanism of the ring cleavage of homogentisate by homogentisate dioxygenase, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out by using two systems in different protonation states of the substrate C2 hydroxyl group. When the substrate C2 hydroxyl group is ionized (the ionized pathway), the superoxo attack on the substrate is the rate-limiting step in the catalytic cycle, with a barrier of 15.9 kcal/mol. Glu396 was found to play an important role in stabilizing the bridge species and its O-O cleavage product by donating a proton via a hydrogen-bonded water molecule. When the substrate C2 hydroxyl group is not ionized (the nonionized pathway), the O-O bond cleavage of the bridge species is the rate-limiting step, with a barrier of 15.3 kcal/mol. The QM/MM-optimized geometries for the dioxygen and alkylperoxo complexes using the nonionized model (for the C2 hydroxyl group) are in agreement with the experimental crystal structures, suggesting that the C2 hydroxyl group is more likely to be nonionized.

  18. Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase

    NARCIS (Netherlands)

    Ridder, L.; Mulholland, A.; Rietjens, I.M.C.M.; Vervoort, J.

    1999-01-01

    The reaction pathway for the aromatic 3-hydroxylation of p-hydroxybenzoate by the reactive C4a-hydroperoxyflavin cofactor intermediate in p-hydroxybenzoate hydroxylase (PHBH) has been investigated by a combined quantum mechanical and molecular mechanical (QM/MM) method. A structural model for the

  19. Mechanism of the superior mechanical strength of nanometer-sized metal single crystals revealed

    KAUST Repository

    Afify, N. D.; Salem, H. G.; Yavari, A.; El Sayed, Tamer S.

    2013-01-01

    Clear understanding of the superior mechanical strength of nanometer-sized metal single crystals is required to derive advanced mechanical components retaining such superiority. Although high quality studies have been reported on nano

  20. Transparent Ethenylene-Bridged Polymethylsiloxane Aerogels: Mechanical Flexibility and Strength and Availability for Addition Reaction.

    Science.gov (United States)

    Shimizu, Taiyo; Kanamori, Kazuyoshi; Maeno, Ayaka; Kaji, Hironori; Doherty, Cara M; Nakanishi, Kazuki

    2017-05-09

    Transparent, low-density ethenylene-bridged polymethylsiloxane [Ethe-BPMS, O 2/2 (CH 3 )Si-CH═CH-Si(CH 3 )O 2/2 ] aerogels from 1,2-bis(methyldiethoxysilyl)ethene have successfully been synthesized via a sol-gel process. A two-step sol-gel process composed of hydrolysis under acidic conditions and polycondensation under basic conditions in a liquid surfactant produces a homogeneous pore structure based on cross-linked nanosized colloidal particles. Visible-light transmittance of the aerogels varies with the concentration of the base catalyst and reaches as high as 87% (at a wavelength of 550 nm for a 10 mm thick sample). Gelation and aging temperature strongly affect the deformation behavior of the resultant aerogels against uniaxial compression, and the obtained aerogels prepared at 80 °C show high elasticity after being unloaded. This highly resilient behavior is primarily derived from the rigidity of ethenylene groups, which is confirmed by a comparison with other aerogels with similar molecular structures, ethylene-bridged polymethylsiloxane and polymethylsilsesquioxane. Applicability of the addition reaction using a Diels-Alder reaction of benzocyclobutene has also been investigated, revealing that a successful addition takes place on the ethenylene linkings, which is verified using Raman and solid-state NMR spectroscopies. Insights into the effect of molecular structure on mechanical properties and the availability of surface functionalization provided in this study are important for realizing transparent aerogels with the desired functionality.

  1. Heterogeneous reaction mechanisms and kinetics relevant to the CVD of semiconductor materials

    Energy Technology Data Exchange (ETDEWEB)

    Creighton, J.R.; Coltrin, M.E.

    1994-03-01

    This report documents the state of the art in experimental and theoretical techniques for determining reaction mechanisms and chemical kinetics of heterogeneous reactions relevant to the chemical vapor deposition of semiconductor materials. It summarizes the most common ultra-high vacuum experimental techniques that are used and the types of rate information available from each. Several case studies of specific chemical systems relevant to the microelectronics industry are described. Theoretical methods for calculating heterogeneous reaction rate constants are also summarized.

  2. Interfacial mechanisms of heterogeneous Fenton reactions catalyzed by iron-based materials: A review.

    Science.gov (United States)

    He, Jie; Yang, Xiaofang; Men, Bin; Wang, Dongsheng

    2016-01-01

    The heterogeneous Fenton reaction can generate highly reactive hydroxyl radicals (OH) from reactions between recyclable solid catalysts and H2O2 at acidic or even circumneutral pH. Hence, it can effectively oxidize refractory organics in water or soils and has become a promising environmentally friendly treatment technology. Due to the complex reaction system, the mechanism behind heterogeneous Fenton reactions remains unresolved but fascinating, and is crucial for understanding Fenton chemistry and the development and application of efficient heterogeneous Fenton technologies. Iron-based materials usually possess high catalytic activity, low cost, negligible toxicity and easy recovery, and are a superior type of heterogeneous Fenton catalysts. Therefore, this article reviews the fundamental but important interfacial mechanisms of heterogeneous Fenton reactions catalyzed by iron-based materials. OH, hydroperoxyl radicals/superoxide anions (HO2/O2(-)) and high-valent iron are the three main types of reactive oxygen species (ROS), with different oxidation reactivity and selectivity. Based on the mechanisms of ROS generation, the interfacial mechanisms of heterogeneous Fenton systems can be classified as the homogeneous Fenton mechanism induced by surface-leached iron, the heterogeneous catalysis mechanism, and the heterogeneous reaction-induced homogeneous mechanism. Different heterogeneous Fenton systems catalyzed by characteristic iron-based materials are comprehensively reviewed. Finally, related future research directions are also suggested. Copyright © 2015. Published by Elsevier B.V.

  3. Development of a skeletal multi-component fuel reaction mechanism based on decoupling methodology

    International Nuclear Information System (INIS)

    Mohan, Balaji; Tay, Kun Lin; Yang, Wenming; Chua, Kian Jon

    2015-01-01

    Highlights: • A compact multi-component skeletal reaction mechanism was developed. • Combined bio-diesel and PRF mechanism was proposed. • The mechanism consists of 68 species and 183 reactions. • Well validated against ignition delay times, flame speed and engine results. - Abstract: A new coupled bio-diesel surrogate and primary reference fuel (PRF) oxidation skeletal mechanism has been developed. The bio-diesel surrogate sub-mechanism consists of oxidation sub-mechanisms of Methyl decanoate (MD), Methyl 9-decenoate (MD9D) and n-Heptane fuel components. The MD and MD9D are chosen to represent the saturated and unsaturated methyl esters respectively in bio-diesel fuels. Then, a reduced iso-Octane oxidation sub-mechanism is added to the bio-diesel surrogate sub-mechanism. Then, all the sub-mechanisms are integrated to a reduced C_2–C_3 mechanism, detailed H_2/CO/C_1 mechanism and reduced NO_x mechanism based on decoupling methodology. The final mechanism consisted of 68 species and 183 reactions. The mechanism was well validated with shock-tube ignition delay times, laminar flame speed and 3D engine simulations.

  4. Effect of compound nuclear reaction mechanism in 12C(6Li,d) reaction at sub-Coulomb energy

    Science.gov (United States)

    Mondal, Ashok; Adhikari, S.; Basu, C.

    2017-09-01

    The angular distribution of the 12C(6Li,d) reaction populating the 6.92 and 7.12 MeV states of 16O at sub-Coulomb energy (Ecm=3 MeV) are analysed in the framework of the Distorted Wave Born Approximation (DWBA). Recent results on excitation function measurements and backward angle angular distributions derive ANC for both the states on the basis of an alpha transfer mechanism. In the present work, we show that considering both forward and backward angle data in the analysis, the 7.12 MeV state at sub-Coulomb energy is populated from Compound nuclear process rather than transfer process. The 6.92 MeV state is however produced from direct reaction mechanism.

  5. Reaction mechanisms in 24.3 MeV/nucleon 238U induced reactions through a comprehensive study of fission

    International Nuclear Information System (INIS)

    Chbihi, A.; Galin; Guerreau, D.; Lewitowicz, M.; Morjean, M.; Pouthas, J.; Piasecki, E.; Kordyasz, A.; Iwanicki, J.; Jastrzebski, J.; Pienkowski, L.; Crema, E.; Gatty, B.; Jacquet, D.; Muchorowska, M.

    1994-01-01

    Nuclear reaction mechanisms for system characterized by very different asymmetries (U+C, Si, Ni, Au) have been investigated at 24.3 MeV/nucleon, using as observables both the fission products and the neutron multiplicity. It is clearly observed that the fusion process-whatever its completeness- can only occur with rather light target nuclei, indicating the persistence of potential energy effects much above the interaction barrier. (authors). 22 refs., 1 fig

  6. Complex nuclear-structure phenomena revealed from the nuclide production in fragmentation reactions

    International Nuclear Information System (INIS)

    Ricciardi, M.V.; Kelic, A.; Napolitani, P.; Schmidt, K.H.; Yordanov, O.; Ignatyuk, A.V.; Rejmund, F.

    2003-12-01

    Complex structural effects in the nuclide production from the projectile fragmentation of 1 A GeV 238 U nuclei in a titanium target are reported. The structure seems to be insensitive to the excitation energy induced in the reaction. This is in contrast to the prominent structural features found in nuclear fission and in transfer reactions, which gradually disappear with increasing excitation energy. Using the statistical model of nuclear reactions, relations to structural effects in nuclear binding and in the nuclear level density are demonstrated. (orig.)

  7. Development and validation of a reduced combined biodiesel–diesel reaction mechanism

    DEFF Research Database (Denmark)

    Ng, Hoon Kiat; Gan, Suyin; Ng, Jo-Han

    2013-01-01

    In this study, a compact combined biodiesel–diesel (CBD) reaction mechanism for diesel engine simulations is proposed through the combination of three component mechanisms using a chemical class-based approach. The proposed mechanism comprises the reaction mechanisms of methyl crotonate (MC...... to characterise the combustion of fossil diesel. Here, the MC and MB mechanisms are reduced before integrating with a compact n-heptane mechanism. CHEMKIN-PRO is used as the solver for the zero-dimensional, closed homogenous reactor with a constant volume in this study. In the first phase, the mechanisms of MC...... ranging from initial temperatures of 750–1350 K, pressures of 40–60 bar and equivalence ratios of 0.4–1.5. The mechanism is generally found to accurately predict the timing and duration of ID for the combustion of each surrogate fuel. This model is also shown to be feasible for use with multidimensional...

  8. Probing the reaction mechanism of IspH protein by x-ray structure analysis

    KAUST Repository

    Gräwert, Tobias

    2009-12-28

    Isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) represent the two central intermediates in the biosynthesis of isoprenoids. The recently discovereddeoxyxylulose 5-phosphate pathway generates a mixture of IPP and DMAPP in its final step by reductive dehydroxylation of 1-hydroxy-2-methyl- 2-butenyl 4-diphosphate. This conversion is catalyzed by IspH protein comprising a central iron-sulfur cluster as electron transfer cofactor in the active site. The five crystal structures of IspH in complex with substrate, converted substrate, products and PPi reported in this article provide unique insights into the mechanism of this enzyme. While IspH protein crystallizes with substrate bound to a [4Fe-4S] cluster, crystals of IspH in complex with IPP, DMAPP or inorganic pyrophosphate feature [3Fe-4S] clusters. The IspH:substrate complex reveals a hairpin conformation of the ligand with the C(1) hydroxyl group coordinated to the unique site in a [4Fe-4S] cluster of aconitase type. The resulting alkoxide complex is coupled to a hydrogen-bonding network, which serves as proton reservoir via a Thr167 proton relay. Prolonged x-ray irradiation leads to cleavage of the C(1)-O bond (initiated by reducing photo electrons). The data suggest a reaction mechanism involving a combination of Lewis-acid activation and proton coupled electron transfer. The resulting allyl radical intermediate can acquire a second electron via the iron-sulfur cluster. The reaction may be terminated by the transfer of a proton from the β-phosphate of the substrate to C(1) (affording DMAPP) or C(3) (affording IPP).

  9. Probing the reaction mechanism of IspH protein by x-ray structure analysis

    KAUST Repository

    Grä wert, Tobias; Span, Ingrid; Eisenreich, Wolfgang; Rohdich, Felix; Eppinger, Jö rg; Bacher, Adelbert; Groll, Michael

    2009-01-01

    Isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) represent the two central intermediates in the biosynthesis of isoprenoids. The recently discovereddeoxyxylulose 5-phosphate pathway generates a mixture of IPP and DMAPP in its final step by reductive dehydroxylation of 1-hydroxy-2-methyl- 2-butenyl 4-diphosphate. This conversion is catalyzed by IspH protein comprising a central iron-sulfur cluster as electron transfer cofactor in the active site. The five crystal structures of IspH in complex with substrate, converted substrate, products and PPi reported in this article provide unique insights into the mechanism of this enzyme. While IspH protein crystallizes with substrate bound to a [4Fe-4S] cluster, crystals of IspH in complex with IPP, DMAPP or inorganic pyrophosphate feature [3Fe-4S] clusters. The IspH:substrate complex reveals a hairpin conformation of the ligand with the C(1) hydroxyl group coordinated to the unique site in a [4Fe-4S] cluster of aconitase type. The resulting alkoxide complex is coupled to a hydrogen-bonding network, which serves as proton reservoir via a Thr167 proton relay. Prolonged x-ray irradiation leads to cleavage of the C(1)-O bond (initiated by reducing photo electrons). The data suggest a reaction mechanism involving a combination of Lewis-acid activation and proton coupled electron transfer. The resulting allyl radical intermediate can acquire a second electron via the iron-sulfur cluster. The reaction may be terminated by the transfer of a proton from the β-phosphate of the substrate to C(1) (affording DMAPP) or C(3) (affording IPP).

  10. Mechanism and kinetics of LiX(X=H, D, T) + H2O reaction

    International Nuclear Information System (INIS)

    Lei Hongjie; Duan Hao; Xing Pifeng; Tang Yongjian

    2011-01-01

    The reaction mechanism of LiX(X=H, D, T) with H 2 O was investigated at MP2/6-311G (d) level using ab initio quantum chemistry in Gaussian 03 software. The equilibrium geometries, harmonic frequencies and energy of various stationary points on the potential energy surfaces were calculated in the lowest singlet states. Considering the quantum correction, the reaction rate constants were calculated using classical transition state theory. The results show the reaction of LiH (LiD, LiT) with H 2 O was considerably dependent on temperature that it is lower, the reaction rate constants are smaller. (authors)

  11. Reaction mechanism of oxygen atoms with unsaturated hydrocarbons by the crossed molecular beams method

    Energy Technology Data Exchange (ETDEWEB)

    Buss, R.J.; Baseman, R.J.; Guozhong, H.; Lee, Y.T.

    1982-04-01

    From a series of studies of the reaction of oxygen atoms with unsaturated hydrocarbons using the crossed molecular beam method, the dominant reaction mechanisms were found to be the simple substitution reactions with oxygen atoms replacing H, Cl, Br atom or alkyl groups. Complication due to secondary reaction was avoided by carrying out experiments under single collisions and observing primary products directly. Primary products were identified by measuring the angular and velocity distributions of products at all the mass numbers which could be detected by the mass spectrometer, and from comparison of these distributions, applying the requirement of energy and momentum conservation.

  12. Reaction Mechanism of Oxygen Atoms with Unsaturated Hydrocarbons by the Crossed-Molecular-Beams Method

    Science.gov (United States)

    Buss, R. J.; Baseman, R. J.; Guozhong, H.; Lee, Y. T.

    1982-04-01

    From a series of studies of the reaction of oxygen atoms with unsaturated hydrocarbons using the crossed molecular beam method, the dominant reaction mechanisms were found to be the simple substitution reactions with oxygen atoms replacing H, Cl, Br atom or alkyl groups. Complication due to secondary reaction was avoided by carrying out experiments under single collisions and observing primary products directly. Primary products were identified by measuring the angular and velocity distributions of products at all the mass numbers which could be detected by the mass spectrometer, and from comparison of these distributions, applying the requirement of energy and momentum conservation.

  13. Determining the reaction in kinematic pairs of certain mechanisms using a digital computer

    Energy Technology Data Exchange (ETDEWEB)

    Chifchieva, V N

    1980-01-01

    In Dorr classifiers, walking excavators, conveyors, sieves and other mechanisms, one finds a triad with a sliding pair. An algorithm is proposed for determining reactions in the kinematic connections of a triad with one, two or three sliding pairs. The algorithm is suitable for use in digital computers. It is based on the transfer function method, and has several advantages over the technnique of determining reactions in kinematic pairs of V. Zinovyev. A concrete example is given of calculating reactions in the connections of a crank and lever mechanism of a walking excavator.

  14. 2013 Gordon Research Conference, Inorganic reaction mechanisms, Galveston, TX, March 3-8 2013

    Energy Technology Data Exchange (ETDEWEB)

    Abu-Omar, Mahdi M. [Purdue Univ., West Lafayette, IN (United States)

    2012-12-08

    The 2013 Gordon Conference on Inorganic Reaction Mechanisms will present cutting-edge research on the molecular aspects of inorganic reactions involving elements from throughout the periodic table and state-of-the art techniques that are used in the elucidation of reaction mechanisms. The Conference will feature a wide range of topics, such as homogeneous and heterogeneous catalysis, metallobiochemistry, electron-transfer in energy reactions, polymerization, nitrogen fixation, green chemistry, oxidation, solar conversion, alkane functionalization, organotransition metal chemistry, and computational chemistry. The talks will cover themes of current interest including energy, materials, and bioinorganic chemistry. Sections cover: Electron-Transfer in Energy Reactions; Catalytic Polymerization and Oxidation Chemistry; Kinetics and Spectroscopy of Heterogeneous Catalysts; Metal-Organic Chemistry and its Application in Synthesis; Green Energy Conversion;Organometallic Chemistry and Activation of Small Molecules; Advances in Kinetics Modeling and Green Chemistry; Metals in Biology and Disease; Frontiers in Catalytic Bond Activation and Cleavage.

  15. Exchange reaction between hydrogen and deuterium. II - Proposal for an heterogeneous initiation mechanism of gaseous phase reactions

    Energy Technology Data Exchange (ETDEWEB)

    Marteau, Chantal; Gaillard-Cusin, Francoise; James, Henri [Centre National de la Recherche Scientifique, 45 - Orleans-la-Source (France). Centre de Recherches sur la Chimie de Combustion et des Hautes Temperatures

    1978-05-01

    Investigation of experimental data related to evolution period exhibited by H/sub 2/-D/sub 2/ exchange process requires to take into account the variation against time of every atomic species -adsorbed or not- implied in the reaction mechanism. The formation of first chain carriers involves: - chemisorption of either gaseous reactant on the surface active centres (..sigma..), e.g.: ..sigma.. + 1/2 H/sub 2/ reversible ..sigma..H; - consecutive generation of atomic species through hetero-homogeneous transfer between chemisorbed species (..sigma..H) and gaseous molecules: ..sigma..H+H/sub 2/..--> sigma..+H/sub 2/+H/sup 0/, ..sigma..H+D/sub 2/..--> sigma..+HD+D/sup 0/. Therefore, it can be shown that the heterogeneous initiation process of a gas phase reaction identifies to a chain linear mechanism. Such an heterogeneous sequence conditions the further proceeding of the homogeneous chain reaction; both evolutions being kinematically connected. Rate constant of hydrogen adsorption on silica glass: ksub(a1) approximately 10/sup 14/ exp(-47/RT)Isup(0,5).molesup(-0,5).S/sup -1/ has been evaluated.

  16. Insights into the π-p → ηn reaction mechanism

    International Nuclear Information System (INIS)

    Durand, J.; Julia-Diaz, B.; Julia-Diaz, B.; Julia-Diaz, B.; Lee, T.S.H.; Sato, T.; Lee, T.S.H.; Sato, T.

    2009-01-01

    A dynamical coupled-channels formalism is used to investigate the eta-meson production mechanism on the proton induced by pions, in the total center-of-mass energy region from threshold up to 2 GeV. We show how and why studying exclusively total cross section data might turn out to be misleading in pinning down the reaction mechanism. (authors)

  17. Formation of amorphous Ti-50at.%Pt by solid state reactions during mechanical alloying

    CSIR Research Space (South Africa)

    Mahlatji, ML

    2013-10-01

    Full Text Available Mechanical alloying of an equiatomic mixture of crystalline elemental powders of Ti and Pt in a high-energy ball mill results in formation of an amorphous alloy by solid-state reactions. Mechanical alloying was carried out in an argon atmosphere...

  18. Interest of uranium complexes for the mechanism study of the McMurry reaction

    International Nuclear Information System (INIS)

    Maury, O.

    1997-01-01

    The reducing coupling reactions of ketones in diols and olefins are generally carried out with titanium or samarium compounds. In this work uranium complexes have been used. They have allowed to study the chemical reaction mechanism. This thesis is divided into three parts: 1) the reduction mechanism of uranium tetrachloride by cyclic voltametry has been studied at first. It has been shown that this reduction is followed by a transfer reaction of chlorides between the reduced specie of the higher electronic density and UCl . 2) In the second part is described: the synthesis, the crystal structure, the reactivity of the chemical agents, the stereochemistry of diols and alkenes formation and the pinacolisation reaction catalysis. 3) In the last part, the limits of the McMurry reaction are given by the study of the aromatic ketones pinacolisation reaction by-products. The obtained results show that the complexes of the metals which present a high reducing and oxo-philic (Ti, Sm, U..) character react in a similar way with the carbonyl compounds. If the uranium compounds are less used than those of the titanium in the field of the organic synthesis applications, they are precious auxiliaries and excellent models for reactions mechanisms study and for the synthesis methods optimization. (O.M.)

  19. Synergetic mechanism of methanol–steam reforming reaction in a catalytic reactor with electric discharges

    International Nuclear Information System (INIS)

    Kim, Taegyu; Jo, Sungkwon; Song, Young-Hoon; Lee, Dae Hoon

    2014-01-01

    Highlights: • Methanol–steam reforming was performed on Cu catalysts under an electric discharge. • Discharge had a synergetic effect on the catalytic reaction for methanol conversion. • Discharge lowered the temperature for catalyst activation or light off. • Discharge controlled the yield and selectivity of species in a reforming process. • Adsorption triggered by a discharge was a possible mechanism for a synergetic effect. - Abstract: Methanol–steam reforming was performed on Cu/ZnO/Al 2 O 3 catalysts under an electric discharge. The discharge occurred between the electrodes where the catalysts were packed. The electric discharge was characterized by the discharge voltage and electric power to generate the discharge. The existence of a discharge had a synergetic effect on the catalytic reaction for methanol conversion. The electric discharge provided modified reaction paths resulting in a lower temperature for catalyst activation or light off. The discharge partially controlled the yield and selectivity of species in a reforming process. The aspect of control was examined in view of the reaction kinetics. The possible mechanisms for the synergetic effect between the catalytic reaction and electric discharge on methanol–steam reforming were addressed. A discrete reaction path, particularly adsorption triggered by an electric discharge, was suggested to be the most likely mechanism for the synergetic effect. These results are expected to provide a guide for understanding the plasma–catalyst hybrid reaction

  20. Mechanism of degradation and discoloration reaction of L-ascorbic acid

    International Nuclear Information System (INIS)

    Kurata, Tadao

    1976-01-01

    The mechanisms of decomposition and coloration reaction of L-ascorbic acid are reviewed. At the initial stage of the decomposition, it can be classified roughly into oxidative and non-oxidative processes of decomposition. ASA forms furfural by being heated and decomposed in strong acid. The mechanism of the production of furfural at varying pH in acidic region was discussed. Furfural was produced through the enol form of 3-deoxy-L-pentosulose(3DP). 3DP seemed to be produced by two different routes: the one route consists of successive reactions from ASA through lactone ring-opening, dehydration, decarboxylation, to 3DP, and the other consists of reactions from the 3-keto form of ASA, through lactone ring-opening, decarboxylation, and dehydration, to the enol form of 3DP. ASA is easily reduced and decomposed through dehydro-ASA(DHA) by the presence of an oxidizing agent. The decomposition of DHA is discussed in cases of the systems of DHA alone, DHA and α-aminoacid, and DHA and amine. DHA was decomposed by the same reaction scheme as the decomposition of ASA and yielded 2-furoic acid. In the presence of an amino acid, DHA was decomposed by the Strecker decomposition, and yielded a red compound and a radical. In the presence of an amine, the discoloration reaction seemed to take place through radical reaction mechanism. The coloration reaction of ASA occurs in an acidic medium, and is accelerated by the oxidative process of decomposition. (Nishino, S.)

  1. Mechanism of the superior mechanical strength of nanometer-sized metal single crystals revealed

    KAUST Repository

    Afify, N. D.

    2013-10-01

    Clear understanding of the superior mechanical strength of nanometer-sized metal single crystals is required to derive advanced mechanical components retaining such superiority. Although high quality studies have been reported on nano-crystalline metals, the superiority of small single crystals has neither been fundamentally explained nor quantified to this date. Here we present a molecular dynamics study of aluminum single crystals in the size range from 4.1 nm to 40.5 nm. We show that the ultimate mechanical strength deteriorates exponentially as the single crystal size increases. The small crystals superiority is explained by their ability to continuously form vacancies and to recover them. © 2013 Published by Elsevier B.V.

  2. Flow chemistry kinetic studies reveal reaction conditions for ready access to unsymmetrical trehalose analogues.

    Science.gov (United States)

    Patel, Mitul K; Davis, Benjamin G

    2010-10-07

    Monofunctionalization of trehalose, a widely-found symmetric plant disaccharide, was studied in a microreactor to give valuable kinetic insights that have allowed improvements in desymmetrization yields and the development of a reaction sequence for large scale monofunctionalizations that allow access to probes of trehalose's biological function.

  3. Reduction of very large reaction mechanisms using methods based on simulation error minimization

    Energy Technology Data Exchange (ETDEWEB)

    Nagy, Tibor; Turanyi, Tamas [Institute of Chemistry, Eoetvoes University (ELTE), P.O. Box 32, H-1518 Budapest (Hungary)

    2009-02-15

    A new species reduction method called the Simulation Error Minimization Connectivity Method (SEM-CM) was developed. According to the SEM-CM algorithm, a mechanism building procedure is started from the important species. Strongly connected sets of species, identified on the basis of the normalized Jacobian, are added and several consistent mechanisms are produced. The combustion model is simulated with each of these mechanisms and the mechanism causing the smallest error (i.e. deviation from the model that uses the full mechanism), considering the important species only, is selected. Then, in several steps other strongly connected sets of species are added, the size of the mechanism is gradually increased and the procedure is terminated when the error becomes smaller than the required threshold. A new method for the elimination of redundant reactions is also presented, which is called the Principal Component Analysis of Matrix F with Simulation Error Minimization (SEM-PCAF). According to this method, several reduced mechanisms are produced by using various PCAF thresholds. The reduced mechanism having the least CPU time requirement among the ones having almost the smallest error is selected. Application of SEM-CM and SEM-PCAF together provides a very efficient way to eliminate redundant species and reactions from large mechanisms. The suggested approach was tested on a mechanism containing 6874 irreversible reactions of 345 species that describes methane partial oxidation to high conversion. The aim is to accurately reproduce the concentration-time profiles of 12 major species with less than 5% error at the conditions of an industrial application. The reduced mechanism consists of 246 reactions of 47 species and its simulation is 116 times faster than using the full mechanism. The SEM-CM was found to be more effective than the classic Connectivity Method, and also than the DRG, two-stage DRG, DRGASA, basic DRGEP and extended DRGEP methods. (author)

  4. Modeling the mechanism of glycosylation reactions between ethanol, 1,2-ethanediol and methoxymethanol.

    Science.gov (United States)

    Azofra, Luis Miguel; Alkorta, Ibon; Toro-Labbé, Alejandro; Elguero, José

    2013-09-07

    The mechanism of the S(N)2 model glycosylation reaction between ethanol, 1,2-ethanediol and methoxymethanol has been studied theoretically at the B3LYP/6-311+G(d,p) computational level. Three different types of reactions have been explored: (i) the exchange of hydroxyl groups between these model systems; (ii) the basic catalysis reactions by combination of the substrates as glycosyl donors (neutral species) and acceptors (enolate species); and (iii) the effect on the reaction profile of an explicit H2O molecule in the reactions considered in (ii). The reaction force, the electronic chemical potential and the reaction electronic flux have been characterized for the reaction path in each case. Energy calculations show that methoxymethanol is the worst glycosyl donor model among the ones studied here, while 1,2-ethanediol is the best, having the lowest activation barrier of 74.7 kJ mol(-1) for the reaction between this one and the ethanolate as the glycosyl acceptor model. In general, the presence of direct interactions between the atoms involved in the penta-coordinated TS increases the activation energies of the processes.

  5. Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions.

    Science.gov (United States)

    Cheng, Gui-Juan; Zhang, Xinhao; Chung, Lung Wa; Xu, Liping; Wu, Yun-Dong

    2015-02-11

    Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.

  6. Reaction mechanisms and rate constants of waste degradation in landfill bioreactor systems with enzymatic-enhancement.

    Science.gov (United States)

    Jayasinghe, P A; Hettiaratchi, J P A; Mehrotra, A K; Kumar, S

    2014-06-01

    Augmenting leachate before recirculation with peroxidase enzymes is a novel method to increase the available carbon, and therefore the food supply to microorganisms at the declining phase of the anaerobic landfill bioreactor operation. In order to optimize the enzyme-catalyzed leachate recirculation process, it is necessary to identify the reaction mechanisms and determine rate constants. This paper presents a kinetic model developed to ascertain the reaction mechanisms and determine the rate constants for enzyme catalyzed anaerobic waste degradation. The maximum rate of reaction (Vmax) for MnP enzyme-catalyzed reactors was 0.076 g(TOC)/g(DS).day. The catalytic turnover number (k(cat)) of the MnP enzyme-catalyzed was 506.7 per day while the rate constant (k) of the un-catalyzed reaction was 0.012 per day. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Atomic-scale processes revealing dynamic twin boundary strengthening mechanisms in face-centered cubic materials

    International Nuclear Information System (INIS)

    Yang, Z.Q.; Chisholm, M.F.; He, L.L.; Pennycook, S.J.; Ye, H.Q.

    2012-01-01

    We report experimental investigations on interactions/reactions between dislocations and twin boundaries in Al. The absorption of screw dislocations via cross-slip and the production of stair-rods via reactions with non-screw dislocations were verified by atomic resolution imaging. Importantly, the resulting partial dislocations moving along twin boundaries can produce secondary sessile defects. These immobile defects act as obstacles to other dislocations and also serve to pin the twin boundaries. These findings show the atomic-level dynamics of the dislocation–twin boundary processes and the unique strengthening mechanism of twin boundaries in face-centered cubic metals.

  8. Kinetics and mechanism of the gas phase reaction of Cl atoms with iodobenzene

    DEFF Research Database (Denmark)

    Andersen, Mads Peter Sulbæk; Ponomarev, DA; Nielsen, OJ

    2001-01-01

    Smog chamber/FTIR techniques were used to study the kinetics and mechanism of the reaction of Cl atoms with iodobenzene (C6H5I) in 20-700 Torr of N-2, air, or O-2 diluent at 296 K. The reaction proceeds with a rate constant k(Cl + QH(5)I) = (3.3 +/- 0.7) x 10(-11) cm(3) molecule(-1) s(-1) to give...

  9. Inelastic collisions of heavy ions and their reaction mechanisms; Collisions inelastiques d'ions lourds et mecanismes de reaction

    Energy Technology Data Exchange (ETDEWEB)

    Scarpaci, J.A

    2004-06-01

    This work is dedicated to the study of inelastic collisions of heavy ions. Most experiments took place in Ganil facility. The 2 first chapters introduce the notion of inelastic scattering of heavy ions. The third chapter deals with target excitation, giant monopolar or dipolar or quadrupolar resonances ant the multi-phonon concept and presents relevant experimental results from the Ca{sup 40} + Ca{sup 40} nuclear reaction at 50 MeV/A. The fourth chapter is dedicated to nuclear processes involved in inelastic collisions: pick-up break-up mechanisms, the angular distribution of emitted protons and the towing mode. These notions are applied to the reaction Zr{sup 90}(Ar{sup 40}, Ar{sup 40}'). The fifth chapter presents the solving of the time dependent Schroedinger equation (TDSE) applied to the wave function of a particle plunged in a variable potential. TDSE solving is applied to the break-up of Be{sup 11}. These calculations have been validated by comparing them with experimental results from the nuclear reaction Ti{sup 48}(Be{sup 11}, Be{sup 10} + n + {gamma}) that is described in the chapter 6. The last chapter presents the advantages of inelastic scattering considered as a tool to study exotic nuclei.

  10. Complex Reaction Kinetics in Chemistry: A Unified Picture Suggested by Mechanics in Physics

    Directory of Open Access Journals (Sweden)

    Elena Agliari

    2018-01-01

    Full Text Available Complex biochemical pathways can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. Among the elementary reactions so far extensively investigated, we recall the Michaelis-Menten and the Hill positive-cooperative kinetics, which apply to molecular binding and are characterized by the absence and the presence, respectively, of cooperative interactions between binding sites. However, there is evidence of reactions displaying a more complex pattern: these follow the positive-cooperative scenario at small substrate concentration, yet negative-cooperative effects emerge as the substrate concentration is increased. Here, we analyze the formal analogy between the mathematical backbone of (classical reaction kinetics in Chemistry and that of (classical mechanics in Physics. We first show that standard cooperative kinetics can be framed in terms of classical mechanics, where the emerging phenomenology can be obtained by applying the principle of least action of classical mechanics. Further, since the saturation function plays in Chemistry the same role played by velocity in Physics, we show that a relativistic scaffold naturally accounts for the kinetics of the above-mentioned complex reactions. The proposed formalism yields to a unique, consistent picture for cooperative-like reactions and to a stronger mathematical control.

  11. Clustering mechanism of oxocarboxylic acids involving hydration reaction: Implications for the atmospheric models

    Science.gov (United States)

    Liu, Ling; Kupiainen-Määttä, Oona; Zhang, Haijie; Li, Hao; Zhong, Jie; Kurtén, Theo; Vehkamäki, Hanna; Zhang, Shaowen; Zhang, Yunhong; Ge, Maofa; Zhang, Xiuhui; Li, Zesheng

    2018-06-01

    The formation of atmospheric aerosol particles from condensable gases is a dominant source of particulate matter in the boundary layer, but the mechanism is still ambiguous. During the clustering process, precursors with different reactivities can induce various chemical reactions in addition to the formation of hydrogen bonds. However, the clustering mechanism involving chemical reactions is rarely considered in most of the nucleation process models. Oxocarboxylic acids are common compositions of secondary organic aerosol, but the role of oxocarboxylic acids in secondary organic aerosol formation is still not fully understood. In this paper, glyoxylic acid, the simplest and the most abundant atmospheric oxocarboxylic acid, has been selected as a representative example of oxocarboxylic acids in order to study the clustering mechanism involving hydration reactions using density functional theory combined with the Atmospheric Clusters Dynamic Code. The hydration reaction of glyoxylic acid can occur either in the gas phase or during the clustering process. Under atmospheric conditions, the total conversion ratio of glyoxylic acid to its hydration reaction product (2,2-dihydroxyacetic acid) in both gas phase and clusters can be up to 85%, and the product can further participate in the clustering process. The differences in cluster structures and properties induced by the hydration reaction lead to significant differences in cluster formation rates and pathways at relatively low temperatures.

  12. Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures.

    Science.gov (United States)

    Sankar, Punnaivanam; Aghila, Gnanasekaran

    2007-01-01

    The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.

  13. Temporal predictive mechanisms modulate motor reaction time during initiation and inhibition of speech and hand movement.

    Science.gov (United States)

    Johari, Karim; Behroozmand, Roozbeh

    2017-08-01

    Skilled movement is mediated by motor commands executed with extremely fine temporal precision. The question of how the brain incorporates temporal information to perform motor actions has remained unanswered. This study investigated the effect of stimulus temporal predictability on response timing of speech and hand movement. Subjects performed a randomized vowel vocalization or button press task in two counterbalanced blocks in response to temporally-predictable and unpredictable visual cues. Results indicated that speech and hand reaction time was decreased for predictable compared with unpredictable stimuli. This finding suggests that a temporal predictive code is established to capture temporal dynamics of sensory cues in order to produce faster movements in responses to predictable stimuli. In addition, results revealed a main effect of modality, indicating faster hand movement compared with speech. We suggest that this effect is accounted for by the inherent complexity of speech production compared with hand movement. Lastly, we found that movement inhibition was faster than initiation for both hand and speech, suggesting that movement initiation requires a longer processing time to coordinate activities across multiple regions in the brain. These findings provide new insights into the mechanisms of temporal information processing during initiation and inhibition of speech and hand movement. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Chemical reaction of hexagonal boron nitride and graphite nanoclusters in mechanical milling systems

    Energy Technology Data Exchange (ETDEWEB)

    Muramatsu, Y.; Grush, M.; Callcott, T.A. [Univ. of Tennessee, Knoxville, TN (United States)] [and others

    1997-04-01

    Synthesis of boron-carbon-nitride (BCN) hybrid alloys has been attempted extensively by many researchers because the BCN alloys are considered an extremely hard material called {open_quotes}super diamond,{close_quotes} and the industrial application for wear-resistant materials is promising. A mechanical alloying (MA) method of hexagonal boron nitride (h-BN) with graphite has recently been studied to explore the industrial synthesis of the BCN alloys. To develop the MA method for the BCN alloy synthesis, it is necessary to confirm the chemical reaction processes in the mechanical milling systems and to identify the reaction products. Therefore, the authors have attempted to confirm the chemical reaction process of the h-BN and graphite in mechanical milling systems using x-ray absorption near edge structure (XANES) methods.

  15. Chemical reaction of hexagonal boron nitride and graphite nanoclusters in mechanical milling systems

    International Nuclear Information System (INIS)

    Muramatsu, Y.; Grush, M.; Callcott, T.A.

    1997-01-01

    Synthesis of boron-carbon-nitride (BCN) hybrid alloys has been attempted extensively by many researchers because the BCN alloys are considered an extremely hard material called open-quotes super diamond,close quotes and the industrial application for wear-resistant materials is promising. A mechanical alloying (MA) method of hexagonal boron nitride (h-BN) with graphite has recently been studied to explore the industrial synthesis of the BCN alloys. To develop the MA method for the BCN alloy synthesis, it is necessary to confirm the chemical reaction processes in the mechanical milling systems and to identify the reaction products. Therefore, the authors have attempted to confirm the chemical reaction process of the h-BN and graphite in mechanical milling systems using x-ray absorption near edge structure (XANES) methods

  16. Investigation of the CH3Cl + CN(-) reaction in water: Multilevel quantum mechanics/molecular mechanics study.

    Science.gov (United States)

    Xu, Yulong; Zhang, Jingxue; Wang, Dunyou

    2015-06-28

    The CH3Cl + CN(-) reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack SN2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show that the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ∼11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.

  17. WNT and DKK Determine Hair Follicle Spacing Through a Reaction-Diffusion Mechanism

    Science.gov (United States)

    Sick, Stefanie; Reinker, Stefan; Timmer, Jens; Schlake, Thomas

    2006-12-01

    Mathematical reaction-diffusion models have been suggested to describe formation of animal pigmentation patterns and distribution of epidermal appendages. However, the crucial signals and in vivo mechanisms are still elusive. Here we identify WNT and its inhibitor DKK as primary determinants of murine hair follicle spacing, using a combined experimental and computational modeling approach. Transgenic DKK overexpression reduces overall appendage density. Moderate suppression of endogenous WNT signaling forces follicles to form clusters during an otherwise normal morphogenetic program. These results confirm predictions of a WNT/DKK-specific mathematical model and provide in vivo corroboration of the reaction-diffusion mechanism for epidermal appendage formation.

  18. Identification of mechanisms in heavy ion reactions by measurement of angular correlations

    International Nuclear Information System (INIS)

    Carlin Filho, N.

    1987-01-01

    The identification of reaction mechanisms in light heavy-ion collisions has been performed within the framework of the three body kinematics, by means of angular correlation measurements. The 16 O+ 27 Al, 16 +O+ 28 Si and 10 B+ 27 Al reactions were investigated at Laboratory bombarding energies of 64 MeV, 64 and 48 MeV, respectively. Contributions of transfer-reemission and projectile sequential decay mechanisms were identified by the analysis of the relative kinetic energy of the final state components, excitation energies of the system at the intermediate stages, and also by means of fits to theoretical predictions for the angular correlations. (author) [pt

  19. Kinetic and mechanism formation reaction of complex compound Cu with di-n-buthildithiocarbamate (dbdtc) ligand

    Science.gov (United States)

    Haryani, S.; Kurniawan, C.; Kasmui

    2018-04-01

    Synthesis of complex compound is one field of research which intensively studied. Metal-dithiocarbamate complexes find wide-ranging applications in nanomaterial and metal separation science, and have potential use as chemotherapeutic, pesticides, and as additives to lubricants. However, the information about is reaction kinetic and mechanism are very much lacking. The research and analyzes results show that reaction synthesis ligand DBDTC and complex compounds Cu-DBDTC. Optimum reaction condition of formation of complex compounds Cu with DBDTC at pH=3, [DBDTC] = 4.10-3 M, and the time of reaction 5 minutes. Based the analysis varian reaction of complex compounds at pH 3 and 4, diffrence significance at the other pH: 5; 5,5; 6; 6,5 ; 7; and 8. The various of mole with reactants comosition difference sigbificance, those the time reaction for 5 and 6 minutes diffrence by significance with the other time, it is 3,4,8, and 10 minutes. The great product to at condition pH 6, the time optimum at 5 minutes and molar ratio of logam: ligand = 1:2. The reaction kinetic equation of complex compound Cu with chelathing ligand DBDTC is V=0.917106 [Cu2+]0.87921 [DBDTC]2.03021. Based on the kinetic data, and formed complex compounds estimation, the mechanism explaining by 2 stages. In the first stage formation of [Cu(DBDTC)], and then [Cu(DBDTC)2] with the last structure geomethry planar rectangle. The result of this research will be more useful if an effort is being done in reaction mechanism by chemical computation method for obtain intermediate, and for constant “k” in same stage, k1.k2. and compound complex constanta (β).

  20. Soft tissue deformation modelling through neural dynamics-based reaction-diffusion mechanics.

    Science.gov (United States)

    Zhang, Jinao; Zhong, Yongmin; Gu, Chengfan

    2018-05-30

    Soft tissue deformation modelling forms the basis of development of surgical simulation, surgical planning and robotic-assisted minimally invasive surgery. This paper presents a new methodology for modelling of soft tissue deformation based on reaction-diffusion mechanics via neural dynamics. The potential energy stored in soft tissues due to a mechanical load to deform tissues away from their rest state is treated as the equivalent transmembrane potential energy, and it is distributed in the tissue masses in the manner of reaction-diffusion propagation of nonlinear electrical waves. The reaction-diffusion propagation of mechanical potential energy and nonrigid mechanics of motion are combined to model soft tissue deformation and its dynamics, both of which are further formulated as the dynamics of cellular neural networks to achieve real-time computational performance. The proposed methodology is implemented with a haptic device for interactive soft tissue deformation with force feedback. Experimental results demonstrate that the proposed methodology exhibits nonlinear force-displacement relationship for nonlinear soft tissue deformation. Homogeneous, anisotropic and heterogeneous soft tissue material properties can be modelled through the inherent physical properties of mass points. Graphical abstract Soft tissue deformation modelling with haptic feedback via neural dynamics-based reaction-diffusion mechanics.

  1. Reaction-diffusion-like formalism for plastic neural networks reveals dissipative solitons at criticality

    Science.gov (United States)

    Grytskyy, Dmytro; Diesmann, Markus; Helias, Moritz

    2016-06-01

    Self-organized structures in networks with spike-timing dependent synaptic plasticity (STDP) are likely to play a central role for information processing in the brain. In the present study we derive a reaction-diffusion-like formalism for plastic feed-forward networks of nonlinear rate-based model neurons with a correlation sensitive learning rule inspired by and being qualitatively similar to STDP. After obtaining equations that describe the change of the spatial shape of the signal from layer to layer, we derive a criterion for the nonlinearity necessary to obtain stable dynamics for arbitrary input. We classify the possible scenarios of signal evolution and find that close to the transition to the unstable regime metastable solutions appear. The form of these dissipative solitons is determined analytically and the evolution and interaction of several such coexistent objects is investigated.

  2. Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces.

    Science.gov (United States)

    Faheem, Muhammad; Heyden, Andreas

    2014-08-12

    We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C-C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

  3. Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer.

    Science.gov (United States)

    Mendieta-Moreno, Jesús I; Trabada, Daniel G; Mendieta, Jesús; Lewis, James P; Gómez-Puertas, Paulino; Ortega, José

    2016-11-03

    The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.

  4. Modified reaction mechanism of aerated n-dodecane liquid flowing over heated metal tubes

    Science.gov (United States)

    Reddy, K. T.; Cernansky, N. P.; Cohen, R. S.

    1988-01-01

    The degradation mechanism of the n-dodecane was studied using a modified jet fuel thermal oxidation tester containing a sample withdrawal system as a reaction vessel. The reaction products were identified using gas chromatography and mass spectorometry. The soluble products were found to consist mainly of C5-C10 n-alkanes and 1-alkenes, C7-C10 aldehydes, tetrahydrofuran derivatives, dodecanol and dodecanone isomers, dodecyl hydroperoxide (ROOH) decomposition products, and C24 alkane isomers. The data from the experiments agreed with those of Hazlett et al. (1977). It was found that alkyl peroxide radical reactions dominate in the autooxidation temperature regime (at T not above 300 C); the dominant path is for the alkyl peroxyl radical to react bimolecularly with fuel to yield primarily alkyl hydroperoxides. The alkyl peroxide radical also undergoes self-termination and unimolecular isomerization and decomposition reactions, to yield smaller amounts of C12 alcohol plus ketone products and tetrahydrofuran derivatives, respectively.

  5. Reaction Mechanisms on Multiwell Potential Energy Surfaces in Combustion (and Atmospheric) Chemistry

    International Nuclear Information System (INIS)

    Osborn, David L.

    2017-01-01

    Chemical reactions occurring on a potential energy surface with multiple wells are ubiquitous in low temperature combustion and the oxidation of volatile organic compounds in earth’s atmosphere. The rich variety of structural isomerizations that compete with collisional stabilization make characterizing such complex-forming reactions challenging. This review describes recent experimental and theoretical advances that deliver increasingly complete views of their reaction mechanisms. New methods for creating reactive intermediates coupled with multiplexed measurements provide many experimental observables simultaneously. Automated methods to explore potential energy surfaces can uncover hidden reactive pathways, while master equation methods enable a holistic treatment of both sequential and well-skipping pathways. Our ability to probe and understand nonequilibrium effects and reaction sequences is increasing. These advances provide the fundamental science base for predictive models of combustion and the atmosphere that are crucial to address global challenges.

  6. Reaction Mechanisms on Multiwell Potential Energy Surfaces in Combustion (and Atmospheric) Chemistry

    Science.gov (United States)

    Osborn, David L.

    2017-05-01

    Chemical reactions occurring on a potential energy surface with multiple wells are ubiquitous in low-temperature combustion and in the oxidation of volatile organic compounds in Earth's atmosphere. The rich variety of structural isomerizations that compete with collisional stabilization makes characterizing such complex-forming reactions challenging. This review describes recent experimental and theoretical advances that deliver increasingly complete views of their reaction mechanisms. New methods for creating reactive intermediates coupled with multiplexed measurements provide many experimental observables simultaneously. Automated methods to explore potential energy surfaces can uncover hidden reactive pathways, and master equation methods enable a holistic treatment of both sequential and well-skipping pathways. Our ability to probe and understand nonequilibrium effects and reaction sequences is increasing. These advances provide the fundamental science base for predictive models of combustion and the atmosphere that are crucial to address global challenges.

  7. Formation of degradation compounds from lignocellulosic biomass in the biorefinery: sugar reaction mechanisms

    DEFF Research Database (Denmark)

    Rasmussen, Helena; Sørensen, Hanne R.; Meyer, Anne S.

    2014-01-01

    , several aldehydes and ketones and many different organic acids and aromatic compounds may be generated during hydrothermal treatment of lignocellulosic biomass. The reaction mechanisms are of interest because the very same compounds that are possible inhibitors for biomass processing enzymes......The degradation compounds formed during pretreatment when lignocellulosic biomass is processed to ethanol or other biorefinery products include furans, phenolics, organic acids, as well as mono- and oligomeric pentoses and hexoses. Depending on the reaction conditions glucose can be converted to 5......-(hydroxymethyl)-2-furaldehyde (HMF) and/or levulinic acid, formic acid and different phenolics at elevated temperatures. Correspondingly, xylose can follow different reaction mechanisms resulting in the formation of furan-2-carbaldehyde (furfural) and/or various C-1 and C-4 compounds. At least four routes...

  8. Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Gray, S.K. [Argonne National Laboratory, IL (United States)

    1993-12-01

    A major goal of this research is to obtain an understanding of the molecular reaction dynamics of three and four atom chemical reactions using numerically accurate quantum dynamics. This work involves: (i) the development and/or improvement of accurate quantum mechanical methods for the calculation and analysis of the properties of chemical reactions (e.g., rate constants and product distributions), and (ii) the determination of accurate dynamical results for selected chemical systems, which allow one to compare directly with experiment, determine the reliability of the underlying potential energy surfaces, and test the validity of approximate theories. This research emphasizes the use of recently developed time-dependent quantum mechanical methods, i.e. wave packet methods.

  9. Expanding the Enzyme Universe: Accessing Non-Natural Reactions by Mechanism-Guided Directed Evolution

    Science.gov (United States)

    Renata, Hans; Wang, Z. Jane

    2015-01-01

    High selectivities and exquisite control over reaction outcomes entice chemists to use biocatalysts in organic synthesis. However, many useful reactions are not accessible because they are not in nature’s known repertoire. We will use this review to outline an evolutionary approach to engineering enzymes to catalyze reactions not found in nature. We begin with examples of how nature has discovered new catalytic functions and how such evolutionary progressions have been recapitulated in the laboratory starting from extant enzymes. We then examine non-native enzyme activities that have been discovered and exploited for chemical synthesis, emphasizing reactions that do not have natural counterparts. The new functions have mechanistic parallels to the native reaction mechanisms that often manifest as catalytic promiscuity and the ability to convert from one function to the other with minimal mutation. We present examples of how non-natural activities have been improved by directed evolution, mimicking the process used by nature to create new catalysts. Examples of new enzyme functions include epoxide opening reactions with non-natural nucleophiles catalyzed by a laboratory-evolved halohydrin dehalogenase, cyclopropanation and other carbene transfer reactions catalyzed by cytochrome P450 variants, and non-natural modes of cyclization by a modified terpene synthase. Lastly, we describe discoveries of non-native catalytic functions that may provide future opportunities for expanding the enzyme universe. PMID:25649694

  10. A full understanding of oxygen reduction reaction mechanism on Au(1 1 1) surface

    Science.gov (United States)

    Yang, Yang; Dai, Changqing; Fisher, Adrian; Shen, Yanchun; Cheng, Daojian

    2017-09-01

    Oxygen reduction and hydrogen peroxide reduction are technologically important reactions in energy-conversion devices. In this work, a full understanding of oxygen reduction reaction (ORR) mechanism on Au(1 1 1) surface is investigated by density functional theory (DFT) calculations, including the reaction mechanisms of O2 dissociation, OOH dissociation, and H2O2 dissociation. Among these ORR mechanisms on Au(1 1 1), the activation energy of \\text{O}2* hydrogenation reaction is much lower than that of \\text{O}2* dissociation, indicating that \\text{O}2* hydrogenation reaction is more appropriate at the first step than \\text{O}2* dissociation. In the following, H2O2 can be formed with the lower activation energy compared with the OOH dissociation reaction, and finally H2O2 could be generated as a detectable product due to the high activation energy of H2O2 dissociation reaction. Furthermore, the potential dependent free energy study suggests that the H2O2 formation is thermodynamically favorable up to 0.4 V on Au(1 1 1), reducing the overpotential for 2e - ORR process. And the elementary step of first H2O formation becomes non-spontaneous at 0.4 V, indicating the difficulty of 4e - reduction pathway. Our DFT calculations show that H2O2 can be generated on Au(1 1 1) and the first electron transfer is the rate determining step. Our results show that gold surface could be used as a good catalyst for small-scale manufacture and on-site production of H2O2.

  11. The oxygen reduction reaction mechanism on Pt(111) from density functional theory calculations

    DEFF Research Database (Denmark)

    Tripkovic, Vladimir; Skulason, Egill; Siahrostami, Samira

    2010-01-01

    We study the oxygen reduction reaction (ORR) mechanism on a Pt(1 1 1) surface using density functional theory calculations We find that at low overpotentials the surface is covered with a half dissociated water layer We estimate the barrier for proton transfer to this surface and the barrier...

  12. Inheritance of the bark reaction resistance mechanism in Pinus monticola infected by Cronartium ribicola

    Science.gov (United States)

    Ray J. Hoff

    1986-01-01

    Necrotic reactions in branch or main stems of western white pine (Pinus monticola Dougl.) caused by infection by the blister rust fungus (Cronartium ribicola J. C. Fisch. ex Rabenh.) are a major mechanism of resistance. Overall, 26 percent of the seedlings eliminated the fungus via this defense system. Heritability based upon crossing family groups averaged 33 percent...

  13. Hydrodeoxygenation by deuterium gas--a powerful way to provide insight into the reaction mechanisms.

    Science.gov (United States)

    Ben, Haoxi; Ferguson, Glen A; Mu, Wei; Pu, Yunqiao; Huang, Fang; Jarvis, Mark; Biddy, Mary; Deng, Yulin; Ragauskas, Arthur J

    2013-11-28

    This study demonstrates the use of isotopic labelling and NMR to study the HDO process. As far as we know, this is the first reported effort to trace the incorporation of hydrogen in the HDO process of lignin pyrolysis oil thereby providing key fundamental insight into its reaction mechanism.

  14. Mechanism and kinetics of the electrocatalytic reaction responsible for the high cost of hydrogen fuel cells.

    Science.gov (United States)

    Cheng, Tao; Goddard, William A; An, Qi; Xiao, Hai; Merinov, Boris; Morozov, Sergey

    2017-01-25

    The sluggish oxygen reduction reaction (ORR) is a major impediment to the economic use of hydrogen fuel cells in transportation. In this work, we report the full ORR reaction mechanism for Pt(111) based on Quantum Mechanics (QM) based Reactive metadynamics (RμD) simulations including explicit water to obtain free energy reaction barriers at 298 K. The lowest energy pathway for 4 e - water formation is: first, *OOH formation; second, *OOH reduction to H 2 O and O*; third, O* hydrolysis using surface water to produce two *OH and finally *OH hydration to water. Water formation is the rate-determining step (RDS) for potentials above 0.87 Volt, the normal operating range. Considering the Eley-Rideal (ER) mechanism involving protons from the solvent, we predict the free energy reaction barrier at 298 K for water formation to be 0.25 eV for an external potential below U = 0.87 V and 0.41 eV at U = 1.23 V, in good agreement with experimental values of 0.22 eV and 0.44 eV, respectively. With the mechanism now fully understood, we can use this now validated methodology to examine the changes upon alloying and surface modifications to increase the rate by reducing the barrier for water formation.

  15. The relationship of microstructure and temperature to fracture mechanics parameters in reaction bonded silicon nitride

    International Nuclear Information System (INIS)

    Jennings, H.M.; Dalgleish, B.J.; Pratt, P.L.

    1978-01-01

    The development of physical properties in reaction bonded silicon nitride has been investigated over a range of temperatures and correlated with microstructure. Fracture mechanics parameters, elastic moduli, strength and critical defect size have been determined. The nitrided microstructure is shown to be directly related to these observed properties and these basic relationships can be used to produce material with improved properties. (orig.) [de

  16. Revealing the Differences Between Free and Complexed Enzyme Mechanisms and Factors Contributing to Cell Wall Recalcitrance

    Energy Technology Data Exchange (ETDEWEB)

    Resch, Michael G.; Donohoe, Byron; Ciesielski, Peter; Nill, Jennifer; McKinney, Kellene; Mittal, Ashutosh; Katahira, Rui; Himmel, Michael; Biddy, Mary; Beckham, Gregg; Decker, Steve

    2014-09-08

    Enzymatic depolymerization of polysaccharides is a key step in the production of fuels and chemicals from lignocellulosic biomass, and discovery of synergistic biomass-degrading enzyme paradigms will enable improved conversion processes. Historically, revealing insights into enzymatic saccharification mechanisms on plant cell walls has been hindered by uncharacterized substrates and low resolution.

  17. Comparison of a two-body threshold (π,2π) reaction mechanism with the usual one-body mechanism in the deuteron

    International Nuclear Information System (INIS)

    Rockmore, R.

    1984-01-01

    A two-body threshold (π +- ,π +- π -+ ) reaction mechanism is suggested in direct analogy with pion absorption. The mechanism involves boson rescattering via Δ excitation. The relative importance of this mechanism and the ordinary one-body mechanism in nuclei is studied in the particular case of S-wave deuteron targets. The contribution of the two-body mechanism to the threshold reaction cross section is found to be less than 1% of the simple one-body estimate

  18. Reaction

    African Journals Online (AJOL)

    abp

    19 oct. 2017 ... Reaction to Mohamed Said Nakhli et al. concerning the article: "When the axillary block remains the only alternative in a 5 year old child". .... Bertini L1, Savoia G, De Nicola A, Ivani G, Gravino E, Albani A et al ... 2010;7(2):101-.

  19. Automated Prediction of Catalytic Mechanism and Rate Law Using Graph-Based Reaction Path Sampling.

    Science.gov (United States)

    Habershon, Scott

    2016-04-12

    In a recent article [ J. Chem. Phys. 2015 , 143 , 094106 ], we introduced a novel graph-based sampling scheme which can be used to generate chemical reaction paths in many-atom systems in an efficient and highly automated manner. The main goal of this work is to demonstrate how this approach, when combined with direct kinetic modeling, can be used to determine the mechanism and phenomenological rate law of a complex catalytic cycle, namely cobalt-catalyzed hydroformylation of ethene. Our graph-based sampling scheme generates 31 unique chemical products and 32 unique chemical reaction pathways; these sampled structures and reaction paths enable automated construction of a kinetic network model of the catalytic system when combined with density functional theory (DFT) calculations of free energies and resultant transition-state theory rate constants. Direct simulations of this kinetic network across a range of initial reactant concentrations enables determination of both the reaction mechanism and the associated rate law in an automated fashion, without the need for either presupposing a mechanism or making steady-state approximations in kinetic analysis. Most importantly, we find that the reaction mechanism which emerges from these simulations is exactly that originally proposed by Heck and Breslow; furthermore, the simulated rate law is also consistent with previous experimental and computational studies, exhibiting a complex dependence on carbon monoxide pressure. While the inherent errors of using DFT simulations to model chemical reactivity limit the quantitative accuracy of our calculated rates, this work confirms that our automated simulation strategy enables direct analysis of catalytic mechanisms from first principles.

  20. The Reaction Mechanism and Rate Constants in the Radiolysis of Fe2+-Cu2+ Solutions

    DEFF Research Database (Denmark)

    Bjergbakke, Erling; Sehested, Knud; Rasmussen, O. Lang

    1976-01-01

    Pulse radiolysis and gamma radiolysis have been used to study the reaction mechanism in the radiolysis of aqueous solutions of Fe2+ and Cu2+. A reaction scheme has been developed and confirmed by computation of the corresponding complete set of differential equations. The rate constants for some ...... 10^{8}$ and $1.3\\times 10^{8}\\ {\\rm mol}^{-1}\\ {\\rm sec}^{-1}$ in pH 2.1 H2 SO4 and HClO4, respectively.......Pulse radiolysis and gamma radiolysis have been used to study the reaction mechanism in the radiolysis of aqueous solutions of Fe2+ and Cu2+. A reaction scheme has been developed and confirmed by computation of the corresponding complete set of differential equations. The rate constants for some...... of the reactions have been determined at different pH's. $k_{{\\rm Cu}^{+}+{\\rm O}_{2}}=4.6\\times 10^{5}$ and $1.0\\times 10^{6}\\ {\\rm mol}^{-1}\\ {\\rm sec}^{-1}$, $k_{{\\rm Cu}^{+}+{\\rm Fe}^{3+}}=5.5\\times 10^{6}$ and $1.3\\times 10^{7}\\ {\\rm mol}^{-1}\\ {\\rm sec}^{-1}$, $k_{{\\rm Cu}({\\rm III)}+{\\rm Fe}^{2+}}=3.3\\times...

  1. Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin.

    Directory of Open Access Journals (Sweden)

    Vasyl V Mykuliak

    2018-04-01

    Full Text Available Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins.

  2. Numerical comparison of hydrogen-air reaction mechanisms for unsteady shockinduced combustion applications

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, P. Pradeep; Kim, Kui Soon; Oh, Se Jong; Choi, Jeong Yeol [Pusan National University, Busan (Korea, Republic of)

    2015-03-15

    An unsteady shock-induced combustion (SIC) is characterized by the regularly oscillating combustion phenomenon behind the shock wave supported by the blunt projectile flying around the speed of Chapman-Jouguet detonation wave. The SIC is the coupling phenomenon between the hypersonic flow and the chemical kinetics, but the effects of chemical kinetics have been rarely reported. We compared hydrogen-air reaction mechanisms for the shock-induced combustion to demonstrate the importance of considering the reaction mechanisms for such complex flows. Seven hydrogen-air reaction mechanisms were considered, those available publically and used in other researches. As a first step in the comparison of the hydrogen combustion, ignition delay time of hydrogen-oxygen mixtures was compared at various initial conditions. Laminar premixed flame speed was also compared with available experimental data and at high pressure conditions. In addition, half-reaction length of ZND (Zeldovich-Neumann-Doering) detonation structure accounts for the length scale in SIC phenomena. Oscillation frequency of the SIC is compared by running the time-accurate 3rd-order Navier-Stokes CFD code fully coupled with the detailed chemistry by using four levels of grid resolutions.

  3. Numerical comparison of hydrogen-air reaction mechanisms for unsteady shockinduced combustion applications

    International Nuclear Information System (INIS)

    Kumar, P. Pradeep; Kim, Kui Soon; Oh, Se Jong; Choi, Jeong Yeol

    2015-01-01

    An unsteady shock-induced combustion (SIC) is characterized by the regularly oscillating combustion phenomenon behind the shock wave supported by the blunt projectile flying around the speed of Chapman-Jouguet detonation wave. The SIC is the coupling phenomenon between the hypersonic flow and the chemical kinetics, but the effects of chemical kinetics have been rarely reported. We compared hydrogen-air reaction mechanisms for the shock-induced combustion to demonstrate the importance of considering the reaction mechanisms for such complex flows. Seven hydrogen-air reaction mechanisms were considered, those available publically and used in other researches. As a first step in the comparison of the hydrogen combustion, ignition delay time of hydrogen-oxygen mixtures was compared at various initial conditions. Laminar premixed flame speed was also compared with available experimental data and at high pressure conditions. In addition, half-reaction length of ZND (Zeldovich-Neumann-Doering) detonation structure accounts for the length scale in SIC phenomena. Oscillation frequency of the SIC is compared by running the time-accurate 3rd-order Navier-Stokes CFD code fully coupled with the detailed chemistry by using four levels of grid resolutions.

  4. Mechanism of the electrochemical hydrogen reaction on smooth tungsten carbide and tungsten electrodes

    International Nuclear Information System (INIS)

    Wiesener, K.; Winkler, E.; Schneider, W.

    1985-01-01

    The course of the electrochemical hydrogen reaction on smooth tungsten-carbide electrodes in hydrogen saturated 2.25 M H 2 SO 4 follows a electrochemical sorption-desorption mechanism in the potential range of -0.4 to +0.1 V. At potentials greater than +0.1 V the hydrogen oxidation is controlled by a preliminary chemical sorption step. Concluding from the similar behaviour of tungsten-carbide and tungsten electrodes after cathodic pretreatment, different tungsten oxides should be involved in the course of the hydrogen reaction on tungsten carbide electrodes. (author)

  5. Mechanisms of reactions of organoaluminium compounds with alkenes and alkynes catalyzed by Zr complexes

    International Nuclear Information System (INIS)

    Parfenova, L V; Khalilov, Leonard M; Dzhemilev, Usein M

    2012-01-01

    The results of studies dealing with mechanisms of hydro-, carbo- and cycloalumination of alkenes and alkynes catalyzed by zirconium complexes are generalized and systematized for the first time. Data about the structures of intermediates responsible for the formation of the target compounds are presented and the available data on the effect of the structure of organoaluminium compounds and the electronic and steric factors determining the catalytic activity of metal complexes in these reactions are considered in detail. Much attention is paid to studies of the influence of reaction conditions on the chemo-, regio- and stereoselectivity of the Zr-containing complex catalysts. The bibliography includes 217 references.

  6. Biogenesis of Triterpene Dimers from Orthoquinones Related to Quinonemethides: Theoretical Study on the Reaction Mechanism

    Directory of Open Access Journals (Sweden)

    Mariana Quesadas-Rojas

    2016-11-01

    Full Text Available The biogenetic origin of triterpene dimers from the Celastraceae family has been proposed as assisted hetero-Diels-Alder reaction (HDA. In this work, computational calculation of HDA between natural quinonemethides (tingenone and isopristimerol and hypothetical orthoquinones has been performed at the M06-2X/6-31G(d level of theory. We have located all the HDA transition states supporting the biogenetic route via HDA cycloadditions. We found that all reactions take place through a concerted inverse electron demand and asynchronous mechanism. The enzymatic assistance for dimer formation was analyzed in terms of the calculated transition state energy barrier.

  7. Mechanism and kinetics in reactions of caffeic acid with radicals by pulse radiolysis and calculation

    International Nuclear Information System (INIS)

    Li, Xifeng; Cai, Zhongli; Katsumura, Yosuke

    2000-01-01

    The interaction of caffeic acid with e aq - , (CH 3 ) 2 (OH) CCH 2 · , CO 2 ·- , H · , ·OH and N 3 · radicals were studied by γ-, pulse radiolysis and molecular orbital calculation. UV-visible spectra of electron/·OH adducts, semi-quinone radicals of caffeic ions, and the stable products from the reactions were derived. The rate constants were determined. The attacked sites and the most favorable structures of the transient radicals were predicted. Reaction mechanisms were proposed. (author)

  8. Study of reaction mechanism for 12C(14N, 6Li) by angular correlation measurement

    International Nuclear Information System (INIS)

    Goldberg, V.Z.; Golovkov, M.S.; Rogatchev, G.V.; Barrov, S.P.; Zurmuhle, R.W.; Liu, Z.; Benton, D.R.; Miao, Y.; Lee, C.; Wimer, N.G.; Murgatroyd, J.T.; Li, X.

    1999-01-01

    An angular correlation for the reaction 12 C ( 14 N, 6 Li) 20 Ne* (α) populating the 8.78 MeV (6 + ) level in 20 Ne is measured at 48 MeV incident 14 N energy. 6 Li is registered for 0-degree geometry in coincidence with α particles from the 20 Ne excited state decay. The results shows that 20% was the upper limit for the contribution of compound nucleus formation. Possible main direct mechanisms of the reaction are discussed [ru

  9. A reaction mechanism for gasoline surrogate fuels for large polycyclic aromatic hydrocarbons

    KAUST Repository

    Raj, Abhijeet

    2012-02-01

    This work aims to develop a reaction mechanism for gasoline surrogate fuels (n-heptane, iso-octane and toluene) with an emphasis on the formation of large polycyclic aromatic hydrocarbons (PAHs). Starting from an existing base mechanism for gasoline surrogate fuels with the largest chemical species being pyrene (C 16H 10), this new mechanism is generated by adding PAH sub-mechanisms to account for the formation and growth of PAHs up to coronene (C 24H 12). The density functional theory (DFT) and the transition state theory (TST) have been adopted to evaluate the rate constants for several PAH reactions. The mechanism is validated in the premixed laminar flames of n-heptane, iso-octane, benzene and ethylene. The characteristics of PAH formation in the counterflow diffusion flames of iso-octane/toluene and n-heptane/toluene mixtures have also been tested for both the soot formation and soot formation/oxidation flame conditions. The predictions of the concentrations of large PAHs in the premixed flames having available experimental data are significantly improved with the new mechanism as compared to the base mechanism. The major pathways for the formation of large PAHs are identified. The test of the counterflow diffusion flames successfully predicts the PAH behavior exhibiting a synergistic effect observed experimentally for the mixture fuels, irrespective of the type of flame (soot formation flame or soot formation/oxidation flame). The reactions that lead to this synergistic effect in PAH formation are identified through the rate-of-production analysis. © 2011 The Combustion Institute.

  10. Development of the Automatic Modeling System for Reaction Mechanisms Using REX+JGG

    Science.gov (United States)

    Takahashi, Takahiro; Kawai, Kohei; Nakai, Hiroyuki; Ema, Yoshinori

    The identification of appropriate reaction models is very helpful for developing chemical vapor deposition (CVD) processes. In this study, we developed an automatic modeling system that analyzes experimental data on the cross- sectional shapes of films deposited on substrates with nanometer- or micrometer-sized trenches. The system then identifies a suitable reaction model to describe the film deposition. The inference engine used by the system to model the reaction mechanism was designed using real-coded genetic algorithms (RCGAs): a generation alternation model named "just generation gap" (JGG) and a real-coded crossover named "real-coded ensemble crossover" (REX). We studied the effect of REX+JGG on the system's performance, and found that the system with REX+JGG was the most accurate and reliable at model identification among the algorithms that we studied.

  11. [Mechanism of reaction catalyzed by RNA-ligase from bacteriophage T4].

    Science.gov (United States)

    Zagrebel'nyĭ, S N; Zernov, Iu P

    1987-01-01

    The dissociation constants of the complexes of RNA-ligase with acceptors, donors and the adenylylated donor A(5')ppAp have been determined on the basis of the inhibition of ATP-pyrophosphate exchange reaction. The dissociation constants of the complexes of the enzyme with "poor" acceptors (oligouridilates) have been shown to be slightly different from those with "good" acceptors (oligoadenylates). The dependence of the reaction velocity of the formation of ligation products on the concentration of acceptors (pA)4, (pU)4 and the adenylylated donor A(5)ppAp has been studied. On the basis of the data obtained the conclusion about the random addition mechanism has been drawn. The reaction takes place in the steady-state conditions in the case of (pA)4 and in the equilibrium conditions--in the case of (pU)4.

  12. A Density Functional Theory Study on the Reaction Mechanism of Terpinolene with O{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hahkjoon [Duksung Women' s University, Seoul (Korea, Republic of)

    2016-02-15

    The energies of chemical species involved in the early stage of the reaction of terpinolene with ozone were calculated to understand the oxidation mechanism of terpinolene with atmospheric O{sub 2} and NO determined experimentally. All the quantum calculations for geometry optimization and frequency calculations in this study were carried out using B3LYP with the 6-31G(d,p) basis (Gaussian 03 software package). In conclusion, quantum chemical calculations were performed to obtain the relative energies and energy barriers for the early stage of the reaction pathways of terpinolene with ozone. The branching ratio for pathways 3 and 4 determined experimentally is in qualitative agreement with the current calculations. The results of these calculations are important for assessing the relative stabilities of the intermediates in the reaction of terpinolene with ozone although detailed RRKM calculations are still needed to fully understand the branching ratios of the final products.

  13. Prediction of Mechanism and Thermochemical Properties of O3 + H2S Atmospheric Reaction

    Directory of Open Access Journals (Sweden)

    Morteza Vahedpour

    2013-01-01

    Full Text Available Ozone and hydrogen sulfide reaction mechanism including a complex was studied at the B3LYP/6-311++G(3df,3pd and CCSD/6-311++G(3df,3pd//B3LYP/6-311++G(3df,3pd levels of computation. The interaction between sulfur atom of hydrogen sulfide and terminal oxygen atom of ozone produces a stable H2S-O3 complex with no barrier. With the decomposition of this complex, four possible product channels have been found. Intrinsic reaction coordinate, topological analyses of atom in molecule, and vibrational frequency calculation have been used to confirm the suggested mechanism. Thermodynamic data at T = 298.15 K and the atmospheric pressure have been calculated. The results show that the production of H2O + SO2 is the main reaction channel with ΔG° = −645.84 kJ/mol. Rate constants of H2S + O3 reaction show two product channels, SO2 + H2O and HSO + HOO, which compete with each other based on the temperature.

  14. An experimental and theoretical study of reaction mechanisms between nitriles and hydroxylamine.

    Science.gov (United States)

    Vörös, Attila; Mucsi, Zoltán; Baán, Zoltán; Timári, Géza; Hermecz, István; Mizsey, Péter; Finta, Zoltán

    2014-10-28

    The industrially relevant reaction between nitriles and hydroxylamine yielding amidoximes was studied in different molecular solvents and in ionic liquids. In industry, this procedure is carried out on the ton scale in alcohol solutions and the above transformation produces a significant amount of unexpected amide by-product, depending on the nature of the nitrile, which can cause further analytical and purification issues. Although there were earlier attempts to propose mechanisms for this transformation, the real reaction pathway is still under discussion. A new detailed reaction mechanistic explanation, based on theoretical and experimental proof, is given to augment the former mechanisms, which allowed us to find a more efficient, side-product free procedure. Interpreting the theoretical results obtained, it was shown that the application of specific imidazolium, phosphonium and quaternary ammonium based ionic liquids could decrease simultaneously the reaction time while eliminating the amide side-product, leading to the targeted product selectively. This robust and economic procedure now affords a fast, selective amide free synthesis of amidoximes.

  15. Mechanism of nuclear dissipation in fission and heavy-ion reactions

    International Nuclear Information System (INIS)

    Nix, J.R.; Sierk, A.J.

    1986-01-01

    Recent advances in the theoretical understanding of nuclear dissipation at intermediate excitation energies are reviewed, with particular emphasis on a new surface-plus-window mechanism that involves interactions of either one or two nucleons with the moving nuclear surface and also, for dumbbell-like shapes encountered in fission and heavy-ion reactions, the transfer of nucleons through the window separating the two portions of the system. This novel dissipation mechanism provides a unified macroscopic description of such diverse phenomena as widths of isoscalar giant quadrupole and giant octupole resonances, mean fission-fragment kinetic energies and excitation energies, dynamical thresholds for compound-nucleus formation, enhancement in neutron emission prior to fission, and widths of mass and charge distributions in deep-inelastic heavy-ion reactions. 41 refs., 8 figs

  16. Elucidation of reaction mechanism for m -cresol hydrodeoxygenation over Fe based catalysts: A kinetic study

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Yongchun; Wang, Yong

    2017-09-01

    Fe based catalysts are promising for hydrodeoxygenation (HDO) of lignin derived phenolics due to their high selectivity for aromatics. In this work, the reaction mechanism of m-cresol HDO on Fe catalysts and the kinetic consequence with Pd addition were elucidated by examining the effect of H2, H2O and m-cresol pressures on toluene formation rate on Fe and PdFe catalysts. A direct CO bond cleavage mechanism is proposed for HDO catalysis on both Fe and PdFe catalysts, while Pd provides a facilitated reaction pathway at the PdFe interface and therefore promotes the catalysis on Fe without changing the high selectivity towards aromatics.

  17. Light particle emission as a probe of reaction mechanism and nuclear excitation

    International Nuclear Information System (INIS)

    Guerreau, D.

    1989-01-01

    The central part of these lectures will be dealing with the problem of energy dissipation. A good understanding of the mechanisms for the dissipation requires to study both peripheral and central collisions or, in other words, to look at the impact paramenter dependence. This should also provide valuable information on the time scale. In order to probe the reaction mechanism and nuclear excitation, one of the most powerful tool is unquestionably the observation of light particle emission, including neutrons and charged particles. Several examples will be discussed related to peripheral collisions (the fate of transfer reactions, the excitation energy generation, the production of projectile-like fragments) as well as inner collisions for which extensive studies have demonstrated the strength of intermediate energy heavy ions for the production of very hot nuclei and detailed study of their decay properties

  18. Theoretical studies of mechanisms of cycloaddition reaction between difluoromethylene carbene and acetone

    Science.gov (United States)

    Lu, Xiu Hui; Yu, Hai Bin; Wu, Wei Rong; Xu, Yue Hua

    Mechanisms of the cycloaddition reaction between singlet difluoromethylene carbene and acetone have been investigated with the second-order Møller-Plesset (MP2)/6-31G* method, including geometry optimization and vibrational analysis. Energies for the involved stationary points on the potential energy surface (PES) are corrected by zero-point energy (ZPE) and CCSD(T)/6-31G* single-point calculations. From the PES obtained with the CCSD(T)//MP2/6-31G* method for the cycloaddition reaction between singlet difluoromethylene carbene and acetone, it can be predicted that path B of reactions 2 and 3 should be two competitive leading channels of the cycloaddition reaction between difluoromethylene carbene and acetone. The former consists of two steps: (i) the two reactants first form a four-membered ring intermediate, INT2, which is a barrier-free exothermic reaction of 97.8 kJ/mol; (ii) the intermediate INT2 isomerizes to a four-membered product P2b via a transition state TS2b with an energy barrier of 24.9 kJ/mol, which results from the methyl group transfer. The latter proceeds in three steps: (i) the two reactants first form an intermediate, INT1c, through a barrier-free exothermic reaction of 199.4 kJ/mol; (ii) the intermediate INT1c further reacts with acetone to form a polycyclic intermediate, INT3, which is also a barrier-free exothermic reaction of 27.4 kJ/mol; and (iii) INT3 isomerizes to a polycyclic product P3 via a transition state TS3 with an energy barrier of 25.8 kJ/mol.

  19. Drift mechanism of mass transfer on heterogeneous reaction in crystalline silicon substrate

    Energy Technology Data Exchange (ETDEWEB)

    Kukushkin, S.A. [Institute of Problems of Mechanical Engineering, Russian Academy of Science, St Petersburg, 199178 (Russian Federation); St. Petersburg National Research University of Information Technologies, Mechanics and Optics, 197101 (Russian Federation); Osipov, A.V., E-mail: Andrey.V.Osipov@gmail.com [Institute of Problems of Mechanical Engineering, Russian Academy of Science, St Petersburg, 199178 (Russian Federation); St. Petersburg National Research University of Information Technologies, Mechanics and Optics, 197101 (Russian Federation)

    2017-05-01

    This work aims to study the pressure dependence of the thickness of the epitaxial silicon carbide film growing from crystalline silicon due to the heterogeneous reaction with gaseous carbon monoxide. It turned out that this dependence exhibits the clear maximum. On further pressure increasing the film thickness decreases. The theoretical model has been developed which explains such a character of the dependence by the fact that the gaseous silicon monoxide reaction product inhibits the drift of the gaseous reagent through the channels of a crystal lattice, thus decreasing their hydraulic diameter. In the proposed hydraulic model, the dependences of the film thickness both on the gas pressure and time have been calculated. It was shown that not only the qualitative but also quantitative correspondence between theoretical and experimental results takes place. As one would expect, due to the Einstein relation, at short growth times the drift model coincides with the diffusion one. Consequences of this drift mechanism of epitaxial film growing are discussed. - Graphical abstract: This work aims to study the pressure dependence of the thickness of the epitaxial silicon carbide film growing from crystalline silicon due to the heterogeneous reaction with gaseous carbon monoxide. It turned out that this dependence exhibits the clear maximum. On further pressure increasing the film thickness decreases. The theoretical model has been developed which explains such a character of the dependence by the fact that the gaseous silicon monoxide reaction product inhibits the drift of the gaseous reagent through the channels of a crystal lattice, thus decreasing their hydraulic diameter. - Highlights: • It is established that the greater pressure, the smaller is the reaction rate. • The reaction product prevents penetration of the reagent into a reaction zone. • For description the hydraulic model of crystal lattice channels is developed. • Theoretical results for polytropic

  20. Reaction mechanism of hydroxymaleimide induced by γ-irradiation in alcohol solvents

    International Nuclear Information System (INIS)

    Nakagawa, Seiko

    2010-01-01

    Methanol and 2-propanol solutions of hydroxymaleimide were irradiated with γ-ray and mechanism of its γ-irradiation-induced reactions was investigated through final-product analyses using high performance liquid chromatography (HPLC) coupled with mass spectroscopy. An addition reaction of a solvent radical toward hydroxymaleimide was dominant among its oxygen-free γ-irradiation-induced reactions in its alcohol solutions while it is known that electron attachment toward hydroxyphthalimide or hydroxysuccinimide is dominant among their γ-irradiation-induced reactions. The radical adduct abstracts hydrogen from solvent molecule to re-produce a solvent radical. Therefore, the degradation efficiency of hydroxymaleimide was more than ten times larger than that of hydroxyphthalimide and hydroxysuccinimide. Dimer was also produced through electron attachment process in the solutions of hydroxymaleimide. In addition, it was found that the degradation efficiency increased with decrease in dose rate. An additional reaction of a solvent radical toward hydroxymaleimide competes with a radical-radical recombination. The latter was reduced, with the former leading to efficient degradation of hydroxymaleimide increased by irradiation at lower dose rate. On the contrary, the production yield of the adduct radical as well as the degradation efficiency of hydroxymaleimide was inhibited in the presence of oxygen.

  1. Reaction mechanism of hydroxymaleimide induced by γ-irradiation in alcohol solvents

    International Nuclear Information System (INIS)

    Nakagawa, Seiko

    2010-01-01

    Methanol and 2-propanol solutions of hydroxymaleimide were irradiated with γ-ray and mechanism of its γ-irradiation-induced reactions was investigated through final-product analyses using high performance liquid chromatography (HPLC) coupled with mass spectroscopy. An addition reaction of a solvent radical toward hydroxymaleimide was dominant among its oxygen-free γ-irradiation-induced reactions in its alcohol solutions while it is known that electron attachment toward hydroxyphthalimide or hydroxysuccinimide is dominant among their γ-irradiation-induced reactions. The radical adduct abstracts hydrogen from solvent molecule to re-produce a solvent radical. Therefore, the degradation efficiency of hydroxymaleimide was more than 10 times larger than that of hydroxyphthalimide and hydroxysuccinimide. Dimer was also produced through electron attachment process in the solutions of hydroxymaleimide. In addition, it was found that the degradation efficiency increased with decreasing the dose rate. An addition reaction of a solvent radical toward hydroxymaleimide competes with a radical-radical recombination. The latter was reduced and the former leading to efficient degradation of hydroxymaleimide increased by irradiation at lower dose rate. On the contrary, the production yield of the adduct radical as well as the degradation efficiency of hydroxymaleimide was inhibited in the presence of oxygen.

  2. Reaction mechanism for the free-edge oxidation of soot by O 2

    KAUST Repository

    Raj, Abhijeet; da Silva, Gabriel; Chung, Suk-Ho

    2012-01-01

    The reaction pathways for the oxidation by O 2 of polycyclic aromatic hydrocarbons present in soot particles are investigated using density functional theory at B3LYP/6-311++G(d,p) level of theory. For this, pyrene radical (4-pyrenyl) is chosen as the model molecule, as most soot models present in the literature employ the reactions involving the conversion of 4-pyrenyl to 4-phenanthryl by O 2 and OH to account for soot oxidation. Several routes for the formation of CO and CO 2 are proposed. The addition of O 2 on a radical site to form a peroxyl radical is found to be barrierless and exothermic with reaction energy of 188kJ/mol. For the oxidation reaction to proceed further, three pathways are suggested, each of which involve the activation energies of 104, 167 and 115kJ/mol relative to the peroxyl radical. The effect of the presence of H atom on a carbon atom neighboring the radical site on the energetics of carbon oxidation is assessed. Those intermediate species formed during oxidation with seven-membered rings or with a phenolic group are found to be highly stable. The rate constants evaluated using transition state theory in the temperature range of 300-3000K for the reactions involved in the mechanism are provided. © 2012 The Combustion Institute.

  3. A Density Functional Theory Study on the Reaction Mechanism of α-Phellandrene with NO_3

    International Nuclear Information System (INIS)

    Kim, Hahk Joon; Park, Ji Ho

    2015-01-01

    In this study, we investigated the relative energies of the chemical species involved in the reaction of α-phellandrene with NO_3 under ambient nighttime conditions to understand the reaction pathway and identify the final products using quantum chemical calculations. The expected main oxidation products are nitrosocabonyl compounds. Although the formation of an oxirane compound is plausible, the reaction might proceed further to produce an aromatic compound. To fully understand α-phellandrene oxidation by NO_3, further study of the detailed reaction mechanism of the formation of an aromatic compound detected by the experiment is needed. Oxidations by OH radical and O_3 are major loss processes for tropospheric monoterpenes during the day. NO_3 radical, which is rapidly photolyzed by sunlight, is a dominant trophospheric oxidant at night because they react rapidly with monoterpens. Some volatile organic compounds produced by the reaction with atmospheric constituents are responsible for the formation of secondary organic aerosols that serve as cloud condensation nuclei inducing a cloud climate effect in the troposphere

  4. Reaction mechanism for the free-edge oxidation of soot by O 2

    KAUST Repository

    Raj, Abhijeet

    2012-11-01

    The reaction pathways for the oxidation by O 2 of polycyclic aromatic hydrocarbons present in soot particles are investigated using density functional theory at B3LYP/6-311++G(d,p) level of theory. For this, pyrene radical (4-pyrenyl) is chosen as the model molecule, as most soot models present in the literature employ the reactions involving the conversion of 4-pyrenyl to 4-phenanthryl by O 2 and OH to account for soot oxidation. Several routes for the formation of CO and CO 2 are proposed. The addition of O 2 on a radical site to form a peroxyl radical is found to be barrierless and exothermic with reaction energy of 188kJ/mol. For the oxidation reaction to proceed further, three pathways are suggested, each of which involve the activation energies of 104, 167 and 115kJ/mol relative to the peroxyl radical. The effect of the presence of H atom on a carbon atom neighboring the radical site on the energetics of carbon oxidation is assessed. Those intermediate species formed during oxidation with seven-membered rings or with a phenolic group are found to be highly stable. The rate constants evaluated using transition state theory in the temperature range of 300-3000K for the reactions involved in the mechanism are provided. © 2012 The Combustion Institute.

  5. Reaction kinetics and mechanisms of organosilicon fungicide flusilazole with sulfate and hydroxyl radicals.

    Science.gov (United States)

    Mercado, D Fabio; Bracco, Larisa L B; Arques, Antonio; Gonzalez, Mónica C; Caregnato, Paula

    2018-01-01

    Flusilazole is an organosilane fungicide used for treatments in agriculture and horticulture for control of diseases. The reaction kinetics and mechanism of flusilazole with sulfate and hydroxyl radicals were studied. The rate constant of the radicals with the fungicide were determined by laser flash photolysis of peroxodisulfate and hydrogen peroxide. The results were 2.0 × 10 9 s -1 M -1 for the reaction of the fungicide with HO and 4.6 × 10 8  s -1  M -1 for the same reaction with SO 4 - radicals. The absorption spectra of organic intermediates detected by laser flash photolysis of S 2 O 8 2- with flusilazole, were identified as α-aminoalkyl and siloxyl radicals and agree very well with those estimated employing the time-dependent density functional theory with explicit account for bulk solvent effects. In the continuous photolysis experiments, performed by photo-Fenton reaction of the fungicide, the main degradation products were: (bis(4-fluorophenyl)-hydroxy-methylsilane) and the non-toxic silicic acid, diethyl bis(trimethylsilyl) ester, in ten and twenty minutes of reaction, respectively. Copyright © 2017. Published by Elsevier Ltd.

  6. Modeling of the Reaction Mechanism of Enzymatic Radical C–C Coupling by Benzylsuccinate Synthase

    Directory of Open Access Journals (Sweden)

    Maciej Szaleniec

    2016-04-01

    Full Text Available Molecular modeling techniques and density functional theory calculations were performed to study the mechanism of enzymatic radical C–C coupling catalyzed by benzylsuccinate synthase (BSS. BSS has been identified as a glycyl radical enzyme that catalyzes the enantiospecific fumarate addition to toluene initiating its anaerobic metabolism in the denitrifying bacterium Thauera aromatica, and this reaction represents the general mechanism of toluene degradation in all known anaerobic degraders. In this work docking calculations, classical molecular dynamics (MD simulations, and DFT+D2 cluster modeling was employed to address the following questions: (i What mechanistic details of the BSS reaction yield the most probable molecular model? (ii What is the molecular basis of enantiospecificity of BSS? (iii Is the proposed mechanism consistent with experimental observations, such as an inversion of the stereochemistry of the benzylic protons, syn addition of toluene to fumarate, exclusive production of (R-benzylsuccinate as a product and a kinetic isotope effect (KIE ranging between 2 and 4? The quantum mechanics (QM modeling confirms that the previously proposed hypothetical mechanism is the most probable among several variants considered, although C–H activation and not C–C coupling turns out to be the rate limiting step. The enantiospecificity of the enzyme seems to be enforced by a thermodynamic preference for binding of fumarate in the pro(R orientation and reverse preference of benzyl radical attack on fumarate in pro(S pathway which results with prohibitively high energy barrier of the radical quenching. Finally, the proposed mechanism agrees with most of the experimental observations, although the calculated intrinsic KIE from the model (6.5 is still higher than the experimentally observed values (4.0 which suggests that both C–H activation and radical quenching may jointly be involved in the kinetic control of the reaction.

  7. A coupled mechanical and chemical damage model for concrete affected by alkali–silica reaction

    Energy Technology Data Exchange (ETDEWEB)

    Pignatelli, Rossella, E-mail: rossellapignatelli@gmail.com [Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano (Italy); Lombardi Ingegneria S.r.l., Via Giotto 36, 20145 Milano (Italy); Comi, Claudia, E-mail: comi@stru.polimi.it [Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano (Italy); Monteiro, Paulo J.M., E-mail: monteiro@ce.berkeley.edu [Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720 (United States)

    2013-11-15

    To model the complex degradation phenomena occurring in concrete affected by alkali–silica reaction (ASR), we formulate a poro-mechanical model with two isotropic internal variables: the chemical and the mechanical damage. The chemical damage, related to the evolution of the reaction, is caused by the pressure generated by the expanding ASR gel on the solid concrete skeleton. The mechanical damage describes the strength and stiffness degradation induced by the external loads. As suggested by experimental results, degradation due to ASR is considered to be localized around reactive sites. The effect of the degree of saturation and of the temperature on the reaction development is also modeled. The chemical damage evolution is calibrated using the value of the gel pressure estimated by applying the electrical diffuse double-layer theory to experimental values of the surface charge density in ASR gel specimens reported in the literature. The chemo-damage model is first validated by simulating expansion tests on reactive specimens and beams; the coupled chemo-mechanical damage model is then employed to simulate compression and flexure tests results also taken from the literature. -- Highlights: •Concrete degradation due to ASR in variable environmental conditions is modeled. •Two isotropic internal variables – chemical and mechanical damage – are introduced. •The value of the swelling pressure is estimated by the diffuse double layer theory. •A simplified scheme is proposed to relate macro- and microscopic properties. •The chemo-mechanical damage model is validated by simulating tests in literature.

  8. Gas-phase thermolysis reaction of formaldehyde diperoxide. Kinetic study and theoretical mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Jorge, Nelly Lidia [Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Av. Las Palmeras 4, 18100 Armilla, Granada (Spain); Area de Quimica Fisica Facultad de Ciencias Exactas y Naturales y Agrimensura, UNNE, Avda. Libertad 5460, 3400 Corrientes (Argentina); Romero, Jorge Marcelo [Area de Quimica Fisica Facultad de Ciencias Exactas y Naturales y Agrimensura, UNNE, Avda. Libertad 5460, 3400 Corrientes (Argentina); Grand, Andre [INAC, SCIB, Laboratoire ' Lesions des Acides Nucleiques' , UMR CEA-UJF E3, CEA-Grenoble, 17 Rue des Martyrs, 38054 Grenoble cedex 9 (France); Hernandez-Laguna, Alfonso, E-mail: ahlaguna@ugr.es [Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Av. Las Palmeras 4, 18100 Armilla, Granada (Spain)

    2012-01-17

    Highlights: Black-Right-Pointing-Pointer Kinetic and mechanism of the gas-phase thermolysis of tetroxane were determined. Black-Right-Pointing-Pointer Gas chromatography and computational potential energy surfaces were performed. Black-Right-Pointing-Pointer A mechanism in steps looked like the most probable mechanism. Black-Right-Pointing-Pointer A spin-orbit coupling appeared at the singlet and triple diradical open structures. Black-Right-Pointing-Pointer A non-adiabatic crossing from the singlet to the triplet state occurred. - Abstract: Gas-phase thermolysis reaction of formaldehyde diperoxide (1,2,4,5-tetroxane) was performed in an injection chamber of a gas chromatograph at a range of 463-503 K. The average Arrhenius activation energy and pre-exponential factor were 29.3 {+-} 0.8 kcal/mol and 5.2 Multiplication-Sign 10{sup 13} s{sup -1}, respectively. Critical points and reaction paths of the ground singlet and first triplet potential energy surfaces (PES) were calculated, using DFT method at BHANDHLYP/6-311+G{sup Asterisk-Operator Asterisk-Operator} level of the theory. Also, G3 calculations were performed on the reactant and products. Reaction by the ground-singlet and first-triplet states turned out to be endothermic and exothermic, respectively. The mechanism in three steps seemed to be the most probable one. An electronically non-adiabatic process appeared, in which a crossing, at an open diradical structure, from the singlet to the triplet state PES occurred, due to a spin-orbit coupling, yielding an exothermic reaction. Theoretical kinetic constant coming from the non- adiabatic transition from the singlet to the triplet state agrees with the experimental values.

  9. Concerted and stepwise mechanisms in cycloaddition reactions: potential surfaces and isotope effects

    International Nuclear Information System (INIS)

    Houk, K.N.; Yi Li; Storer, Joey; Raimondi, Laura; Beno, Brett

    1994-01-01

    CASSCF/6-31G * calculations have been performed on concerted and stepwise Diels-Alder reactions of butadiene with ethene, the dimerization of butadiene, and the dimerization of cyclobutadiene. The relative energies of concerted and stepwise mechanisms are compared, and the factors influencing these ''energies of concert'' are discussed. The comparison of calculated isotope effects to experimental data provides support for theoretical results. (Author)

  10. Gas-phase thermolysis reaction of formaldehyde diperoxide. Kinetic study and theoretical mechanisms

    International Nuclear Information System (INIS)

    Jorge, Nelly Lidia; Romero, Jorge Marcelo; Grand, André; Hernández-Laguna, Alfonso

    2012-01-01

    Highlights: ► Kinetic and mechanism of the gas-phase thermolysis of tetroxane were determined. ► Gas chromatography and computational potential energy surfaces were performed. ► A mechanism in steps looked like the most probable mechanism. ► A spin–orbit coupling appeared at the singlet and triple diradical open structures. ► A non-adiabatic crossing from the singlet to the triplet state occurred. - Abstract: Gas-phase thermolysis reaction of formaldehyde diperoxide (1,2,4,5-tetroxane) was performed in an injection chamber of a gas chromatograph at a range of 463–503 K. The average Arrhenius activation energy and pre-exponential factor were 29.3 ± 0.8 kcal/mol and 5.2 × 10 13 s −1 , respectively. Critical points and reaction paths of the ground singlet and first triplet potential energy surfaces (PES) were calculated, using DFT method at BHANDHLYP/6-311+G ∗∗ level of the theory. Also, G3 calculations were performed on the reactant and products. Reaction by the ground-singlet and first-triplet states turned out to be endothermic and exothermic, respectively. The mechanism in three steps seemed to be the most probable one. An electronically non-adiabatic process appeared, in which a crossing, at an open diradical structure, from the singlet to the triplet state PES occurred, due to a spin–orbit coupling, yielding an exothermic reaction. Theoretical kinetic constant coming from the non- adiabatic transition from the singlet to the triplet state agrees with the experimental values.

  11. Mechanism of catalytic action of oxide systems in reactions of aldehyde oxidation to carboxylic acids

    International Nuclear Information System (INIS)

    Andrushkevich, T.V.

    1997-01-01

    Mechanism of selective action of oxide catalysts (on the base of V 2 O 4 , MoO 3 ) of aldehyde oxidation to acids is considered, reaction acrolein oxidation to acrylic acid is taken as an example. Multistage mechanism of the process is established; it involves consequent transformation of coordination-bonded aldehyde into carbonyl-bonded aldehyde and symmetric carboxylate. Principles of active surface construction are formulated, they take into account the activity of stabilization center of concrete intermediate compound and bond energy of oxygen with surface. (author)

  12. Thermal runaway reaction hazards and mechanisms of hydroxylamine with acid/base contaminants

    International Nuclear Information System (INIS)

    Wei Chunyang; Saraf, Sanjeev R.; Rogers, William J.; Sam Mannan, M.

    2004-01-01

    Hydroxylamine (HA) has been involved in two incidents since 1999 because of its thermal instability and incompatibility. In this study, thermal runaway reactions of hydroxylamine with various concentrations of KOH and HCl were studied using the reactive system screening tool (RSST) and automatic pressure tracking adiabatic calorimeter (APTAC). The thermokinetic data, such as onset temperature, heat of reaction, maximum self-heat rate, maximum pressure rate, and non-condensable gas pressure, were compared with those of hydroxylamine solution without added impurity. Our study shows that the thermal decomposition behavior of hydroxylamine is affected by the presence of acid/base, and mixing of hydroxylamine with acid/base may cause thermal decomposition at lower temperatures. Different decomposition pathways can be initiated by hydrogen ion and hydroxide ion. The decomposition mechanisms of hydroxylamine in alkaline and acidic solutions are proposed based on the products, information from the literature, and quantum mechanical calculations. The experimental results are discussed in terms of the proposed reaction mechanisms

  13. The oxidative response and viable reaction mechanism of the textile dyes by fenton reagent

    International Nuclear Information System (INIS)

    Masooda, Q.; Hijira, T.; Sitara, M.; Sehar, M.; Sundus, A.; Mohsin, A.

    2017-01-01

    The mechanism of the degradation of the Reactive Red 239 and Reactive Blue 19 by Fenton reagent was studied by advanced oxidation process in aqueous medium. The spectroscopic technique was adopted for the measurements of dye concentration. Moreover they were determined at 540 nm and 590 nm, respectively. Kinetics of the reaction was studied under the effect of concentration of reactive dyes, concentration of oxidant were followed under pseudo first order condition and found to influence the catalytic mechanism. The pH of the medium, vibrant response of several cations and anions and influence of ionic strength on the reaction kinetics were also monitored. Physical evidences for the degradation and mineralization of the dyes were evaluated by Lime water test, Ring Test and TLC test also confirmed the degradation of dye. Inhibitory effects of dyes were observed by CO3-, HCO3-, HPO42-, Cl-, I- Al3+ and Na+. Thermodynamic activation parameters in the oxidation reaction were studied and mode of mechanism was suggested on the basic of these parameters. This study explored the safe and eco friendly degradation of the textile dyes under Pseudo first order rate constant. It was observed that Fenton assisted degradation of the dyes under controlled conditions was found to be favorable for the treatment of textile wastewater. Moreover compared to other chemical methods it is effective and harmless to the environment. (author)

  14. Close correlation between the reaction mechanism and inner structure of loosely halo-nuclei

    International Nuclear Information System (INIS)

    Liu Jianye; Tianshui Normal Univ., Tianshui; National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou; Guo Wenjun; Ren Zhongzhou; National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou; Xing Yongzhong; National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou

    2006-01-01

    It was based on the comparisons of the variance properties of fragment multiplicities FM's and nuclear stoppings R's for the neutron-halo colliding system with those of FZ's and R's for the proton-halo colliding system with the increases of beam energy in more detail, the closely correlations between the reaction mechanism and the inner structures of halo-nuclei is found. From above comparisons it is found that the variance properties of fragment multiplicities and nuclear stopping with the increases of beam energy are quite different for the neutron-halo and proton halo colliding systems, such as the effects of loosely bound neutron-halo structure on the fragment multiplicities and nuclear stopping are obviously larger than those for the proton-halo colliding system. This is due to that the structures of halo-neutron nucleus 11 Li is more loosely than that of the proton-halo nucleus 23 Al. In this case, the fragment multiplicity and nuclear stopping of halo nuclei may be used as a possible probe for studying the reaction mechanism and the correlation between the reaction mechanism and the inner structure of halo-nuclei. (authors)

  15. Double-lock ratchet mechanism revealing the role of  SER-344 in FoF1 ATP synthase

    KAUST Repository

    Beke-Somfai, T.; Lincoln, P.; Norden, B.

    2011-01-01

    In a majority of living organisms, FoF1 ATP synthase performs the fundamental process of ATP synthesis. Despite the simple net reaction formula, ADP+Pi→ATP+H2O, the detailed step-by-step mechanism of the reaction yet remains to be resolved owing

  16. Kinetics and mechanism of oxygen reduction reaction at CoPd system synthesized on XC72

    International Nuclear Information System (INIS)

    Tarasevich, M.R.; Chalykh, A.E.; Bogdanovskaya, V.A.; Kuznetsova, L.N.; Kapustina, N.A.; Efremov, B.N.; Ehrenburg, M.R.; Reznikova, L.A.

    2006-01-01

    Studies are presented of the kinetics and mechanism of oxygen electroreduction reaction on CoPd catalysts synthesized on carbon black XC72. As shown both in model conditions and in the tests within the cathodes of hydrogen-oxygen fuel cells with proton conducting electrolyte, CoPd/C system features a higher activity, as compared to Co/C. The highest activity in the oxygen reduction reaction is demonstrated by the catalysts with the Pd:Co atomic ratio being 7:3 and 4:1. The structural studies (XPS and XRD, and also the data of CO desorption measurements) evidence the CoPd alloy formation, which is reflected in the negative shift of the bonding energy maximum as compared to Pd/C and in the appearance of the additional CO desorption maximums on the voltammograms. It is found by means of structural research that CoPd alloy is formed in the course of the catalyst synthesis which features a higher catalytic activity of the binary systems. Besides, CoPd/C catalyst is more stable in respect to corrosion than Pd supported on carbon black. The measurements on the rotating disc electrode and rotating ring-disc electrode evidence that CoPd/C system provides the predominant oxygen reduction to water in the practically important range of potentials (E > 0.7 V). The proximity of kinetic parameters of the oxygen reduction reaction on CoPd/C and Pt/C catalysts points to the similar reaction mechanism. The slow step of the reaction is the addition of the first electron to the adsorbed and previously protonated O 2 molecule. The assumptions are offered about the reasons causing the higher activity and selectivity of the binary catalyst towards oxygen reduction to water, as compared to Co/C. The studies of the most active catalysts within the fuel cell cathodes are performed

  17. The Hexadehydro-Diels-Alder Cycloisomerization Reaction Proceeds by a Stepwise Mechanism.

    Science.gov (United States)

    Wang, Tao; Niu, Dawen; Hoye, Thomas R

    2016-06-29

    We report here experiments showing that the hexadehydro-Diels-Alder (HDDA) cycloisomerization reaction proceeds in a stepwise manner-i.e., via a diradical intermediate. Judicious use of substituent effects was decisive. We prepared (i) a series of triyne HDDA substrates that differed only in the R group present on the remote terminus of the diynophilic alkyne and (ii) an analogous series of dienophilic alkynes (n-C7H15COC≡CR) for use in classical Diels-Alder (DA) reactions (with 1,3-cyclopentadiene). The R groups were CF3, CHO, COMe/Et, CO2Me, CONMe2/Et2, H, and 1-propynyl. The relative rates of both the HDDA cyclization reactions and the simple DA cycloadditions were measured. The reactivity trends revealed a dramatic difference in the behaviors of the CF3 (slowest HDDA and nearly fastest DA) and 1-propynyl (fastest HDDA and slowest DA) containing members of each series. These differences can be explained by invoking radical-stabilizing energies rather than electron-withdrawing effects as the dominating feature of the HDDA reaction.

  18. (3He,α) reaction mechanism at high energy and neutron inner shell structure

    International Nuclear Information System (INIS)

    Wiele, J. van de.

    1980-01-01

    The ( 3 He,α) reaction on 12 C, 16 O, 28 Si, 58 Ni, 90 Zr, 118 Sn, 124 Sn and 208 Pb targets has been studied at Esub( 3 He) = 217 MeV (or 205 MeV) in order to investigate the reaction mechanism at high energy and large momentum transfer. The reaction yields large cross sections at very forward angles and strongly enhances the largest orbital momentum transfer. The angular distribution shapes are well reproduced in the frame-work of the Z-R- D.W.B.A. analysis if we use a unique empirical α-potential: Vsub(α)(Esub(α)) = Vsub( 3 He)(3/4 Esub(α)) + Vsub(n)(1/4 Esub(α)). The excitation energy spectra have been measured up to 100 MeV in the residual light and medium nuclei and up to about 16 MeV in heavy nuclei. In addition to the well-known low-lying levels, peaks or broad structures are observed for each nucleus at higher excitation energies. They are attributed to pick up from inner shells: 1s( 11 C and 15 O), 1p( 27 Si), 1d5/2 + 1p( 57 Ni), 1f7/2( 89 Zr) 1g9/2 117 Sn, 123 Sn and 1h11/2( 207 Pb). Selectivity and localization of direct and indirect pick up ( 3 He,α) reactions were studied. Finite range calculations show that this reaction is not very sensitive to the details of the range from function but only to D 0 coefficient and range R. A microscopic α-nucleus optical potential calculated with n-n dependent and independent density forces is able to reproduce both elastic scattering and pick up reaction angular distributions [fr

  19. Elimination Reactions of (E)-2,4,6-Trinitrobenzaldehyde O-benzoyloximes Promoted by R2NH in MeCN. Change of Reaction Mechanism

    International Nuclear Information System (INIS)

    Cho, Bong Rae; Pyun, Sang Yong

    2010-01-01

    We have studied the nitrile-forming elimination reactions from 1 promoted by R 2 NH in MeCN. The reaction proceeded by (E1cb) irr mechanism. Change of the β-aryl group from 2,4-dinitrophenyl to a more strongly electron-withdrawing 2,4,6-trinitrophenyl increased the reaction rate by 470-fold, shifted the transition state toward more reactant-like, and changed the reaction mechanism from E2 to (E1cb) irr . To the best of our knowledge, this is the first example of nitrile-forming elimination reaction that proceeds by the (E1cb) irr mechanism in MeCN. Noteworthy is the carbanion stabilizing ability of the 2,4,6-trinitrophenyl group in aprotic solvent. Nitrile-forming elimination reactions of (E)-benzaldoxime derivatives have been extensively investigated under various conditions. The reactions proceeded by the E2 mechanism in MeCN despite the fact that the reactants have syn stereochemistry, poor leaving, and sp 2 hybridized β-carbon atom, all of which favor E1cb- or E1cb-like transition state. Moreover, the transition state structures were relatively insensitive to the variation of the reactant structures. The results have been attributed to the poor anion solvating ability of MeCN, which favors E2 transition state with maximum charge dispersal. For eliminations from strongly activated (E)-2,4-(NO 2 ) 2 C 6 H 3 CH=NOC(O)C 6 H 4 X, a change in the reaction mechanism from E2 to (E1cb) irr was observed as the base-solvent was changed from R 2 NH in MeCN to R 2 NH/R 2 NH 2 + in 70 mol % MeCN(aq). A combination of a strong electron-withdrawing β-aryl group and anion-solvating protic solvent was required for the mechanistic change

  20. Kinetics and Mechanism of the Reaction of Hydoxyl Radicals with Acetonitrile under Atmospheric Conditions

    Science.gov (United States)

    Hynes, A. J.; Wine, P. H.

    1997-01-01

    scheme to extract kinetic information about the adduct reations with O2 and branching ratios for OH regeneration. A plausible mechanism for OH regeneration in (2) involves OH addition to the nitrogen atom followed by O2 addition to the cyano carbon atom, isomeriazation and decomposition to D2CO + DOCN + OH. Our results suggest that the OH + CH3CN reaction occurs via a complex mechanism involving both bimolecular and termolecular pathways, analogous to the mechanisms for the the important atmospheric reactions of OH with CO and HNO3.

  1. Reciprocal osmotic challenges reveal mechanisms of divergence in phenotypic plasticity in the killifish Fundulus heteroclitus.

    Science.gov (United States)

    Brennan, Reid S; Galvez, Fernando; Whitehead, Andrew

    2015-04-15

    The killifish Fundulus heteroclitus is an estuarine species with broad physiological plasticity, enabling acclimation to diverse stressors. Previous work suggests that freshwater populations expanded their physiology to accommodate low salinity environments; however, it is unknown whether this compromises their tolerance to high salinity. We used a comparative approach to investigate the mechanisms of a derived freshwater phenotype and the fate of an ancestral euryhaline phenotype after invasion of a freshwater environment. We compared physiological and transcriptomic responses to high- and low-salinity stress in fresh and brackish water populations and found an enhanced plasticity to low salinity in the freshwater population coupled with a reduced ability to acclimate to high salinity. Transcriptomic data identified genes with a conserved common response, a conserved salinity-dependent response and responses associated with population divergence. Conserved common acclimation responses revealed stress responses and alterations in cell-cycle regulation as important mechanisms in the general osmotic response. Salinity-specific responses included the regulation of genes involved in ion transport, intracellular calcium, energetic processes and cellular remodeling. Genes diverged between populations were primarily those showing salinity-specific expression and included those regulating polyamine homeostasis and the cell cycle. Additionally, when populations were matched with their native salinity, expression patterns were consistent with the concept of 'transcriptomic resilience', suggesting local adaptation. These findings provide insight into the fate of a plastic phenotype after a shift in environmental salinity and help to reveal mechanisms allowing for euryhalinity. © 2015. Published by The Company of Biologists Ltd.

  2. Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins II reactions at side-chain loci in model systems

    International Nuclear Information System (INIS)

    Garrison, W.M.

    1983-11-01

    The major emphasis in radiation biology at the molecular level has been on the nucleic acid component of the nucleic acid-protein complex because of its primary genetic importance. But there is increasing evidence that radiation damage to the protein component also has important biological implications. Damage to capsid protein now appears to be a major factor in the radiation inactivation of phage and other viruses. And, there is increasing evidence that radiation-chemical change in the protein component of chromation leads to changes in the stability of the repressor-operator complexes involved in gene expression. Knowledge of the radiation chemistry of protein is also of importance in other fields such as the application of radiation sterilization to foods and drugs. Recent findings that a class of compounds, the α,α'-diaminodicarboxylic acids, not normally present in food proteins, are formed in protein radiolysis is of particular significance since certain of their peptide derivatives have been showing to exhibit immunological activity. The purpose of this review is to bring together and to correlate our present knowledge of products and mechanisms in the radiolysis of peptides, polypeptides and proteins both aqueous and solid-state. In part 1 we presented a discussion of the radiation-induced reactions of the peptide main-chain in model peptide and polypeptide systems. Here in part 2 the emphasis is on the competing radiation chemistry at side-chain loci of peptide derivatives of aliphatic, aromatic-unsaturated and sulfur-containing amino acids in similar systems. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis, and ESR spectroscopy are included

  3. Theoretical Research on the Mechanism of the Dimerization Reactions of Alkyl Ketene

    Directory of Open Access Journals (Sweden)

    Zhiguo Zhang

    2013-01-01

    Full Text Available A quantum chemical method was employed to investigate the mechanism of dimerization reactions of alkyl ketene. All the geometric configurations of the stationary points on the reactions path were optimized with Gaussian03 employing density functional theory at the B3LYP/6-311G++(d, p level by energy gradient technique. The transition states were also investigated through synchronous transit method, and its reasonability was confirmed by using frequency analysis and intrinsic reaction coordinate analysis. The results can be summed up as follows: according to the frontier orbital theory, the dimerization reaction (3 to generate four-membered carbon cyclic product P3 is forbidden. Two different dimerization processes of alkyl ketene are all concerted but nonsynchronous, taking place through twisted four-membered cyclic transition states. The activation energies were calculated to be 34.54 and 61.73 kJ/mol, respectively for the two ketene dimerization processes. Calculation results satisfactorily explained the experimental facts.

  4. Calcium-Magnesium-Aluminosilicate (CMAS) Reactions and Degradation Mechanisms of Advanced Environmental Barrier Coatings

    Science.gov (United States)

    Ahlborg, Nadia L.; Zhu, Dongming

    2013-01-01

    The thermochemical reactions between calcium-magnesium-aluminosilicate- (CMAS-) based road sand and several advanced turbine engine environmental barrier coating (EBC) materials were studied. The phase stability, reaction kinetics and degradation mechanisms of rare earth (RE)-silicates Yb2SiO5, Y2Si2O7, and RE-oxide doped HfO2 and ZrO2 under the CMAS infiltration condition at 1500 C were investigated, and the microstructure and phase characteristics of CMAS-EBC specimens were examined using Scanning Electron Microscopy (SEM) and X-ray Diffraction (XRD). Experimental results showed that the CMAS dissolved RE-silicates to form crystalline, highly non-stoichiometric apatite phases, and in particular attacking the silicate grain boundaries. Cross-section images show that the CMAS reacted with specimens and deeply penetrated into the EBC grain boundaries and formed extensive low-melting eutectic phases, causing grain boundary recession with increasing testing time in the silicate materials. The preliminary results also showed that CMAS reactions also formed low melting grain boundary phases in the higher concentration RE-oxide doped HfO2 systems. The effect of the test temperature on CMAS reactions of the EBC materials will also be discussed. The faster diffusion exhibited by apatite and RE-doped oxide phases and the formation of extensive grain boundary low-melting phases may limit the CMAS resistance of some of the environmental barrier coatings at high temperatures.

  5. Characteristics and mechanism of explosive reactions of Purex solvents with Nitric Acid at elevated temperatures

    Energy Technology Data Exchange (ETDEWEB)

    Miyata, Teijiro [Radiation Application Development Association, Tokai, Ibaraki (Japan); Takada, Junichi; Koike, Tadao; Tsukamoto, Michio; Watanabe, Koji [Department of Fuel Cycle Safety Research, Nuclear Safety Research Center, Tokai Research Establishment, Japan Atomic Energy Research Institute, Tokai, Ibaraki (Japan); Ida, Masaaki [JGC PLANTECH CO., LTD (Japan); Nakagiri, Naotaka [JGC Corp., Tokyo (Japan); Nishio, Gunji [Research Organization for Information Science and Technology, Tokai, Ibaraki (Japan)

    2000-03-01

    This investigation was undertaken to make clear the energetic properties and mechanism of explosive decomposition of Purex solvent systems (TBP/n-Dodecane/HNO{sub 3}) by Nitric Acid at elevated temperatures using a calorimetric technique (DSC, ARC) and a chromatographic technique (GC, GC/MS). The measurement of exothermic events of solvent-HNO{sub 3} reactions using DSC with a stainless steel sealed cell showed distinct two peaks with maxima at around 170 and 320degC, respectively. The peak at around 170degC was mainly attributed to the reactions of dealkylation products (n-butyl nitrate) of TBP and the solvent with nitric acid, and the peak at around 320degC was attributed to the exothermic decomposition of nitrated dodecanes formed in the foregoing exothermic reaction of dodecane with nitric acid. By using the data obtained in ARC experiments, activation energies of 123.2 and 152.5 kJ/mol were determined for the exothermic reaction of TBP with nitric acid and for the exothermic pyrolysis of n-butyl nitrate, respectively. Some possible pathways were considered for the explosive decomposition of TBP by nitric acid at elevated temperatures. (author)

  6. Memorable Experiences with Sad Music—Reasons, Reactions and Mechanisms of Three Types of Experiences

    Science.gov (United States)

    Peltola, Henna-Riikka

    2016-01-01

    Reactions to memorable experiences of sad music were studied by means of a survey administered to a convenience (N = 1577), representative (N = 445), and quota sample (N = 414). The survey explored the reasons, mechanisms, and emotions of such experiences. Memorable experiences linked with sad music typically occurred in relation to extremely familiar music, caused intense and pleasurable experiences, which were accompanied by physiological reactions and positive mood changes in about a third of the participants. A consistent structure of reasons and emotions for these experiences was identified through exploratory and confirmatory factor analyses across the samples. Three types of sadness experiences were established, one that was genuinely negative (Grief-Stricken Sorrow) and two that were positive (Comforting Sorrow and Sweet Sorrow). Each type of emotion exhibited certain individual differences and had distinct profiles in terms of the underlying reasons, mechanisms, and elicited reactions. The prevalence of these broad types of emotional experiences suggested that positive experiences are the most frequent, but negative experiences were not uncommon in any of the samples. The findings have implications for measuring emotions induced by music and fiction in general, and call attention to the non-pleasurable aspects of these experiences. PMID:27300268

  7. Reaction mechanism for the symmetric breakup of 24Mg following an interaction with 12C

    International Nuclear Information System (INIS)

    Gyapong, G.J.; Watson, D.L.; Catford, W.N.; Clarke, N.M.; Bennett, S.J.; Freer, M.; Fulton, B.R.; Jones, C.D.; Leddy, M.; Murgatroyd, J.T.; Rae, W.D.M.; Simmons, P.

    1994-01-01

    Data on the yield of the symmetric breakup of 24 Mg as a function of beam energy are presented and compared with detailed calculations of the energy dependence. The 24 Mg states seen in symmetric breakup agree with previously observed breakup states having spin and parities J π =4 + ,(6 + ),8 + . The data allow the variations of yield for indivual states to be judged, as the beam energy is varied. The variation in the yield of the 4 + states is compared in detail with calculations assuming several possible compound nuclear or direct reaction mechanisms. It is concluded that a massive ( 12 C) transfer or a simple statistical compound process are unlikely mechanisms, but that each of several other mechanisms is consistent with the data. ((orig.))

  8. Deciding where to attend: Large-scale network mechanisms underlying attention and intention revealed by graph-theoretic analysis.

    Science.gov (United States)

    Liu, Yuelu; Hong, Xiangfei; Bengson, Jesse J; Kelley, Todd A; Ding, Mingzhou; Mangun, George R

    2017-08-15

    The neural mechanisms by which intentions are transformed into actions remain poorly understood. We investigated the network mechanisms underlying spontaneous voluntary decisions about where to focus visual-spatial attention (willed attention). Graph-theoretic analysis of two independent datasets revealed that regions activated during willed attention form a set of functionally-distinct networks corresponding to the frontoparietal network, the cingulo-opercular network, and the dorsal attention network. Contrasting willed attention with instructed attention (where attention is directed by external cues), we observed that the dorsal anterior cingulate cortex was allied with the dorsal attention network in instructed attention, but shifted connectivity during willed attention to interact with the cingulo-opercular network, which then mediated communications between the frontoparietal network and the dorsal attention network. Behaviorally, greater connectivity in network hubs, including the dorsolateral prefrontal cortex, the dorsal anterior cingulate cortex, and the inferior parietal lobule, was associated with faster reaction times. These results, shown to be consistent across the two independent datasets, uncover the dynamic organization of functionally-distinct networks engaged to support intentional acts. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Reaction Mechanisms and HCCI Combustion Processes of Mixtures of n-Heptane and the Butanols

    Directory of Open Access Journals (Sweden)

    Hu eWang

    2015-03-01

    Full Text Available A reduced primary reference fuel (PRF-Alcohol-Di-tert-butyl Peroxide (DTBP mechanism with 108 species and 435 reactions, including sub-mechanisms of PRF, methanol, ethanol, DTBP and the four butanol isomers, is proposed for homogeneous charge compression ignition (HCCI engine combustion simulations of butanol isomers/n-heptane mixtures. HCCI experiments fuelled with butanol isomer/n-heptane mixtures on two different engines are conducted for the validation of proposed mechanism. The mechanism has been validated against shock tube ignition delays, laminar flame speeds, species profiles in premixed flames and engine HCCI combustion data, and good agreements with experimental results are demonstrated under various validation conditions. It is found that although the reactivity of neat tert-butanol is the lowest, mixtures of tert-butanol/n-heptane exhibit the highest reactivity among the butanol isomer/n-heptane mixtures if the n-heptane blending ratio exceeds 20% (mole. Kinetic analysis shows that the highest C-H bond energy in the tert-butanol molecule is partially responsible for this phenomenon. It is also found that the reaction tC4H9OH+CH3O2 =tC4H9O+CH3O2H plays important role and eventually produces the OH radical to promote the ignition and combustion. The proposed mechanism is able to capture HCCI combustion processes of the butanol/n-heptane mixtures under different operating conditions. In addition, the trend that tert-butanol /n-heptane has the highest reactivity is also captured in HCCI combustion simulations. The results indicate that the current mechanism can be used for HCCI engine predictions of PRF and alcohol fuels.

  10. Quantum mechanical/molecular mechanical modeling finds Diels-Alder reactions are accelerated less on the surface of water than in water.

    Science.gov (United States)

    Thomas, Laura L; Tirado-Rives, Julian; Jorgensen, William L

    2010-03-10

    Quantum and molecular mechanics calculations for the Diels-Alder reactions of cyclopentadiene with 1,4-naphthoquinone, methyl vinyl ketone, and acrylonitrile have been carried out at the vacuum-water interface and in the gas phase. In conjunction with previous studies of these cycloadditions in dilute solution, a more complete picture of aqueous environmental effects emerges with implications for the origin of observed rate accelerations using heterogeneous aqueous suspensions, "on water" conditions. The pure TIP4P water slab maintains the bulk density and hydrogen-bonding properties in central water layers. The bulk region merges to vacuum over a ca. 5 A band with progressive diminution of the density and hydrogen bonding. The relative free energies of activation and transition structures for the reactions at the interface are found to be intermediate between those calculated in the gas phase and in bulk water; i.e., for the reaction with 1,4-naphthoquinone, the DeltaDeltaG(++) values relative to the gas phase are -3.6 and -7.3 kcal/mol at the interface and in bulk water, respectively. Thus, the results do not support the notion that a water surface is more effective than bulk water for catalysis of such pericyclic reactions. The trend is in qualitative agreement with expectations based on density considerations and estimates of experimental rate constants for the gas phase, a heterogeneous aqueous suspension, and a dilute aqueous solution for the reaction of cyclopentadiene with methyl vinyl ketone. Computed energy pair distributions reveal a uniform loss of 0.5-1.0 hydrogen bond for the reactants and transition states in progressing from bulk water to the vacuum-water interface. Orientational effects are apparent at the surface; e.g., the carbonyl group in the methyl vinyl ketone transition structure is preferentially oriented into the surface. Also, the transition structure for the 1,4-naphthoquinone case is buried more in the surface, and the free energy of

  11. Multi-level quantum mechanics theories and molecular mechanics study of the double-inversion mechanism of the F- + CH3I reaction in aqueous solution.

    Science.gov (United States)

    Liu, Peng; Zhang, Jingxue; Wang, Dunyou

    2017-06-07

    A double-inversion mechanism of the F - + CH 3 I reaction was discovered in aqueous solution using combined multi-level quantum mechanics theories and molecular mechanics. The stationary points along the reaction path show very different structures to the ones in the gas phase due to the interactions between the solvent and solute, especially strong hydrogen bonds. An intermediate complex, a minimum on the potential of mean force, was found to serve as a connecting-link between the abstraction-induced inversion transition state and the Walden-inversion transition state. The potentials of mean force were calculated with both the DFT/MM and CCSD(T)/MM levels of theory. Our calculated free energy barrier of the abstraction-induced inversion is 69.5 kcal mol -1 at the CCSD(T)/MM level of theory, which agrees with the one at 72.9 kcal mol -1 calculated using the Born solvation model and gas-phase data; and our calculated free energy barrier of the Walden inversion is 24.2 kcal mol -1 , which agrees very well with the experimental value at 25.2 kcal mol -1 in aqueous solution. The calculations show that the aqueous solution makes significant contributions to the potentials of mean force and exerts a big impact on the molecular-level evolution along the reaction pathway.

  12. Evolution of reaction mechanisms for the reaction 36Ar + 58Ni studied from 32 to 95 A*MeV with the INDRA multidetector

    International Nuclear Information System (INIS)

    De Filippo, E.

    1995-03-01

    In the context of the multifragmentation study program with the 4π INDRA detector at GANIL, the reaction 36 Ar + 58 Ni has been studied at seven different energies ranging from 32 to 95 A*MeV. After a brief description of the detector characteristics and of the data treatment, results on the evolution of intermediate mass fragments (IMF) distributions with incident energy and a first outlook about reaction mechanisms are presented. (author). 15 refs., 10 figs

  13. Mechanism and kinetics in reactions of caffeic acid with radicals by pulse radiolysis and calculation

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xifeng; Cai, Zhongli; Katsumura, Yosuke [Tokyo Univ., Tokai, Ibaraki (Japan). Nuclear Engineering Research Lab

    2000-03-01

    The interaction of caffeic acid with e{sub aq}{sup -}, (CH{sub 3}){sub 2}(OH) CCH{sub 2}{sup {center_dot}}, CO{sub 2}{sup {center_dot}}{sup -}, H{sup {center_dot}}, {center_dot}OH and N{sub 3}{sup {center_dot}} radicals were studied by {gamma}-, pulse radiolysis and molecular orbital calculation. UV-visible spectra of electron/{center_dot}OH adducts, semi-quinone radicals of caffeic ions, and the stable products from the reactions were derived. The rate constants were determined. The attacked sites and the most favorable structures of the transient radicals were predicted. Reaction mechanisms were proposed. (author)

  14. Reaction Mechanism of Tar Evolution in Biomass Steam Gasification for Hydrogen Production

    International Nuclear Information System (INIS)

    Shingo Katayama; Masahiro Suzuki; Atsushi Tsutsumi

    2006-01-01

    Reaction mechanism of tar evolution in steam gasification of biomass was investigated with a continuous cross-flow moving bed type differential reactor, in which tar and gases can be fractionated according to reaction time. We estimated that time profile of tar and gas evolution in the gasification of cellulose, xylan, and lignin, and compared it with experimental product time profile of real biomass gasification. The experimental tar evolution rate is different from estimated tar evolution rate. The estimated tar evolution rate has a peak at 20 s. On the other hand, the experimental tar evolution rate at 20 s is little, and tar at initial stage includes more water-soluble and water-insoluble compounds. It can be concluded that in the real biomass steam gasification the evolution of tar from cellulose and lignin component was found to be precipitated by that from hemi-cellulose component. (authors)

  15. Heterogeneous kinetics, products, and mechanisms of ferulic acid particles in the reaction with NO3 radicals

    Science.gov (United States)

    Liu, Changgeng; Zhang, Peng; Wen, Xiaoying; Wu, Bin

    2017-03-01

    Methoxyphenols, as an important component of wood burning, are produced by lignin pyrolysis and considered to be the potential tracers for wood smoke emissions. In this work, the heterogeneous reaction between ferulic acid particles and NO3 radicals was investigated. Six products including oxalic acid, 4-vinylguaiacol, vanillin, 5-nitrovanillin, 5-nitroferulic acid, and caffeic acid were confirmed by gas chromatography-mass spectrometry (GC-MS). In addition, the reaction mechanisms were proposed and the main pathways were NO3 electrophilic addition to olefin and the meta-position to the hydroxyl group. The uptake coefficient of NO3 radicals on ferulic acid particles was 0.17 ± 0.02 and the effective rate constant under experimental conditions was (1.71 ± 0.08) × 10-12 cm3 molecule-1 s-1. The results indicate that ferulic acid degradation by NO3 can be an important sink at night.

  16. Revealing Nanoscale Passivation and Corrosion Mechanisms of Reactive Battery Materials in Gas Environments.

    Science.gov (United States)

    Li, Yuzhang; Li, Yanbin; Sun, Yongming; Butz, Benjamin; Yan, Kai; Koh, Ai Leen; Zhao, Jie; Pei, Allen; Cui, Yi

    2017-08-09

    Lithium (Li) metal is a high-capacity anode material (3860 mAh g -1 ) that can enable high-energy batteries for electric vehicles and grid-storage applications. However, Li metal is highly reactive and repeatedly consumed when exposed to liquid electrolyte (during battery operation) or the ambient environment (throughout battery manufacturing). Studying these corrosion reactions on the nanoscale is especially difficult due to the high chemical reactivity of both Li metal and its surface corrosion films. Here, we directly generate pure Li metal inside an environmental transmission electron microscope (TEM), revealing the nanoscale passivation and corrosion process of Li metal in oxygen (O 2 ), nitrogen (N 2 ), and water vapor (H 2 O). We find that while dry O 2 and N 2 (99.9999 vol %) form uniform passivation layers on Li, trace water vapor (∼1 mol %) disrupts this passivation and forms a porous film on Li metal that allows gas to penetrate and continuously react with Li. To exploit the self-passivating behavior of Li in dry conditions, we introduce a simple dry-N 2 pretreatment of Li metal to form a protective layer of Li nitride prior to battery assembly. The fast ionic conductivity and stable interface of Li nitride results in improved battery performance with dendrite-free cycling and low voltage hysteresis. Our work reveals the detailed process of Li metal passivation/corrosion and demonstrates how this mechanistic insight can guide engineering solutions for Li metal batteries.

  17. Elastoviscous Transitions of Articular Cartilage Reveal a Mechanism of Synergy between Lubricin and Hyaluronic Acid.

    Directory of Open Access Journals (Sweden)

    Edward D Bonnevie

    Full Text Available When lubricated by synovial fluid, articular cartilage provides some of the lowest friction coefficients found in nature. While it is known that macromolecular constituents of synovial fluid provide it with its lubricating ability, it is not fully understood how two of the main molecules, lubricin and hyaluronic acid, lubricate and interact with one another. Here, we develop a novel framework for cartilage lubrication based on the elastoviscous transition to show that lubricin and hyaluronic acid lubricate by distinct mechanisms. Such analysis revealed nonspecific interactions between these molecules in which lubricin acts to concentrate hyaluronic acid near the tissue surface and promotes a transition to a low friction regime consistent with the theory of viscous boundary lubrication. Understanding the mechanics of synovial fluid not only provides insight into the progression of diseases such as arthritis, but also may be applicable to the development of new biomimetic lubricants.

  18. Revealing −1 Programmed Ribosomal Frameshifting Mechanisms by Single-Molecule Techniques and Computational Methods

    Directory of Open Access Journals (Sweden)

    Kai-Chun Chang

    2012-01-01

    Full Text Available Programmed ribosomal frameshifting (PRF serves as an intrinsic translational regulation mechanism employed by some viruses to control the ratio between structural and enzymatic proteins. Most viral mRNAs which use PRF adapt an H-type pseudoknot to stimulate −1 PRF. The relationship between the thermodynamic stability and the frameshifting efficiency of pseudoknots has not been fully understood. Recently, single-molecule force spectroscopy has revealed that the frequency of −1 PRF correlates with the unwinding forces required for disrupting pseudoknots, and that some of the unwinding work dissipates irreversibly due to the torsional restraint of pseudoknots. Complementary to single-molecule techniques, computational modeling provides insights into global motions of the ribosome, whose structural transitions during frameshifting have not yet been elucidated in atomic detail. Taken together, recent advances in biophysical tools may help to develop antiviral therapies that target the ubiquitous −1 PRF mechanism among viruses.

  19. A general reaction mechanism for carbapenem hydrolysis by mononuclear and binuclear metallo-β-lactamases.

    Science.gov (United States)

    Lisa, María-Natalia; Palacios, Antonela R; Aitha, Mahesh; González, Mariano M; Moreno, Diego M; Crowder, Michael W; Bonomo, Robert A; Spencer, James; Tierney, David L; Llarrull, Leticia I; Vila, Alejandro J

    2017-09-14

    Carbapenem-resistant Enterobacteriaceae threaten human health, since carbapenems are last resort drugs for infections by such organisms. Metallo-β-lactamases (MβLs) are the main mechanism of resistance against carbapenems. Clinically approved inhibitors of MBLs are currently unavailable as design has been limited by the incomplete knowledge of their mechanism. Here, we report a biochemical and biophysical study of carbapenem hydrolysis by the B1 enzymes NDM-1 and BcII in the bi-Zn(II) form, the mono-Zn(II) B2 Sfh-I and the mono-Zn(II) B3 GOB-18. These MβLs hydrolyse carbapenems via a similar mechanism, with accumulation of the same anionic intermediates. We characterize the Michaelis complex formed by mono-Zn(II) enzymes, and we identify all intermediate species, enabling us to propose a chemical mechanism for mono and binuclear MβLs. This common mechanism open avenues for rationally designed inhibitors of all MβLs, notwithstanding the profound differences between these enzymes' active site structure, β-lactam specificity and metal content.Carbapenem-resistant bacteria pose a major health threat by expressing metallo-β-lactamases (MβLs), enzymes able to hydrolyse these life-saving drugs. Here the authors use biophysical and computational methods and show that different MβLs share the same reaction mechanism, suggesting new strategies for drug design.

  20. From Sound to Significance: Exploring the Mechanisms Underlying Emotional Reactions to Music.

    Science.gov (United States)

    Juslin, Patrik N; Barradas, Gonçalo; Eerola, Tuomas

    2015-01-01

    A common approach to studying emotional reactions to music is to attempt to obtain direct links between musical surface features such as tempo and a listener's responses. However, such an analysis ultimately fails to explain why emotions are aroused in the listener. In this article we explore an alternative approach, which aims to account for musical emotions in terms of a set of psychological mechanisms that are activated by different types of information in a musical event. This approach was tested in 4 experiments that manipulated 4 mechanisms (brain stem reflex, contagion, episodic memory, musical expectancy) by selecting existing musical pieces that featured information relevant for each mechanism. The excerpts were played to 60 listeners, who were asked to rate their felt emotions on 15 scales. Skin conductance levels and facial expressions were measured, and listeners reported subjective impressions of relevance to specific mechanisms. Results indicated that the target mechanism conditions evoked emotions largely as predicted by a multimechanism framework and that mostly similar effects occurred across the experiments that included different pieces of music. We conclude that a satisfactory account of musical emotions requires consideration of how musical features and responses are mediated by a range of underlying mechanisms.

  1. Kinetic mechanism of human DNA ligase I reveals magnesium-dependent changes in the rate-limiting step that compromise ligation efficiency.

    Science.gov (United States)

    Taylor, Mark R; Conrad, John A; Wahl, Daniel; O'Brien, Patrick J

    2011-07-01

    DNA ligase I (LIG1) catalyzes the ligation of single-strand breaks to complete DNA replication and repair. The energy of ATP is used to form a new phosphodiester bond in DNA via a reaction mechanism that involves three distinct chemical steps: enzyme adenylylation, adenylyl transfer to DNA, and nick sealing. We used steady state and pre-steady state kinetics to characterize the minimal mechanism for DNA ligation catalyzed by human LIG1. The ATP dependence of the reaction indicates that LIG1 requires multiple Mg(2+) ions for catalysis and that an essential Mg(2+) ion binds more tightly to ATP than to the enzyme. Further dissection of the magnesium ion dependence of individual reaction steps revealed that the affinity for Mg(2+) changes along the reaction coordinate. At saturating concentrations of ATP and Mg(2+) ions, the three chemical steps occur at similar rates, and the efficiency of ligation is high. However, under conditions of limiting Mg(2+), the nick-sealing step becomes rate-limiting, and the adenylylated DNA intermediate is prematurely released into solution. Subsequent adenylylation of enzyme prevents rebinding to the adenylylated DNA intermediate comprising an Achilles' heel of LIG1. These ligase-generated 5'-adenylylated nicks constitute persistent breaks that are a threat to genomic stability if they are not repaired. The kinetic and thermodynamic framework that we have determined for LIG1 provides a starting point for understanding the mechanism and specificity of mammalian DNA ligases.

  2. Mechanisms of emission of particles charged in 6Li + 6Li and 6Li + 10B reactions at low energies

    International Nuclear Information System (INIS)

    Quebert, Jean

    1964-01-01

    The lithium 6 nucleus is a projectile of interest to study nuclear reactions at low energy due to the possibility to obtain high heats of reaction, and to its structure which can play an important role in the projectile-target interaction. This research thesis focused on the study of two low-energy reactions provoked by lithium projectiles. These reactions are studied within the framework of the theoretical model of aggregates. The first part presents the experimental conditions of both reactions, reports the development and analysis of nuclear plates, and the transformation of a given type of particle histogram into a spectrum in the mass centre system. The next parts report the study of the 6 Li + 6 Li reaction (previous results, kinematic analysis, spectrum of secondary particles, theoretical analysis of results) and of the 6 Li + 10 B reaction (previous results, experimental results, study of the continuous spectrum of alpha particle, reaction mechanisms)

  3. A Systems Biology Approach Reveals Converging Molecular Mechanisms that Link Different POPs to Common Metabolic Diseases.

    Science.gov (United States)

    Ruiz, Patricia; Perlina, Ally; Mumtaz, Moiz; Fowler, Bruce A

    2016-07-01

    A number of epidemiological studies have identified statistical associations between persistent organic pollutants (POPs) and metabolic diseases, but testable hypotheses regarding underlying molecular mechanisms to explain these linkages have not been published. We assessed the underlying mechanisms of POPs that have been associated with metabolic diseases; three well-known POPs [2,3,7,8-tetrachlorodibenzodioxin (TCDD), 2,2´,4,4´,5,5´-hexachlorobiphenyl (PCB 153), and 4,4´-dichlorodiphenyldichloroethylene (p,p´-DDE)] were studied. We used advanced database search tools to delineate testable hypotheses and to guide laboratory-based research studies into underlying mechanisms by which this POP mixture could produce or exacerbate metabolic diseases. For our searches, we used proprietary systems biology software (MetaCore™/MetaDrug™) to conduct advanced search queries for the underlying interactions database, followed by directional network construction to identify common mechanisms for these POPs within two or fewer interaction steps downstream of their primary targets. These common downstream pathways belong to various cytokine and chemokine families with experimentally well-documented causal associations with type 2 diabetes. Our systems biology approach allowed identification of converging pathways leading to activation of common downstream targets. To our knowledge, this is the first study to propose an integrated global set of step-by-step molecular mechanisms for a combination of three common POPs using a systems biology approach, which may link POP exposure to diseases. Experimental evaluation of the proposed pathways may lead to development of predictive biomarkers of the effects of POPs, which could translate into disease prevention and effective clinical treatment strategies. Ruiz P, Perlina A, Mumtaz M, Fowler BA. 2016. A systems biology approach reveals converging molecular mechanisms that link different POPs to common metabolic diseases. Environ

  4. Exchange reaction between hydrogen and deuterium. I. Importance of surface reactions in the steady-state mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Marteau, C; Gaillard-Cusin, F; James, H [Centre National de la Recherche Scientifique, 45 - Orleans-la-Source (France). Centre de Recherches sur la Chimie de Combustion et des Hautes Temperatures

    1978-05-01

    Investigation of heterogeneous initiation process of gas phase linear chain reactions is carried out through the study of H/sub 2/-D/sub 2/ exchange reaction. Experimental data under study concern mainly the stationary rate of HD formation and the prestationary proceeding. Steady-state method accounts for the first one of these data; it allows to clearly compare the wall process part to the part played by the homogeneous chain reaction towards HD formation. Activation energy of exchange elementary step between chemisorbed hydrogen (on silica) and gaseous deuterium has been evaluated: Esub(e1)=52+-1 Kcal/mole.

  5. Kinetics modeling and reaction mechanism of ferrate(VI) oxidation of benzotriazoles.

    Science.gov (United States)

    Yang, Bin; Ying, Guang-Guo; Zhang, Li-Juan; Zhou, Li-Jun; Liu, Shan; Fang, Yi-Xiang

    2011-03-01

    Benzotriazoles (BTs) are high production volume chemicals with broad application in various industrial processes and in households, and have been found to be omnipresent in aquatic environments. We investigated oxidation of five benzotriazoles (BT: 1H-benzotriazole; 5MBT: 5-methyl-1H-benzotriazole; DMBT: 5,6-dimethyl-1H-benzotriazole hydrate; 5CBT: 5-chloro-1H-benzotriazole; HBT: 1-hydroxybenzotriazole) by aqueous ferrate (Fe(VI)) to determine reaction kinetics as a function of pH (6.0-10.0), and interpreted the reaction mechanism of Fe(VI) with BTs by using a linear free-energy relationship. The pK(a) values of BT and DMBT were also determined using UV-Visible spectroscopic method in order to calculate the species-specific rate constants, and they were 8.37 ± 0.0 and 8.98 ± 0.08 respectively. Each of BTs reacted moderately with Fe(VI) with the k(app) ranged from 7.2 to 103.8 M(-1)s(-1) at pH 7.0 and 24 ± 1 °C. When the molar ratio of Fe(VI) and BTs increased up to 30:1, the removal rate of BTs reached about >95% in buffered milli-Q water or secondary wastewater effluent. The electrophilic oxidation mechanism of the above reaction was illustrated by using a linear free-energy relationship between pH-dependence of species-specific rate constants and substituent effects (σ(p)). Fe(VI) reacts initially with BTs by electrophilic attack at the 1,2,3-triazole moiety of BT, 5MBT, DMBT and 5CBT, and at the N-OH bond of HBT. Moreover, for BT, 5MBT, DMBT and 5CBT, the reactions with the species HFeO(4)(-) predominantly controled the reaction rates. For HBT, the species H(2)FeO(4) with dissociated HBT played a major role in the reaction. The results showed that Fe(VI) has the ability to degrade benzotriazoles in water. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. Studying mechanism of radical reactions: From radiation to nitroxides as research tools

    Science.gov (United States)

    Maimon, Eric; Samuni, Uri; Goldstein, Sara

    2018-02-01

    Radicals are part of the chemistry of life, and ionizing radiation chemistry serves as an indispensable research tool for elucidation of the mechanism(s) underlying their reactions. The ever-increasing understanding of their involvement in diverse physiological and pathological processes has expanded the search for compounds that can diminish radical-induced damage. This review surveys the areas of research focusing on radical reactions and particularly with stable cyclic nitroxide radicals, which demonstrate unique antioxidative activities. Unlike common antioxidants that are progressively depleted under oxidative stress and yield secondary radicals, nitroxides are efficient radical scavengers yielding in most cases their respective oxoammonium cations, which are readily reduced back in the tissue to the nitroxide thus continuously being recycled. Nitroxides, which not only protect enzymes, cells, and laboratory animals from diverse kinds of biological injury, but also modify the catalytic activity of heme enzymes, could be utilized in chemical and biological systems serving as a research tool for elucidating mechanisms underlying complex chemical and biochemical processes.

  7. Asymmetric effect of mechanical stress on the forward and reverse reaction catalyzed by an enzyme.

    Directory of Open Access Journals (Sweden)

    Collin Joseph

    Full Text Available The concept of modulating enzymatic activity by exerting a mechanical stress on the enzyme has been established in previous work. Mechanical perturbation is also a tool for probing conformational motion accompanying the enzymatic cycle. Here we report measurements of the forward and reverse kinetics of the enzyme Guanylate Kinase from yeast (Saccharomyces cerevisiae. The enzyme is held in a state of stress using the DNA spring method. The observation that mechanical stress has different effects on the forward and reverse reaction kinetics suggests that forward and reverse reactions follow different paths, on average, in the enzyme's conformational space. Comparing the kinetics of the stressed and unstressed enzyme we also show that the maximum speed of the enzyme is comparable to the predictions of the relaxation model of enzyme action, where we use the independently determined dissipation coefficient [Formula: see text] for the enzyme's conformational motion. The present experiments provide a mean to explore enzyme kinetics beyond the static energy landscape picture of transition state theory.

  8. Improved removal performance and mechanism investigation of papermaking wastewater treatment using manganese enhanced Fenton reaction.

    Science.gov (United States)

    Wang, Yingcai; Wang, Can; Shi, Shuai; Fang, Shuai

    2018-06-01

    The effects of Mn(II) on Fenton system to treat papermaking wastewater and the mechanism of Mn(II) enhanced Fenton reaction were investigated in this study. The chemical oxygen demand (COD) removal efficiency was enhanced in the presence of Mn(II), which increased by 19% compared with that of the Fenton system alone. The pseudo-first order reaction kinetic rate constant of Mn(II)/Fenton system was 2.11 times higher than that of Fenton system. 67%-81% COD were removed with the increasing Mn(II) concentration from 0 to 0.8 g/L. COD removal efficiency was also enhanced in a wider pH range (3-7), which indicated the operation parameters of Fenton technology could be broadened to a milder condition. The study of the mechanism showed that Mn(II) participated in the oxidation and coagulation stages in Fenton system. In the oxidation stage, Mn(II) promotes the production of HO 2 •/ O 2 • - , then HO 2 •/ O 2 • - reacts with Fe(III) to accelerate the formation of Fe(II), and finally accelerates the production of HO•. Meantime MnMnO 3 and Fe(OH) 3 forms in the coagulation stage, facilitating the removal of suspended substances and a large amount of COD, which enhances the overall COD removal of papermaking wastewater. This study provided a detailed mechanism to improve practical applications of Fenton technology.

  9. The investigation on electrochemical reaction mechanism of CuF2 thin film with lithium

    International Nuclear Information System (INIS)

    Cui Yanhua; Xue Mingzhe; Zhou Yongning; Peng Shuming; Wang Xiaolin; Fu Zhengwen

    2011-01-01

    Crystalline CuF 2 thin films were prepared by pulsed laser deposition under room temperature. The physical and electrochemical properties of the as-deposited thin films have been investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), galvanostatic cycling and cyclic voltammetry (CV). Reversible capacity of 544 mAh g -1 was achieved in the potential range of 1.0-4.0 V. A reversible couple of redox peaks at 3.0 V and 3.7 V was firstly observed. By using ex situ XRD and TEM techniques, an insertion process followed by a fully conversion reaction to Cu and LiF was revealed in the lithium electrochemical reaction of CuF 2 thin film electrode. The reversible insertion reaction above 2.8 V could provide a capacity of about 125 mAh g -1 , which makes CuF 2 a potential cathode material for rechargeable lithium batteries.

  10. Kinetics and mechanism of the reaction of recombination of vinyl and hydroxyl radicals

    Science.gov (United States)

    Knyazev, Vadim D.

    2017-10-01

    The recombination of the vinyl (C2H3) and the hydroxyl (OH) radicals was studied computationally using quantum chemistry and master equation/RRKM. The reaction mechanism includes the initial addition, several isomerization steps, and decomposition via seven different channels. The spectrum of products demonstrates temperature dependence in the 300-3000 K range. At low temperatures (below 1600 K), CH3 + HCO products are dominant but at elevated temperatures vinoxy radical (CH2CHO) and hydrogen atom become more important. The acetyl (CH3CO) + H products and formation of vinylidene (CH2C:) and water products are minor but non-negligible.

  11. Phaseolin expression in tobacco chloroplast reveals an autoregulatory mechanism in heterologous protein translation.

    Science.gov (United States)

    De Marchis, Francesca; Bellucci, Michele; Pompa, Andrea

    2016-02-01

    Plastid DNA engineering is a well-established research area of plant biotechnology, and plastid transgenes often give high expression levels. However, it is still almost impossible to predict the accumulation rate of heterologous protein in transplastomic plants, and there are many cases of unsuccessful transgene expression. Chloroplasts regulate their proteome at the post-transcriptional level, mainly through translation control. One of the mechanisms to modulate the translation has been described in plant chloroplasts for the chloroplast-encoded subunits of multiprotein complexes, and the autoregulation of the translation initiation of these subunits depends on the availability of their assembly partners [control by epistasy of synthesis (CES)]. In Chlamydomonas reinhardtii, autoregulation of endogenous proteins recruited in the assembly of functional complexes has also been reported. In this study, we revealed a self-regulation mechanism triggered by the accumulation of a soluble recombinant protein, phaseolin, in the stroma of chloroplast-transformed tobacco plants. Immunoblotting experiments showed that phaseolin could avoid this self-regulation mechanism when targeted to the thylakoids in transplastomic plants. To inhibit the thylakoid-targeted phaseolin translation as well, this protein was expressed in the presence of a nuclear version of the phaseolin gene with a transit peptide. Pulse-chase and polysome analysis revealed that phaseolin mRNA translation on plastid ribosomes was repressed due to the accumulation in the stroma of the same soluble polypeptide imported from the cytosol. We suggest that translation autoregulation in chloroplast is not limited to heteromeric protein subunits but also involves at least some of the foreign soluble recombinant proteins, leading to the inhibition of plastome-encoded transgene expression in chloroplast. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  12. Dissipative structure of mechanically stimulated reaction; Kikaiteki reiki hanno ni okeru san`itsu kozo

    Energy Technology Data Exchange (ETDEWEB)

    Hida, M. [Okayama Univ., Okayama (Japan). Faculty of Engineering

    1994-12-20

    Recently various studies have been conducted concerning the state changes of materials obtained through mechanical alloying (MA) or mechano-chemical (MC) processing. What is noticeable is the quasi-steady state of almost all the materials obtained through various processes including MA and MC, and that the super cooling, supersaturating and high residue distortion realized under unbalanced conditions have not been clarified. In other words, the tracing capability to the external binding conditions is low. In this report, the appearance of the high temperature phase and high pressure phase obtained through MA or MC processing, the forming of amorphous, the mesomerism of the amorphous materials, the interesting phenomena generated by combination between the mechanical disturbance and chemical reactions were discussed with concrete examples, and a steady dissipative organization theory was approached from the viewpoint of dissipative structure development which is equal to the forming process of the quasi-steady phase. 34 refs., 2 figs.

  13. Surface/subsurface observation and removal mechanisms of ground reaction bonded silicon carbide

    Science.gov (United States)

    Yao, Wang; Zhang, Yu-Min; Han, Jie-cai; Zhang, Yun-long; Zhang, Jian-han; Zhou, Yu-feng; Han, Yuan-yuan

    2006-01-01

    Reaction Bonded Silicon Carbide (RBSiC) has long been recognized as a promising material for optical applications because of its unique combination of favorable properties and low-cost fabrication. Grinding of silicon carbide is difficult because of its high hardness and brittleness. Grinding often induces surface and subsurface damage, residual stress and other types of damage, which have great influence on the ceramic components for optical application. In this paper, surface integrity, subsurface damage and material removal mechanisms of RBSiC ground using diamond grinding wheel on creep-feed surface grinding machine are investigated. The surface and subsurface are studied with scanning electron microscopy (SEM) and optical microscopy. The effects of grinding conditions on surface and subsurface damage are discussed. This research links the surface roughness, surface and subsurface cracks to grinding parameters and provides valuable insights into the material removal mechanism and the dependence of grind induced damage on grinding conditions.

  14. Conversion of glucose into 5-hydroxymethylfurfural in different solvents and catalysts: Reaction kinetics and mechanism

    Directory of Open Access Journals (Sweden)

    Cunshan Zhou

    2017-06-01

    Full Text Available Synthesis of 5-hydroxymethylfurfural (HMF from glucose was done in H2O, dimethylsulfoxide (DMSO and 1-butyl-3-methylimidazolium chloride ([Bmim]Cl catalyzed by metal (III chloride (FeCl3·6H2O, CrCl3·6H2O and AlCl3. The effects of solvent/catalyst system and temperature/time on the performance of the reaction are studied. HMF yield in the different solvents follows a decreasing order as DMSO > [Bmim]Cl > H2O. The highest HMF yield is achieved by CrCl3·6H2O, followed by AlCl3 and then FeCl3·6H2O. An optimal temperature/time is found at 393 K or 403 K and a time between 30 min and 480 min. Under the optimal reaction conditions, HMF yields of 54.43% and 52.86% are obtained in DMSO with CrCl3·6H2O at 403 K and 480 min and AlCl3 at 393 K and 240 min, respectively. The mechanism of the halide chlorides catalyzed glucose conversion reaction is proposed. The kinetic model is established to describe the HMF formation and the experimental data conform to the model.

  15. THEORETICAL RESEARCH ON THE MULTI-CHANNEL REACTION MECHANISM AND KINETICS OF HNCS WITH OH-

    Directory of Open Access Journals (Sweden)

    Li-Jie Hou

    Full Text Available We presented a theoretical study on the detailed reaction mechanism and kinetics of the HNCS molecule with the OH-. The barrierless minimum energy path and the most favorable entrance channel have been determined by study the thermodynamic and kinetic characters of the channel with low energy barrier. The B3LYP/6-311++G** method was employed for all the geometrical optimizations and a multi-level extrapolation method based on the G3 energies was employed for further energy refinements. In addition, the analysis of the combining interaction between hydroxide ion and HNCS was performed by natural bond orbitals (NBO analysis. The calculation results indicated that the reaction of OH- with HNCS had four channels, and the channel of H-atom in HNCS direct extraction to OH- (OH-+HNCS→IM1→TS3→IM4→P2(SCN- +H2O in singlet state was the main channel with the low potential energy and high equilibrium constant and reaction rate constant. SCN- and H2O were main products.

  16. Automatic analysis and reduction of reaction mechanisms for complex fuel combustion

    Energy Technology Data Exchange (ETDEWEB)

    Nilsson, Daniel

    2001-05-01

    This work concentrates on automatic procedures for simplifying chemical models for realistic fuels using skeletal mechanism construction and Quasi Steady-State Approximation (QSSA) applied to detailed reaction mechanisms. To automate the selection of species for removal or approximation, different indices for species ranking have thus been proposed. Reaction flow rates are combined with sensitivity information for targeting a certain quantity, and used to determine a level of redundancy for automatic skeletal mechanism construction by exclusion of redundant species. For QSSA reduction, a measure of species lifetime can be used for species ranking as-is, weighted by concentrations or molecular transport timescales, and/or combined with species sensitivity. Maximum values of the indices are accumulated over ranges of parameters, (e.g. fuel-air ratio and octane number), and species with low accumulated index values are selected for removal or steady-state approximation. In the case of QSSA, a model with a certain degree of reduction is automatically implemented as FORTRAN code by setting a certain index limit. The code calculates source terms of explicitly handled species from reaction rates and the steady-state concentrations by internal iteration. Homogeneous-reactor and one-dimensional laminar-flame models were used as test cases. A staged combustor fuelled by ethylene with monomethylamine addition is modelled by two homogeneous reactors in sequence, i.e. a PSR (Perfectly Stirred Reactor) followed by a PFR (Plug Flow Reactor). A modified PFR model was applied for simulation of a Homogeneous Charge Compression Ignition (HCCI) engine fuelled with four-component natural gas, whereas a two-zone model was required for a knocking Spark Ignition (SI) engine powered by Primary Reference Fuel (PRF). Finally, a laminar one-dimensional model was used to simulate premixed flames burning methane and an aeroturbine kerosene surrogate consisting of n-decane and toluene. In

  17. Spatiotemporal mechanical variation reveals critical role for rho kinase during primitive streak morphogenesis.

    Science.gov (United States)

    Henkels, Julia; Oh, Jaeho; Xu, Wenwei; Owen, Drew; Sulchek, Todd; Zamir, Evan

    2013-02-01

    Large-scale morphogenetic movements during early embryo development are driven by complex changes in biochemical and biophysical factors. Current models for amniote primitive streak morphogenesis and gastrulation take into account numerous genetic pathways but largely ignore the role of mechanical forces. Here, we used atomic force microscopy (AFM) to obtain for the first time precise biomechanical properties of the early avian embryo. Our data reveal that the primitive streak is significantly stiffer than neighboring regions of the epiblast, and that it is stiffer than the pre-primitive streak epiblast. To test our hypothesis that these changes in mechanical properties are due to a localized increase of actomyosin contractility, we inhibited actomyosin contractility via the Rho kinase (ROCK) pathway using the small-molecule inhibitor Y-27632. Our results using several different assays show the following: (1) primitive streak formation was blocked; (2) the time-dependent increase in primitive streak stiffness was abolished; and (3) convergence of epiblast cells to the midline was inhibited. Taken together, our data suggest that actomyosin contractility is necessary for primitive streak morphogenesis, and specifically, ROCK plays a critical role. To better understand the underlying mechanisms of this fundamental process, future models should account for the findings presented in this study.

  18. Automatic generation of predictive dynamic models reveals nuclear phosphorylation as the key Msn2 control mechanism.

    Science.gov (United States)

    Sunnåker, Mikael; Zamora-Sillero, Elias; Dechant, Reinhard; Ludwig, Christina; Busetto, Alberto Giovanni; Wagner, Andreas; Stelling, Joerg

    2013-05-28

    Predictive dynamical models are critical for the analysis of complex biological systems. However, methods to systematically develop and discriminate among systems biology models are still lacking. We describe a computational method that incorporates all hypothetical mechanisms about the architecture of a biological system into a single model and automatically generates a set of simpler models compatible with observational data. As a proof of principle, we analyzed the dynamic control of the transcription factor Msn2 in Saccharomyces cerevisiae, specifically the short-term mechanisms mediating the cells' recovery after release from starvation stress. Our method determined that 12 of 192 possible models were compatible with available Msn2 localization data. Iterations between model predictions and rationally designed phosphoproteomics and imaging experiments identified a single-circuit topology with a relative probability of 99% among the 192 models. Model analysis revealed that the coupling of dynamic phenomena in Msn2 phosphorylation and transport could lead to efficient stress response signaling by establishing a rate-of-change sensor. Similar principles could apply to mammalian stress response pathways. Systematic construction of dynamic models may yield detailed insight into nonobvious molecular mechanisms.

  19. Proteomic Analysis Reveals the Leaf Color Regulation Mechanism in Chimera Hosta "Gold Standard" Leaves.

    Science.gov (United States)

    Yu, Juanjuan; Zhang, Jinzheng; Zhao, Qi; Liu, Yuelu; Chen, Sixue; Guo, Hongliang; Shi, Lei; Dai, Shaojun

    2016-03-08

    Leaf color change of variegated leaves from chimera species is regulated by fine-tuned molecular mechanisms. Hosta "Gold Standard" is a typical chimera Hosta species with golden-green variegated leaves, which is an ideal material to investigate the molecular mechanisms of leaf variegation. In this study, the margin and center regions of young and mature leaves from Hosta "Gold Standard", as well as the leaves from plants after excess nitrogen fertilization were studied using physiological and comparative proteomic approaches. We identified 31 differentially expressed proteins in various regions and development stages of variegated leaves. Some of them may be related to the leaf color regulation in Hosta "Gold Standard". For example, cytosolic glutamine synthetase (GS1), heat shock protein 70 (Hsp70), and chloroplastic elongation factor G (cpEF-G) were involved in pigment-related nitrogen synthesis as well as protein synthesis and processing. By integrating the proteomics data with physiological results, we revealed the metabolic patterns of nitrogen metabolism, photosynthesis, energy supply, as well as chloroplast protein synthesis, import and processing in various leaf regions at different development stages. Additionally, chloroplast-localized proteoforms involved in nitrogen metabolism, photosynthesis and protein processing implied that post-translational modifications were crucial for leaf color regulation. These results provide new clues toward understanding the mechanisms of leaf color regulation in variegated leaves.

  20. Endogenous molecular network reveals two mechanisms of heterogeneity within gastric cancer

    Science.gov (United States)

    Li, Site; Zhu, Xiaomei; Liu, Bingya; Wang, Gaowei; Ao, Ping

    2015-01-01

    Intratumor heterogeneity is a common phenomenon and impedes cancer therapy and research. Gastric cancer (GC) cells have generally been classified into two heterogeneous cellular phenotypes, the gastric and intestinal types, yet the mechanisms of maintaining two phenotypes and controlling phenotypic transition are largely unknown. A qualitative systematic framework, the endogenous molecular network hypothesis, has recently been proposed to understand cancer genesis and progression. Here, a minimal network corresponding to such framework was found for GC and was quantified via a stochastic nonlinear dynamical system. We then further extended the framework to address the important question of intratumor heterogeneity quantitatively. The working network characterized main known features of normal gastric epithelial and GC cell phenotypes. Our results demonstrated that four positive feedback loops in the network are critical for GC cell phenotypes. Moreover, two mechanisms that contribute to GC cell heterogeneity were identified: particular positive feedback loops are responsible for the maintenance of intestinal and gastric phenotypes; GC cell progression routes that were revealed by the dynamical behaviors of individual key components are heterogeneous. In this work, we constructed an endogenous molecular network of GC that can be expanded in the future and would broaden the known mechanisms of intratumor heterogeneity. PMID:25962957

  1. Integrative Genomics Reveals Mechanisms of Copy Number Alterations Responsible for Transcriptional Deregulation in Colorectal Cancer

    Science.gov (United States)

    Camps, Jordi; Nguyen, Quang Tri; Padilla-Nash, Hesed M.; Knutsen, Turid; McNeil, Nicole E.; Wangsa, Danny; Hummon, Amanda B.; Grade, Marian; Ried, Thomas; Difilippantonio, Michael J.

    2016-01-01

    To evaluate the mechanisms and consequences of chromosomal aberrations in colorectal cancer (CRC), we used a combination of spectral karyotyping, array comparative genomic hybridization (aCGH), and array-based global gene expression profiling on 31 primary carcinomas and 15 established cell lines. Importantly, aCGH showed that the genomic profiles of primary tumors are recapitulated in the cell lines. We revealed a preponderance of chromosome breakpoints at sites of copy number variants (CNVs) in the CRC cell lines, a novel mechanism of DNA breakage in cancer. The integration of gene expression and aCGH led to the identification of 157 genes localized within high-level copy number changes whose transcriptional deregulation was significantly affected across all of the samples, thereby suggesting that these genes play a functional role in CRC. Genomic amplification at 8q24 was the most recurrent event and led to the overexpression of MYC and FAM84B. Copy number dependent gene expression resulted in deregulation of known cancer genes such as APC, FGFR2, and ERBB2. The identification of only 36 genes whose localization near a breakpoint could account for their observed deregulated expression demonstrates that the major mechanism for transcriptional deregulation in CRC is genomic copy number changes resulting from chromosomal aberrations. PMID:19691111

  2. Species-Specific Mechanisms of Neuron Subtype Specification Reveal Evolutionary Plasticity of Amniote Brain Development

    Directory of Open Access Journals (Sweden)

    Tadashi Nomura

    2018-03-01

    Full Text Available Summary: Highly ordered brain architectures in vertebrates consist of multiple neuron subtypes with specific neuronal connections. However, the origin of and evolutionary changes in neuron specification mechanisms remain unclear. Here, we report that regulatory mechanisms of neuron subtype specification are divergent in developing amniote brains. In the mammalian neocortex, the transcription factors (TFs Ctip2 and Satb2 are differentially expressed in layer-specific neurons. In contrast, these TFs are co-localized in reptilian and avian dorsal pallial neurons. Multi-potential progenitors that produce distinct neuronal subtypes commonly exist in the reptilian and avian dorsal pallium, whereas a cis-regulatory element of avian Ctip2 exhibits attenuated transcription suppressive activity. Furthermore, the neuronal subtypes distinguished by these TFs are not tightly associated with conserved neuronal connections among amniotes. Our findings reveal the evolutionary plasticity of regulatory gene functions that contribute to species differences in neuronal heterogeneity and connectivity in developing amniote brains. : Neuronal heterogeneity is essential for assembling intricate neuronal circuits. Nomura et al. find that species-specific transcriptional mechanisms underlie diversities of excitatory neuron subtypes in mammalian and non-mammalian brains. Species differences in neuronal subtypes and connections suggest functional plasticity of regulatory genes for neuronal specification during amniote brain evolution. Keywords: Ctip2, Satb2, multi-potential progenitors, transcriptional regulation, neuronal connectivity

  3. Reaction pathway and oxidation mechanisms of dibutyl phthalate by persulfate activated with zero-valent iron

    Energy Technology Data Exchange (ETDEWEB)

    Li, Huanxuan [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China); Wan, Jinquan, E-mail: ppjqwan@scut.edu.cn [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China); State Key Lab Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640 (China); Ma, Yongwen [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China); State Key Lab Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640 (China); Wang, Yan [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China)

    2016-08-15

    This study investigated reaction pathway and oxidation mechanisms of dibutyl phthalate (DBP) by persulfate (PS) activated with zero-valent iron (ZVI). The DBP degradation was studied at three pH values (acidic, neutral and basic) in the presence of different organic scavengers. Using a chemical probe method, both sulfate radical (SO{sub 4}·{sup −}) and hydroxyl radical (·OH) were found to be primary oxidants at pH 3.0 and pH 7.0, respectively while ·OH was the major specie to oxidize DBP at pH 11.0. A similar result was found in an experiment of Electron Spin Resonance spin-trapping where in addition to ·OH, superoxide radical (O{sub 2}·{sup −}) was detected at pH 11.0. The transformation of degradation products including dimethyl phthalate (DMP), diethyl phthalate (DEP), phthalic anhydride, and acetophenone exhibited diverse variation during the reaction processes. The phthalic anhydride concentration appeared to be maximum at all pHs. Another eleven intermediate products were also found at pH 3.0 by GC–MS and HPLC analysis, and their degradation mechanisms and pathways were proposed. It was suggested that dealkylation, hydroxylation, decarboxylation and hydrogen extraction were the dominant degradation mechanisms of DBP at pH 3.0. - Highlights: • Both SO{sub 4}{sup −}· and ·OH were found to be the major active species at pH 3.0 and pH 7.0. • ·OH and ·O2– were the primary oxidants pH 11.0. • The intermediate products were investigated as well as the degradation pathway. • Dealkylation, hydroxylation, decarboxylation, H-extraction were the major mechanisms.

  4. Study of transfer reactions (α,t), (α,3He) in the f-p shell: mechanism and spectroscopic use

    International Nuclear Information System (INIS)

    Roussel, P.

    1968-05-01

    We describe an experimental study of (α,t), (α, 3 He) reactions at 44 MeV using a solid-state identifier, on the target-nuclei 54 Fe and 58,60,62,64 Ni. A critical study of optical model and of disturbed wave analysis has been performed. We show the complementarity of different transfer-reactions, the ambiguity of spectroscopic factors, the importance of the problem of the reaction mechanism. (author) [fr

  5. Theoretical study on the mechanism of the reaction of FOX-7 with OH and NO2 radicals: bimolecular reactions with low barrier during the decomposition of FOX-7

    Science.gov (United States)

    Zhang, Ji-Dong; Zhang, Li-Li

    2017-12-01

    The decomposition of 1,1-diamino-2,2-dinitroethene (FOX-7) attracts great interests, while the studies on bimolecular reactions during the decomposition of FOX-7 are scarce. This study for the first time investigated the bimolecular reactions of OH and NO2 radicals, which are pyrolysis products of ammonium perchlorate (an efficient oxidant usually used in solid propellant), with FOX-7 by computational chemistry methods. The molecular geometries and energies were calculated using the (U)B3LYP/6-31++G(d,p) method. The rate constants of the reactions were calculated by canonical variational transition state theory. We found three mechanisms (H-abstraction, OH addition to C and N atom) for the reaction of OH + FOX-7 and two mechanisms (O abstraction and H abstraction) for the reaction of NO2 + FOX-7. OH radical can abstract H atom or add to C atom of FOX-7 with barriers near to zero, which means OH radical can effectively degrade FOX-7. The O abstraction channel of the reaction of NO2 + FOX-7 results in the formation of NO3 radical, which has never been detected experimentally during the decomposition of FOX-7.

  6. Rationalizing the mechanism of HMDS degradation in air and effective control of the reaction byproducts

    Science.gov (United States)

    Seguin, Kevin; Dallas, Andrew J.; Weineck, Gerald

    2008-03-01

    The concern over molecular contamination on the surfaces of optics continues to grow. Most recently, this concern has focused on siloxane contamination resulting from hexamethyldisilazane (HMDS) which is commonly used as a wafer treatment to improve photoresist adhesion onto wafers. From this process, HMDS vapor can be found within FABs and process tools where it has been linked to issues related to lens hazing. This type of surface contamination is significantly detrimental to the imaging process and is generally corrected by extensive surface cleaning or even lens replacement. Additionally, this type of repair also requires adjustment of the optical axis, thereby contributing to an extended downtime. HMDS is known to be very sensitive to the presence of water and is therefore believed to degrade in humid airstreams. This research focuses on rationalizing the reaction mechanisms of HMDS in dry and humid airstreams and in the presence of several adsorbent surfaces. It is shown that HMDS hydrolyzes in humid air to trimethylsilanol (TMS) and ammonia (NH 3). Furthermore, it is shown that TMS can dimerize in air, or on specific types of adsorption media, to form hexamethyldisiloxane (HMDSO). Additionally, we report on the relative impact of these reaction mechanisms on the removal of both HMDS and its hydrolysis products (TMS, HMDSO and NH 3).

  7. Study of the mechanism of Pb + Au reaction at 29 A.MeV

    International Nuclear Information System (INIS)

    Aboufirassi, M.

    1994-07-01

    The aim of this thesis is to demonstrate the binary character of Pb + Au reaction at 29 A.MeV and to study the decay modes of very excited nuclei produced. The experiment set up was performed at the GANIL in the scattering chamber NAUTILUS. It was composed by multi detectors of fragments (Z ≥8) and multi detectors of light charged particles. (Z<8). The analysis of events which lead to detection of more then 80 % of both total charge and total parallel momentum proved that two body final state is still present at this incident energy. This mechanism is similar to the mechanism of heavy ion reaction at low bombarding energy. We have shown that complete damping occurred leading to excitation energy as high as 6 Me V/u. The decay modes of deep inelastic products are evaporation residue or binary fission or multifragmentation. Analysing the fission products, we have estimated the aligned spin of deep inelastic products (45 h). Finally, the study of light charged particles detected with fission fragments has demonstrated that these particles are emitted essentially before fission. The temperature value of hot nuclei emitted at foreword angle is deduced of light particle spectra. (author)

  8. Viewing loved faces inhibits defense reactions: a health-promotion mechanism?

    Directory of Open Access Journals (Sweden)

    Pedro Guerra

    Full Text Available We have known for decades that social support is associated with positive health outcomes. And yet, the neurophysiological mechanisms underlying this association remain poorly understood. The link between social support and positive health outcomes is likely to depend on the neurophysiological regulatory mechanisms underlying reward and defensive reactions. The present study examines the hypothesis that emotional social support (love provides safety cues that activate the appetitive reward system and simultaneously inhibit defense reactions. Using the startle probe paradigm, 54 undergraduate students (24 men viewed black and white photographs of loved (romantic partner, father, mother, and best friend, neutral (unknown, and unpleasant (mutilated faces. Eye-blink startle, zygomatic major activity, heart rate, and skin conductance responses to the faces, together with subjective ratings of valence, arousal, and dominance, were obtained. Viewing loved faces induced a marked inhibition of the eye-blink startle response accompanied by a pattern of zygomatic, heart rate, skin conductance, and subjective changes indicative of an intense positive emotional response. Effects were similar for men and women, but the startle inhibition and the zygomatic response were larger in female participants. A comparison between the faces of the romantic partner and the parent who shares the partner's gender further suggests that this effect is not attributable to familiarity or arousal. We conclude that this inhibitory capacity may contribute to the health benefits associated with social support.

  9. Viewing loved faces inhibits defense reactions: a health-promotion mechanism?

    Science.gov (United States)

    Guerra, Pedro; Sánchez-Adam, Alicia; Anllo-Vento, Lourdes; Ramírez, Isabel; Vila, Jaime

    2012-01-01

    We have known for decades that social support is associated with positive health outcomes. And yet, the neurophysiological mechanisms underlying this association remain poorly understood. The link between social support and positive health outcomes is likely to depend on the neurophysiological regulatory mechanisms underlying reward and defensive reactions. The present study examines the hypothesis that emotional social support (love) provides safety cues that activate the appetitive reward system and simultaneously inhibit defense reactions. Using the startle probe paradigm, 54 undergraduate students (24 men) viewed black and white photographs of loved (romantic partner, father, mother, and best friend), neutral (unknown), and unpleasant (mutilated) faces. Eye-blink startle, zygomatic major activity, heart rate, and skin conductance responses to the faces, together with subjective ratings of valence, arousal, and dominance, were obtained. Viewing loved faces induced a marked inhibition of the eye-blink startle response accompanied by a pattern of zygomatic, heart rate, skin conductance, and subjective changes indicative of an intense positive emotional response. Effects were similar for men and women, but the startle inhibition and the zygomatic response were larger in female participants. A comparison between the faces of the romantic partner and the parent who shares the partner's gender further suggests that this effect is not attributable to familiarity or arousal. We conclude that this inhibitory capacity may contribute to the health benefits associated with social support.

  10. Reaction mechanisms and kinetics of the iminovinylidene radical with NO: Ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Hsiao, Ming-Kai; Chung, Yi-Hua; Hung, Yu-Ming; Chen, Hui-Lung, E-mail: chl3@faculty.pccu.edu.tw [Department of Chemistry and Institute of Applied Chemistry, Chinese Culture University, Taipei 111, Taiwan (China)

    2014-05-28

    The nitric oxide (NO) is a notorious compound for polluting environment. Recent year, removing nitric oxide from the atmosphere becomes a focus of the investigation. In our work, we study the iminovinylidene (HNCC) radical reacted with NO molecule. The mechanism and kinetic for reaction of the HNCC radical with the NO molecule is investigated via considering the possible channels of the N and O atoms of NO attacking the N and C atoms of the HNCC based on the high level ab initio molecular orbital calculations in conjunction with variational TST and RRKM calculations. The species involved have been optimized at the B3LYP/6-311++G(3df,2p) level and their single-point energies are refined by the CCSD(T)/aug-cc-PVQZ//B3LYP/6-311++G(3df,2p) method. The calculated potential energy surfaces indicated that energetically the most favorable channel for the HNCC + NO reaction was predicted to be the formation of HNC+CNO (P8) product via the addition reaction of the C atom of HNCC radical and the N atom of NO with the head to head orientation. To rationalize the scenario of the calculated results, we also employ the Fukui functions and HSAB theory to seek for a possible explanation. In addition, the reaction rate constants were calculated using VariFlex code, and the results show that the total rate coefficient, k{sub total}, at Ar pressure 760 Torr can be represented with an equation: k{sub total} = 6.433 × 10{sup −11} T {sup 0.100} exp(0.275 kcal mol{sup −1}/RT) at T = 298–3000 K, in units of cm{sup 3} molecule{sup −1} s{sup −1}.

  11. Reaction Mechanism for m- Xylene Oxidation in the Claus Process by Sulfur Dioxide

    KAUST Repository

    Sinha, Sourab

    2015-09-24

    In the Claus process, the presence of aromatic contaminants such benzene, toluene, and xylenes (BTX), in the H2S feed stream has a detrimental effect on catalytic reactors, where BTX form soot particles and clog and deactivate the catalysts. Among BTX, xylenes are proven to be most damaging contaminant for catalysts. BTX oxidation in the Claus furnace, before they enter catalyst beds, provides a solution to this problem. A reaction kinetics study on m-xylene oxidation by SO2, an oxidant present in Claus furnace, is presented. The density functional theory is used to study the formation of m-xylene radicals (3-methylbenzyl, 2,6-dimethylphenyl, 2,4-dimethylphenyl, and 3,5-dimethylphenyl) through H-abstraction and their oxidation by SO2. The mechanism begins with SO2 addition on the radicals through an O-atom rather than the S-atom with the release of 180.0-183.1 kJ/mol of reaction energies. This exothermic reaction involves energy barriers in the range 3.9-5.2 kJ/mol for several m-xylene radicals. Thereafter, O-S bond scission takes place to release SO, and the O-atom remaining on aromatics leads to CO formation. Among four m-xylene radicals, the resonantly stabilized 3-methylbenzyl exhibited the lowest SO2 addition and SO elimination rates. The reaction rate constants are provided to facilitate Claus process simulations to find conditions suitable for BTX oxidation. © 2015 American Chemical Society.

  12. Reaction Mechanism for m- Xylene Oxidation in the Claus Process by Sulfur Dioxide

    KAUST Repository

    Sinha, Sourab; Raj, Abhijeet; Al Shoaibi, Ahmed S.; Chung, Suk-Ho

    2015-01-01

    In the Claus process, the presence of aromatic contaminants such benzene, toluene, and xylenes (BTX), in the H2S feed stream has a detrimental effect on catalytic reactors, where BTX form soot particles and clog and deactivate the catalysts. Among BTX, xylenes are proven to be most damaging contaminant for catalysts. BTX oxidation in the Claus furnace, before they enter catalyst beds, provides a solution to this problem. A reaction kinetics study on m-xylene oxidation by SO2, an oxidant present in Claus furnace, is presented. The density functional theory is used to study the formation of m-xylene radicals (3-methylbenzyl, 2,6-dimethylphenyl, 2,4-dimethylphenyl, and 3,5-dimethylphenyl) through H-abstraction and their oxidation by SO2. The mechanism begins with SO2 addition on the radicals through an O-atom rather than the S-atom with the release of 180.0-183.1 kJ/mol of reaction energies. This exothermic reaction involves energy barriers in the range 3.9-5.2 kJ/mol for several m-xylene radicals. Thereafter, O-S bond scission takes place to release SO, and the O-atom remaining on aromatics leads to CO formation. Among four m-xylene radicals, the resonantly stabilized 3-methylbenzyl exhibited the lowest SO2 addition and SO elimination rates. The reaction rate constants are provided to facilitate Claus process simulations to find conditions suitable for BTX oxidation. © 2015 American Chemical Society.

  13. Ablation characteristics and reaction mechanism of insulation materials under slag deposition condition

    Science.gov (United States)

    Guan, Yiwen; Li, Jiang; Liu, Yang

    2017-07-01

    Current understanding of the physical and chemical processes involved in the ablation of insulation materials by highly aluminized solid propellants is limited. The study on the heat transfer and ablation principle of ethylene propylene diene monomer (EPDM) materials under slag deposition condition is essential for future design or modification of large solid rocket motors (SRMs) for launch application. In this paper, the alumina liquid flow pattern and the deposition principle in full-scale SRM engines are discussed. The interaction mechanism between the alumina droplets and the wall are analyzed. Then, an experimental method was developed to simulate the insulation material ablation under slag deposition condition. Experimental study was conducted based on a laboratory-scale device. Meanwhile, from the analysis of the cross-sectional morphology and chemical composition of the charring layer after ablation, the reaction mechanism of the charring layer under deposition condition was discussed, and the main reaction equation was derived. The numerical simulation and experimental results show the following. (i) The alumina droplet flow in the deposition section of the laboratory-scale device is similar to that of a full-scale SRM. (ii) The charring layer of the EPDM insulator displays a porous tight/loose structure under high-temperature slag deposition condition. (iii) A seven-step carbothermal reduction in the alumina is derived and established under high-pressure and high-temperature environment in the SRM combustion chamber. (iv) The analysis using thermodynamic software indicates that the reaction of the alumina and charring layer initially forms Al4C3 during the operation. Then, Al element and Al2OC compound are subsequently produced with the reduction in the release of gas CO as well with continuous environmental heating.

  14. Exploring Reaction Mechanism on Generalized Force Modified Potential Energy Surfaces (G-FMPES) for Diels-Alder Reaction

    Science.gov (United States)

    Jha, Sanjiv; Brown, Katie; Subramanian, Gopinath

    We apply a recent formulation for searching minimum energy reaction path (MERP) and saddle point to atomic systems subjected to an external force. We demonstrate the effect of a loading modality resembling hydrostatic pressure on the trans to cis conformational change of 1,3-butadiene, and the simplest Diels-Alder reaction between ethylene and 1,3-butadiene. The calculated MERP and saddle points on the generalized force modified potential energy surface (G-FMPES) are compared with the corresponding quantities on an unmodified potential energy surface. Our study is performed using electronic structure calculations at the HF/6-31G** level as implemented in the AIMS-MOLPRO code. Our calculations suggest that the added compressive pressure lowers the energy of cis butadiene. The activation energy barrier for the concerted Diels-Alder reaction is found to decrease progressively with increasing compressive pressure.

  15. Mechanisms before Reactions: A Mechanistic Approach to the Organic Chemistry Curriculum Based on Patterns of Electron Flow

    Science.gov (United States)

    Flynn, Alison B.; Ogilvie, William W.

    2015-01-01

    A significant redesign of the introductory organic chemistry curriculum at the authors' institution is described. There are two aspects that differ greatly from a typical functional group approach. First, organic reaction mechanisms and the electron-pushing formalism are taught before students have learned a single reaction. The conservation of…

  16. EFFECT OF FLUORINE AND CHLORINE IONS ON THE REACTION SINTERING OF MECHANICALLY ACTIVATED ZIRCON-ALUMINA MIXTURE

    Directory of Open Access Journals (Sweden)

    R. Zamani Foroshani

    2015-09-01

    Full Text Available The aim of this work was to study the effect of fluorine and chlorine ions on the formation of mullite during the reaction sintering of mechanically activated zircon-alumina powder mixture. The results showed that mechanical activation of zirconalumina powder mixture for 20 h led to grain refinement and partial amorphization. In the presence of fluorine and chlorine ions, complete formation of mullite in the mechanically activated sample occurred after 2 h of reaction sintering at 1300oC and 1400oC, respectively. In the sample lacking fluorine and chlorine ions, mullitization was not completed even after 2 h of reaction sintering at 1400oC. It was concluded that presence of fluorine and chlorine ions enhance the dissociation of zircon and formation of mullite during the reaction sintering of mechanically activated zircon-alumina mixture.

  17. Subsurface damage mechanism of high speed grinding process in single crystal silicon revealed by atomistic simulations

    International Nuclear Information System (INIS)

    Li, Jia; Fang, Qihong; Zhang, Liangchi; Liu, Youwen

    2015-01-01

    stress status. The dislocation nucleation and motion induced plastic deformation during grinding process can better reveal subsurface damage mechanism considering to stress and temperature acting on the dislocations

  18. Transcriptome profiling of a curdlan-producing Agrobacterium reveals conserved regulatory mechanisms of exopolysaccharide biosynthesis

    Directory of Open Access Journals (Sweden)

    Ruffing Anne M

    2012-02-01

    Full Text Available Abstract Background The ability to synthesize exopolysaccharides (EPS is widespread among microorganisms, and microbial EPS play important roles in biofilm formation, pathogen persistence, and applications in the food and medical industries. Although it is well established that EPS synthesis is invariably in response to environmental cues, it remains largely unknown how various environmental signals trigger activation of the biochemical synthesis machinery. Results We report here the transcriptome profiling of Agrobacterium sp. ATCC 31749, a microorganism that produces large amounts of a glucose polymer known as curdlan under nitrogen starvation. Transcriptome analysis revealed a nearly 100-fold upregulation of the curdlan synthesis operon upon transition to nitrogen starvation, thus establishing the prominent role that transcriptional regulation plays in the EPS synthesis. In addition to known mechanisms of EPS regulation such as activation by c-di-GMP, we identify novel mechanisms of regulation in ATCC 31749, including RpoN-independent NtrC regulation and intracellular pH regulation by acidocalcisomes. Furthermore, we show evidence that curdlan synthesis is also regulated by conserved cell stress responses, including polyphosphate accumulation and the stringent response. In fact, the stringent response signal, pppGpp, appears to be indispensible for transcriptional activation of curdlan biosynthesis. Conclusions This study identifies several mechanisms regulating the synthesis of curdlan, an EPS with numerous applications. These mechanisms are potential metabolic engineering targets for improving the industrial production of curdlan from Agrobacterium sp. ATCC 31749. Furthermore, many of the genes identified in this study are highly conserved across microbial genomes, and we propose that the molecular elements identified in this study may serve as universal regulators of microbial EPS synthesis.

  19. Data integration reveals key homeostatic mechanisms following low dose radiation exposure

    Energy Technology Data Exchange (ETDEWEB)

    Tilton, Susan C.; Matzke, Melissa M. [Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99338 (United States); Sowa, Marianne B.; Stenoien, David L.; Weber, Thomas J. [Health Impacts and Exposure Science, Pacific Northwest National Laboratory, Richland, WA 99338 (United States); Morgan, William F. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99338 (United States); Waters, Katrina M., E-mail: katrina.waters@pnnl.gov [Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99338 (United States)

    2015-05-15

    The goal of this study was to define pathways regulated by low dose radiation to understand how biological systems respond to subtle perturbations in their environment and prioritize pathways for human health assessment. Using an in vitro 3-D human full thickness skin model, we have examined the temporal response of dermal and epidermal layers to 10 cGy X-ray using transcriptomic, proteomic, phosphoproteomic and metabolomic platforms. Bioinformatics analysis of each dataset independently revealed potential signaling mechanisms affected by low dose radiation, and integrating data shed additional insight into the mechanisms regulating low dose responses in human tissue. We examined direct interactions among datasets (top down approach) and defined several hubs as significant regulators, including transcription factors (YY1, MYC and CREB1), kinases (CDK2, PLK1) and a protease (MMP2). These data indicate a shift in response across time — with an increase in DNA repair, tissue remodeling and repression of cell proliferation acutely (24–72 h). Pathway-based integration (bottom up approach) identified common molecular and pathway responses to low dose radiation, including oxidative stress, nitric oxide signaling and transcriptional regulation through the SP1 factor that would not have been identified by the individual data sets. Significant regulation of key downstream metabolites of nitrative stress was measured within these pathways. Among the features identified in our study, the regulation of MMP2 and SP1 was experimentally validated. Our results demonstrate the advantage of data integration to broadly define the pathways and networks that represent the mechanisms by which complex biological systems respond to perturbation. - Highlights: • Low dose ionizing radiation altered homeostasis in 3D skin tissue model. • Global gene/protein/metabolite data integrated using complementary statistical approaches • Time and location-specific change in matrix regulation

  20. Chemical dynamics simulations of X- + CH3Y → XCH3 + Y- gas-phase S(N)2 nucleophilic substitution reactions. Nonstatistical dynamics and nontraditional reaction mechanisms.

    Science.gov (United States)

    Manikandan, Paranjothy; Zhang, Jiaxu; Hase, William L

    2012-03-29

    Extensive classical chemical dynamics simulations of gas-phase X(-) + CH(3)Y → XCH(3) + Y(-) S(N)2 nucleophilic substitution reactions are reviewed and discussed and compared with experimental measurements and predictions of theoretical models. The primary emphasis is on reactions for which X and Y are halogen atoms. Both reactions with the traditional potential energy surface (PES), which include pre- and postreaction potential energy minima and a central barrier, and reactions with nontraditional PESs are considered. These S(N)2 reactions exhibit important nonstatistical atomic-level dynamics. The X(-) + CH(3)Y → X(-)---CH(3)Y association rate constant is less than the capture model as a result of inefficient energy transfer from X(-)+ CH(3)Y relative translation to CH(3)Y rotation and vibration. There is weak coupling between the low-frequency intermolecular modes of the X(-)---CH(3)Y complex and higher frequency CH(3)Y intramolecular modes, resulting in non-RRKM kinetics for X(-)---CH(3)Y unimolecular decomposition. Recrossings of the [X--CH(3)--Y](-) central barrier is important. As a result of the above dynamics, the relative translational energy and temperature dependencies of the S(N)2 rate constants are not accurately given by statistical theory. The nonstatistical dynamics results in nonstatistical partitioning of the available energy to XCH(3) +Y(-) reaction products. Besides the indirect, complex forming atomic-level mechanism for the S(N)2 reaction, direct mechanisms promoted by X(-) + CH(3)Y relative translational or CH(3)Y vibrational excitation are possible, e.g., the roundabout mechanism.

  1. Non-ionic iodinated contrast media related immediate reactions: A mechanism study of 27 patients.

    Science.gov (United States)

    Zhai, Liqin; Guo, Xiangjie; Zhang, Haoyue; Jin, Qianqian; Zeng, Qiang; Tang, Xiaoxian; Gao, Cairong

    2017-01-01

    The underlying mechanism of non-ionic iodinated contrast media-related immediate reactions was evaluated in this study. Patients presenting at least grade II immediate reactions after non-ionic iodinated contrast media injection were enrolled. Basophil activation was evaluated by flow cytometry. The plasma concentration of human terminal complement complex SC5b-9, as well as concentrations of serum chymase, tryptase, human mast cell carboxypeptidase A3, human prostaglandin D2, and total IgE were measured by enzyme-linked immunosorbent assay. The basophil activation percentage was significantly higher in the study group than in the control group (17.94±21.06% vs 3.45±1.49%). The plasma concentration of human terminal complement complex SC5b-9 and concentrations of serum chymase, human mast cell carboxypeptidase A3, prostaglandin D2, tryptase, and total IgE were also significantly increased (236.99±318.21 vs 49.70±30.41ng/mL, 0.41±0.49 vs 0.09±0.06ng/mL, 1.17±0.67 vs 0.30±0.17ng/mL, 203.52±137.27 vs 102.28±48.72pg/mL, 3.81±0.22 vs 2.70±0.16ng/mL, 102.00±51.84 vs 19.97±2.75ng/mL, respectively). Both mast cells and basophils were activated in non-ionic iodinated contrast media to mediate immediate hypersensitivity, and mast cells may be involved. Different mechanisms, including IgE-dependent, complement-dependent, and direct membrane effects, contributed to mast cell and basophil activation. Individual patients may use a single or combined mechanism involving single or combined mast cells and basophils. Immediate reactions following non-ionic iodinated contrast media injection may be a mechanically heterogenous disease. Copyright © 2016. Published by Elsevier B.V.

  2. Comparative proteomics and codon substitution analysis reveal mechanisms of differential resistance to hypoxia in congeneric snails

    KAUST Repository

    Mu, Huawei; Sun, Jin; Cheung, Siu Gin; Fang, Ling; Zhou, Haiyun; Luan, Tiangang; Zhang, Huoming; Wong, Chris K.C.; Qiu, Jian-Wen

    2017-01-01

    Although high-throughput proteomics has been widely applied to study mechanisms of environmental adaptation, the conclusions from studies that are based on one species can be confounded by phylogeny. We compare the freshwater snail Pomacea canaliculata (a notorious invasive species) and its congener Pomacea diffusa (a non-invasive species) to understand the molecular mechanisms of their differential resistance to hypoxia. A 72-h acute exposure experiment showed that P. canaliculata is more tolerant to hypoxia than P. diffusa. The two species were then exposed to three levels of dissolved oxygen (6.7, 2.0 and 1.0mgL−1) for 8h, and their gill proteins were analyzed using iTRAQ-coupled LC-MS/MS. The two species showed striking differences in protein expression profiles, with the more hypoxia tolerant P. canaliculata having more up-regulated proteins in signal transduction and down-regulated proteins in glycolysis and the tricarboxylic acid cycle. Evolutionary analysis revealed five orthologous genes encoding differentially expressed proteins having clear signal of positive selection, indicating selection has acted on some of the hypoxia responsive genes. Our case study has highlighted the potential of integrated proteomics and comparative evolutionary analysis for understanding the genetic basis of adaptation to global environmental change in non-model species. SignificanceRapid globalization in recent decades has greatly facilitated species introduction around the world. Successfully established introduced species, so-called invasive species, have threatened the invaded ecosystems. There has been substantial interest in studying how invasive species respond to extreme environmental conditions because the results can help not only predict their range of expansion and manage their impact, but also may reveal the adaptive mechanisms underlying their invasiveness. Our study has adopted a comparative approach to study the differential physiological and proteomic

  3. Comparative proteomics and codon substitution analysis reveal mechanisms of differential resistance to hypoxia in congeneric snails

    KAUST Repository

    Mu, Huawei

    2017-11-06

    Although high-throughput proteomics has been widely applied to study mechanisms of environmental adaptation, the conclusions from studies that are based on one species can be confounded by phylogeny. We compare the freshwater snail Pomacea canaliculata (a notorious invasive species) and its congener Pomacea diffusa (a non-invasive species) to understand the molecular mechanisms of their differential resistance to hypoxia. A 72-h acute exposure experiment showed that P. canaliculata is more tolerant to hypoxia than P. diffusa. The two species were then exposed to three levels of dissolved oxygen (6.7, 2.0 and 1.0mgL−1) for 8h, and their gill proteins were analyzed using iTRAQ-coupled LC-MS/MS. The two species showed striking differences in protein expression profiles, with the more hypoxia tolerant P. canaliculata having more up-regulated proteins in signal transduction and down-regulated proteins in glycolysis and the tricarboxylic acid cycle. Evolutionary analysis revealed five orthologous genes encoding differentially expressed proteins having clear signal of positive selection, indicating selection has acted on some of the hypoxia responsive genes. Our case study has highlighted the potential of integrated proteomics and comparative evolutionary analysis for understanding the genetic basis of adaptation to global environmental change in non-model species. SignificanceRapid globalization in recent decades has greatly facilitated species introduction around the world. Successfully established introduced species, so-called invasive species, have threatened the invaded ecosystems. There has been substantial interest in studying how invasive species respond to extreme environmental conditions because the results can help not only predict their range of expansion and manage their impact, but also may reveal the adaptive mechanisms underlying their invasiveness. Our study has adopted a comparative approach to study the differential physiological and proteomic

  4. Trophic cascades triggered by overfishing reveal possible mechanisms of ecosystem regime shifts.

    Science.gov (United States)

    Daskalov, Georgi M; Grishin, Alexander N; Rodionov, Sergei; Mihneva, Vesselina

    2007-06-19

    Large-scale transitions between alternative states in ecosystems are known as regime shifts. Once described as healthy and dominated by various marine predators, the Black Sea ecosystem by the late 20th century had experienced anthropogenic impacts such as heavy fishing, cultural eutrophication, and invasions by alien species. We studied changes related to these "natural experiments" to reveal the mechanisms of regime shifts. Two major shifts were detected, the first related to a depletion of marine predators and the second to an outburst of the alien comb jelly Mnemiopsis leidyi; both shifts were triggered by intense fishing resulting in system-wide trophic cascades. The complex nature of ecosystem responses to human activities calls for more elaborate approaches than currently provided by traditional environmental and fisheries management. This implies challenging existing practices and implementing explanatory models of ecosystem interactions that can better reconcile conservation and ecosystem management ideals.

  5. The mechanics of anaphase B in a basidiomycete as revealed by laser microbeam microsurgery

    International Nuclear Information System (INIS)

    Bayles, C.J.; Aist, J.R.; Berns, M.W.

    1993-01-01

    Bayles, C. J., Aist, J. R., and Berns, M. W. 1993. The mechanics of anaphase B in a basidiomycete as revealed by laser microbeam microsurgery. Experimental Mycology 17, 191-199. Cytoplasmic forces were found to be actively pulling on the spindle pole bodies during anaphase B in the dikaryotic, basidiomycete fungus, Helicobasidium mompa. When the spindle of one nucleus was severed with a laser microbeam at mid anaphase B, its two spindle pole bodies separated at a much faster rate than did those of the intact spindle in the other nucleus of the same cell. Since astral microtubule populations apparently reach their maximum during anaphase B in this fungus, we suggest that these microtubules may be involved in the cytoplasmic pulling forces. The spindle appears to act primarily as a governor, regulating the rate at which the spindle pole bodies are separated

  6. Epitope-dependent mechanisms of CD27 neutralization revealed by X-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Obmolova, Galina; Teplyakov, Alexey; Malia, Thomas J.; Wunderler, Nicole; Kwok, Deborah; Barone, Linda; Sweet, Raymond; Ort, Tatiana; Scully, Michael; Gilliland, Gary L. (Janssen)

    2017-03-01

    CD27 is a T and B cell co-stimulatory protein of the TNF receptor superfamily dependent on the availability of the TNF-like ligand CD70. Two anti-CD27 neutralizing monoclonal antibodies were obtained from mouse hybridoma and subsequently humanized and optimized for binding the target. The two antibodies are similar in terms of their CD27-binding affinity and ability to block NF-κB signaling, however their clearance rates in monkeys are very different. The pharmacokinetics profiles could be epitope dependent. To identify the epitopes, we determined the crystal structure of the ternary complex between CD27 and the Fab fragments of these non-competing antibodies. The structure reveals the binding modes of the antibodies suggesting that their mechanisms of action are distinctly different and provides a possible explanation of the in vivo data.

  7. Electrochemistry and capillary condensation theory reveal the mechanism of corrosion in dense porous media.

    Science.gov (United States)

    Stefanoni, Matteo; Angst, Ueli M; Elsener, Bernhard

    2018-05-09

    Corrosion in carbonated concrete is an example of corrosion in dense porous media of tremendous socio-economic and scientific relevance. The widespread research endeavors to develop novel, environmentally friendly cements raise questions regarding their ability to protect the embedded steel from corrosion. Here, we propose a fundamentally new approach to explain the scientific mechanism of corrosion kinetics in dense porous media. The main strength of our model lies in its simplicity and in combining the capillary condensation theory with electrochemistry. This reveals that capillary condensation in the pore structure defines the electrochemically active steel surface, whose variability upon changes in exposure relative humidity is accountable for the wide variability in measured corrosion rates. We performed experiments that quantify this effect and find good agreement with the theory. Our findings are essential to devise predictive models for the corrosion performance, needed to guarantee the safety and sustainability of traditional and future cements.

  8. Potent neutralization of hepatitis A virus reveals a receptor mimic mechanism and the receptor recognition site.

    Science.gov (United States)

    Wang, Xiangxi; Zhu, Ling; Dang, Minghao; Hu, Zhongyu; Gao, Qiang; Yuan, Shuai; Sun, Yao; Zhang, Bo; Ren, Jingshan; Kotecha, Abhay; Walter, Thomas S; Wang, Junzhi; Fry, Elizabeth E; Stuart, David I; Rao, Zihe

    2017-01-24

    Hepatitis A virus (HAV) infects ∼1.4 million people annually and, although there is a vaccine, there are no licensed therapeutic drugs. HAV is unusually stable (making disinfection problematic) and little is known of how it enters cells and releases its RNA. Here we report a potent HAV-specific monoclonal antibody, R10, which neutralizes HAV infection by blocking attachment to the host cell. High-resolution cryo-EM structures of HAV full and empty particles and of the complex of HAV with R10 Fab reveal the atomic details of antibody binding and point to a receptor recognition site at the pentamer interface. These results, together with our observation that the R10 Fab destabilizes the capsid, suggest the use of a receptor mimic mechanism to neutralize virus infection, providing new opportunities for therapeutic intervention.

  9. Electrophysiological potentials reveal cortical mechanisms for mental imagery, mental simulation, and grounded (embodied cognition

    Directory of Open Access Journals (Sweden)

    Haline E. Schendan

    2012-09-01

    Full Text Available Grounded cognition theory proposes that cognition, including meaning, is grounded in sensorimotor processing. The mechanism for grounding cognition is mental simulation, which is a type of mental imagery that re-enacts modal processing. To reveal top-down, cortical mechanisms for mental simulation of shape, event-related potentials were recorded to face and object pictures preceded by mental imagery of a picture. Mental imagery of the identical face or object (congruous condition facilitated not only categorical perception (VPP/N170 but also later visual knowledge (N3[00] complex and linguistic knowledge (N400 for faces more than objects, and strategic semantic analysis (late positive complex between 200 and 700 ms. The later effects resembled semantic congruity effects with pictures. Mental imagery also facilitated category decisions, as a P3(00 peaked earlier for congruous than incongruous (other category pictures, resembling the case when identical pictures repeat immediately. Thus mental imagery mimics semantic congruity and immediate repetition priming processes with pictures. Perception control results showed the opposite for faces and were in the same direction for objects: Perceptual repetition adapts (and so impairs processing of perceived faces from categorical perception onwards, but primes processing of objects during categorical perception, visual knowledge processes, and strategic semantic analysis. For both imagery and perception, differences between faces and objects support domain-specificity and indicate that cognition is grounded in modal processing. Altogether, this direct neural evidence reveals that top-down processes of mental imagery sustain an imagistic representation that mimics perception well enough to prime subsequent perception and cognition. This also suggests that automatic mental simulation of the visual shape of faces and objects operates between 200 and 400 ms, and strategic mental simulation operates between

  10. Gene expression analysis reveals new possible mechanisms of vancomycin-induced nephrotoxicity and identifies gene markers candidates.

    Science.gov (United States)

    Dieterich, Christine; Puey, Angela; Lin, Sylvia; Lyn, Sylvia; Swezey, Robert; Furimsky, Anna; Fairchild, David; Mirsalis, Jon C; Ng, Hanna H

    2009-01-01

    Vancomycin, one of few effective treatments against methicillin-resistant Staphylococcus aureus, is nephrotoxic. The goals of this study were to (1) gain insights into molecular mechanisms of nephrotoxicity at the genomic level, (2) evaluate gene markers of vancomycin-induced kidney injury, and (3) compare gene expression responses after iv and ip administration. Groups of six female BALB/c mice were treated with seven daily iv or ip doses of vancomycin (50, 200, and 400 mg/kg) or saline, and sacrificed on day 8. Clinical chemistry and histopathology demonstrated kidney injury at 400 mg/kg only. Hierarchical clustering analysis revealed that kidney gene expression profiles of all mice treated at 400 mg/kg clustered with those of mice administered 200 mg/kg iv. Transcriptional profiling might thus be more sensitive than current clinical markers for detecting kidney damage, though the profiles can differ with the route of administration. Analysis of transcripts whose expression was changed by at least twofold compared with vehicle saline after high iv and ip doses of vancomycin suggested the possibility of oxidative stress and mitochondrial damage in vancomycin-induced toxicity. In addition, our data showed changes in expression of several transcripts from the complement and inflammatory pathways. Such expression changes were confirmed by relative real-time reverse transcription-polymerase chain reaction. Finally, our results further substantiate the use of gene markers of kidney toxicity such as KIM-1/Havcr1, as indicators of renal injury.

  11. Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53.

    Directory of Open Access Journals (Sweden)

    Kristina Kirschner

    2015-03-01

    Full Text Available The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage and chronically activated (in senescent or pro-apoptotic conditions p53. Compared to the classical 'acute' p53 binding profile, 'chronic' p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory 'p53 hubs' where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the 'lipogenic phenotype', a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms.

  12. Talaromyces marneffei Genomic, Transcriptomic, Proteomic and Metabolomic Studies Reveal Mechanisms for Environmental Adaptations and Virulence

    Directory of Open Access Journals (Sweden)

    Susanna K. P. Lau

    2017-06-01

    Full Text Available Talaromyces marneffei is a thermally dimorphic fungus causing systemic infections in patients positive for HIV or other immunocompromised statuses. Analysis of its ~28.9 Mb draft genome and additional transcriptomic, proteomic and metabolomic studies revealed mechanisms for environmental adaptations and virulence. Meiotic genes and genes for pheromone receptors, enzymes which process pheromones, and proteins involved in pheromone response pathway are present, indicating its possibility as a heterothallic fungus. Among the 14 Mp1p homologs, only Mp1p is a virulence factor binding a variety of host proteins, fatty acids and lipids. There are 23 polyketide synthase genes, one for melanin and two for mitorubrinic acid/mitorubrinol biosynthesis, which are virulence factors. Another polyketide synthase is for biogenesis of the diffusible red pigment, which consists of amino acid conjugates of monascorubin and rubropunctatin. Novel microRNA-like RNAs (milRNAs and processing proteins are present. The dicer protein, dcl-2, is required for biogenesis of two milRNAs, PM-milR-M1 and PM-milR-M2, which are more highly expressed in hyphal cells. Comparative transcriptomics showed that tandem repeat-containing genes were overexpressed in yeast phase, generating protein polymorphism among cells, evading host’s immunity. Comparative proteomics between yeast and hyphal cells revealed that glyceraldehyde-3-phosphate dehydrogenase, up-regulated in hyphal cells, is an adhesion factor for conidial attachment.

  13. Ten-year review reveals changing trends and severity of allergic reactions to nuts and other foods.

    Science.gov (United States)

    Johnson, Jennifer; Malinovschi, Andrei; Alving, Kjell; Lidholm, Jonas; Borres, Magnus P; Nordvall, Lennart

    2014-08-01

    Over the past few decades, the incidence of food allergies has risen and Sweden has increased its import of peanuts and exotic nuts, such as cashew nuts, which may cause severe allergic reactions. This study aimed to retrospectively investigate paediatric emergency visits due to food reactions over a 10-year period, focusing on reactions to peanuts and tree nuts. Emergency visits to Uppsala University Children's Hospital, Sweden, between September 2001 and December 2010, were reviewed, and cases containing diagnostic codes for anaphylaxis, allergic reactions or allergy and hypersensitivity not caused by drugs or biological substances were retrieved. We analysed 703 emergency visits made by 578 individuals with food allergies. Peanuts and tree nuts accounted for 50% of the food allergies and were more frequently associated with adrenaline treatment and hospitalisation than other foods. Cashew nut reactions increased over the study period, and together with peanuts, they were responsible for more anaphylactic reactions than hazelnuts. Peanut and tree nut reactions were more likely to result in adrenaline treatment and hospitalisation than other food reactions. Peanut and cashew nut reactions were more likely to cause anaphylaxis than hazelnuts. Cashew nut reactions increased during the study period. ©2014 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

  14. Testing two-nucleon transfer reaction mechanism with elementary modes of excitation in exotic nuclei

    CERN Document Server

    Broglia, R A; Idini, A; Barranco, F; Vigezzi, E

    2015-01-01

    Nuclear Field Theory of structure and reactions is confronted with observations made on neutron halo dripline nuclei, resulting in the prediction of a novel (symbiotic) mode of nuclear excitation, and on the observation of the virtual effect of the halo phenomenon in the apparently non-halo nucleus $^7$Li. This effect is forced to become real by intervening the virtual process with an external (t,p) field which, combined with accurate predictive abilities concerning the absolute differential cross section, reveals an increase of a factor 2 in the cross section due to the presence of halo ground state correlations, and is essential to reproduce the value of the observed $d \\sigma(^7$Li(t,p)$^9$Li)/d$\\Omega$.

  15. Tribology. Mechanisms of antiwear tribofilm growth revealed in situ by single-asperity sliding contacts.

    Science.gov (United States)

    Gosvami, N N; Bares, J A; Mangolini, F; Konicek, A R; Yablon, D G; Carpick, R W

    2015-04-03

    Zinc dialkyldithiophosphates (ZDDPs) form antiwear tribofilms at sliding interfaces and are widely used as additives in automotive lubricants. The mechanisms governing the tribofilm growth are not well understood, which limits the development of replacements that offer better performance and are less likely to degrade automobile catalytic converters over time. Using atomic force microscopy in ZDDP-containing lubricant base stock at elevated temperatures, we monitored the growth and properties of the tribofilms in situ in well-defined single-asperity sliding nanocontacts. Surface-based nucleation, growth, and thickness saturation of patchy tribofilms were observed. The growth rate increased exponentially with either applied compressive stress or temperature, consistent with a thermally activated, stress-assisted reaction rate model. Although some models rely on the presence of iron to catalyze tribofilm growth, the films grew regardless of the presence of iron on either the tip or substrate, highlighting the critical role of stress and thermal activation. Copyright © 2015, American Association for the Advancement of Science.

  16. Cartilaginous Metabolomic Study Reveals Potential Mechanisms of Osteophyte Formation in Osteoarthritis.

    Science.gov (United States)

    Xu, Zhongwei; Chen, Tingmei; Luo, Jiao; Ding, Shijia; Gao, Sichuan; Zhang, Jian

    2017-04-07

    Osteophyte is one of the inevitable consequences of progressive osteoarthritis with the main characteristics of cartilage degeneration and endochondral ossification. The pathogenesis of osteophyte formation is not fully understood to date. In this work, metabolomic approaches were employed to explore potential mechanisms of osteophyte formation by detecting metabolic variations between extracts of osteophyte cartilage tissues (n = 32) and uninvolved control cartilage tissues (n = 34), based on the platform of ultraperformance liquid chromatography tandem quadrupole time-of-flight mass spectrometry, as well as the use of multivariate statistic analysis and univariate statistic analysis. The osteophyte group was significantly separated from the control group by the orthogonal partial least-squares discriminant analysis models, indicating that metabolic state of osteophyte cartilage had been changed. In total, 28 metabolic variations further validated by mass spectrum (MS) match, tandom mass spectrum (MS/MS) match, and standards match mainly included amino acids, sulfonic acids, glycerophospholipids, and fatty acyls. These metabolites were related to some specific physiological or pathological processes (collagen dissolution, boundary layers destroyed, self-restoration triggered, etc.) which might be associated with the procedure of osteophyte formation. Pathway analysis showed phenylalanine metabolism (PI = 0.168, p = 0.004) was highly correlative to this degenerative process. Our findings provided a direction for targeted metabolomic study and an insight into further reveal the molecular mechanisms of ostophyte formation.

  17. Comparative genomic analysis of isoproturon-mineralizing sphingomonads reveals the isoproturon catabolic mechanism.

    Science.gov (United States)

    Yan, Xin; Gu, Tao; Yi, Zhongquan; Huang, Junwei; Liu, Xiaowei; Zhang, Ji; Xu, Xihui; Xin, Zhihong; Hong, Qing; He, Jian; Spain, Jim C; Li, Shunpeng; Jiang, Jiandong

    2016-12-01

    The worldwide use of the phenylurea herbicide, isoproturon (IPU), has resulted in considerable concern about its environmental fate. Although many microbial metabolites of IPU are known and IPU-mineralizing bacteria have been isolated, the molecular mechanism of IPU catabolism has not been elucidated yet. In this study, complete genes that encode the conserved IPU catabolic pathway were revealed, based on comparative analysis of the genomes of three IPU-mineralizing sphingomonads and subsequent experimental validation. The complete genes included a novel hydrolase gene ddhA, which is responsible for the cleavage of the urea side chain of the IPU demethylated products; a distinct aniline dioxygenase gene cluster adoQTA1A2BR, which has a broad substrate range; and an inducible catechol meta-cleavage pathway gene cluster adoXEGKLIJC. Furthermore, the initial mono-N-demethylation genes pdmAB were further confirmed to be involved in the successive N-demethylation of the IPU mono-N-demethylated product. These IPU-catabolic genes were organized into four transcription units and distributed on three plasmids. They were flanked by multiple mobile genetic elements and highly conserved among IPU-mineralizing sphingomonads. The elucidation of the molecular mechanism of IPU catabolism will enhance our understanding of the microbial mineralization of IPU and provide insights into the evolutionary scenario of the conserved IPU-catabolic pathway. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  18. Determining Role of the Chain Mechanism in the Temperature Dependence of the Gas-Phase Rate of Combustion Reactions

    Science.gov (United States)

    Azatyan, V. V.; Bolod'yan, I. A.; Kopylov, N. P.; Kopylov, S. N.; Prokopenko, V. M.; Shebeko, Yu. N.

    2018-05-01

    It is shown that the strong dependence of the rate of gas-phase combustion reactions on temperature is determined by the high values of the reaction rate constants of free atoms and radicals. It is established that with a branched chain mechanism, a special role in the reaction rate temperature dependence is played by positive feedback between the concentrations of active intermediate species and the rate of their change. The role of the chemical mechanism in the temperature dependence of the process rate with and without inhibitors is considered.

  19. Signature gene expression reveals novel clues to the molecular mechanisms of dimorphic transition in Penicillium marneffei.

    Directory of Open Access Journals (Sweden)

    Ence Yang

    2014-10-01

    Full Text Available Systemic dimorphic fungi cause more than one million new infections each year, ranking them among the significant public health challenges currently encountered. Penicillium marneffei is a systemic dimorphic fungus endemic to Southeast Asia. The temperature-dependent dimorphic phase transition between mycelium and yeast is considered crucial for the pathogenicity and transmission of P. marneffei, but the underlying mechanisms are still poorly understood. Here, we re-sequenced P. marneffei strain PM1 using multiple sequencing platforms and assembled the genome using hybrid genome assembly. We determined gene expression levels using RNA sequencing at the mycelial and yeast phases of P. marneffei, as well as during phase transition. We classified 2,718 genes with variable expression across conditions into 14 distinct groups, each marked by a signature expression pattern implicated at a certain stage in the dimorphic life cycle. Genes with the same expression patterns tend to be clustered together on the genome, suggesting orchestrated regulations of the transcriptional activities of neighboring genes. Using qRT-PCR, we validated expression levels of all genes in one of clusters highly expressed during the yeast-to-mycelium transition. These included madsA, a gene encoding MADS-box transcription factor whose gene family is exclusively expanded in P. marneffei. Over-expression of madsA drove P. marneffei to undergo mycelial growth at 37°C, a condition that restricts the wild-type in the yeast phase. Furthermore, analyses of signature expression patterns suggested diverse roles of secreted proteins at different developmental stages and the potential importance of non-coding RNAs in mycelium-to-yeast transition. We also showed that RNA structural transition in response to temperature changes may be related to the control of thermal dimorphism. Together, our findings have revealed multiple molecular mechanisms that may underlie the dimorphic transition

  20. Comparative proteomic and metabolomic analysis reveal the antiosteoporotic molecular mechanism of icariin from Epimedium brevicornu maxim.

    Science.gov (United States)

    Xue, Liming; Jiang, Yiping; Han, Ting; Zhang, Naidan; Qin, Luping; Xin, Hailiang; Zhang, Qiaoyan

    2016-11-04

    Icariin, a principal flavonoid glycoside of Epimedium brevicornu Maxim, has been widely proved to possess antiosteoporotic activity with promoting bone formation and decreasing bone resorption. However, the involving mechanisms remain unclear. To clear a global insight of signal pathways involved in anti-osteoporotic mechanism of icariin at proteins and metabolites level by integrating the proteomics and NMR metabonomics, in a systems biology approach. Mice were divided into sham, OVX model and icariin-treated OVX group, after 90 days treatment, difference gel electrophoresis combined with MALDI-TOF/TOF proteomics analysis on bone femur and serum metabolomics were carried out for monitor intracellular processes and elucidate anti-osteoporotic mechanism of icariin. Osteoblast and osteoclast were applied to evaluate the potential signal pathways. Twenty three proteins in bone femur, and 8 metabolites in serum, were significantly altered and identified, involving in bone remodeling, energy metabolism, cytoskeleton, lipid metabolism, MAPK signaling, Ca 2+ signaling et, al. Furthermore, animal experiment show icariin could enhance the BMD and BMC, decrease CTX-I level in ovariectomized mice. The mitochondrial membrane potential and the intracellular ATP levels were increased significantly, and the cytoskeleton were improved in icariin-treatment osteoblast and osteoclast. Icariin also increased mRNA expression of Runx2 and osterix of OB, decreased CTR and CAII mRNA expression and protein expression of P38 and JNK. However, icariin did not reveal any inhibition of the collagenolytic activity of cathepsin K, mRNA expression of MMP-9 and protein expression of ERK in osteoclast. we consider icariin as multi-targeting compounds for treating with osteoporosis, involve initiating osteoblastogenesis, inhibiting adipogenesis, and preventing osteoclast differentiation. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  1. Structural evolution and reaction mechanism of lithium nickelate (LiNiO2 during the carbonation reaction

    Directory of Open Access Journals (Sweden)

    Daniela González-Varela

    2018-03-01

    Full Text Available Lithium nickelate (LiNiO2 was synthesized using the lithium excess method, and then characterized by X-ray diffraction, scanning electron microscopy and N2 adsorption-desorption. Finally, differential thermal and thermogravimetric analyses were performed in CO2 presence, at high temperatures. Results show that LiNiO2 is able to react with CO2 through a complex structural evolution process, where lithium atoms are released to produce Li2CO3, while some nickel atoms are rearranged on different Li1-xNi1+xO2 crystalline phases. LiNiO2-CO2 reaction kinetic parameters were determined assuming a first-order reaction, where kinetic constants tended to increase as a function of temperature. However, kinetic constant values did not follow a linear trend. This atypical behavior was attributed to LiNiO2 sintering and crystalline evolution performed as a function of temperature.

  2. Atmospheric reaction of Cl + methacrolein: a theoretical study on the mechanism, and pressure- and temperature-dependent rate constants.

    Science.gov (United States)

    Sun, Cuihong; Xu, Baoen; Zhang, Shaowen

    2014-05-22

    Methacrolein is a major degradation product of isoprene, the reaction of methacrolein with Cl atoms may play some roles in the degradation of isoprene where these species are relatively abundant. However, the energetics and kinetics of this reaction, which govern the reaction branching, are still not well understood so far. In the present study, two-dimensional potential energy surfaces were constructed to analyze the minimum energy path of the barrierless addition process between Cl and the C═C double bond of methacrolein, which reveals that the terminal addition intermediate is directly formed from the addition reaction. The terminal addition intermediate can further yield different products among which the reaction paths abstracting the aldehyde hydrogen atom and the methyl hydrogen atom are dominant reaction exits. The minimum reaction path for the direct aldehydic hydrogen atom abstraction is also obtained. The reaction kinetics was calculated by the variational transition state theory in conjunction with the master equation method. From the theoretical model we predicted that the overall rate constant of the Cl + methacrolein reaction at 297 K and atmospheric pressure is koverall = 2.3× 10(-10) cm(3) molecule(-1) s(-1), and the branching ratio of the aldehydic hydrogen abstraction is about 12%. The reaction is pressure dependent at P pressure limit at about 100 Torr. The calculated results could well account for the experimental observations.

  3. High Electrocatalytic Response of a Mechanically Enhanced NbC Nanocomposite Electrode Towards Hydrogen Evolution Reaction

    KAUST Repository

    Coy, Emerson

    2017-08-22

    Resistant and efficient electrocatalysts for hydrogen evolution reaction (HER) are desired to replace scarce and commercially expensive platinum electrodes. Thin film electrodes of metal-carbides are a promising alternative due to their reduced price and similar catalytic properties. However, most of the studied structures to date neglect long lasting chemical and structural stability, focusing only on electrochemical efficiency. Herein we report on a new approach to easily deposit and control the micro/nanostructure of thin film electrodes based on niobium carbide (NbC) and their electrocatalytic response. We will show that, by improving the mechanical properties of the NbC electrodes, microstructure and mechanical resilience can be obtained whilst maintaining high electro catalytic response. We also address the influence of other parameters such as conductivity and chemical composition on the overall performance of the thin film electrodes. Finally, we show that nanocomposite NbC electrodes are promising candidates towards HER , and furthermore, that the methodology presented here is suitable to produce other transition metal carbides (TM-C) with improved catalytic and mechanical properties.

  4. Elucidation of Mechanisms and Selectivities of Metal-Catalyzed Reactions using Quantum Chemical Methodology.

    Science.gov (United States)

    Santoro, Stefano; Kalek, Marcin; Huang, Genping; Himo, Fahmi

    2016-05-17

    solving complex problems and proposing new detailed reaction mechanisms that rationalize the experimental findings. For each of the considered reactions, a consistent mechanism is presented, the experimentally observed selectivities are reproduced, and their sources are identified. Reproducing selectivities requires high accuracy in computing relative transition state energies. As demonstrated by the results summarized in this Account, this accuracy is possible with the use of the presented methodology, benefiting of course from a large extent of cancellation of systematic errors. It is argued that as the employed models become larger, the number of rotamers and isomers that have to be considered for every stationary point increases and a careful assessment of their energies is therefore necessary in order to ensure that the lowest energy conformation is located. This issue constitutes a bottleneck of the investigation in some cases and is particularly important when analyzing selectivities, since small energy differences need to be reproduced.

  5. Dissociation reactions of the 11Be one-neutron halo: the interplay between structure and reaction mechanism

    International Nuclear Information System (INIS)

    Anne, R.; Lewitowicz, M.; Saint-Laurent, M.G.; Arnell, S.E.; Jonson, B.; Nilsson, T.; Nyman, G.; Wilhelmsen Rolander, K.; Esbensen, H.; Wolski, D.

    1992-01-01

    Reactions of a radioactive 11 Be beam at 41 MeV/u have been investigated. The absolute magnitude of the differential cross-sections of the forward neutrons in the exclusive ( 10 Be + n) channel can be accounted for quantitatively in a simple model. The narrow distribution from high-Z targets turns out to arise from Coulomb dissociation whereas the broad distribution from the beryllium target is due to diffraction dissociation

  6. Quantum and Statistical Mechanics Applied to Singlet Carbenes, Pericyclic Reactions, and Condensed Phase Phenomena

    Science.gov (United States)

    Evanseck, Jeffrey Donald

    The completed research covers a broad range of theoretical applications in organic chemistry. It is divided into three chapters which covers the chemistry of singlet carbenes (Chapter 1), substituent effects in pericyclic rearrangements (Chapter 2), and the effects of solvent on the reactivity of organic reactions (Chapter 3). The selectivity between 1,2- and 1,4-intramolecular additions to restricted diene systems has been investigated. A decrease in activation energy for the intramolecular cycloaddition is noted for systems which approach the idealized geometry found with intermolecular addition of carbenes to olefins. Direct substitution at the carbene site dramatically effects the predicted activation barriers for 1,2-hydrogen shifts. An excellent correlation between the activation energy and a substituents sigma_sp {rm R}{rm o} parameters has been demonstrated. The long standing problem of orbital alignment influences on the selectivity of 1,2-hydrogen arrangements shows significant geometric distortions, yet has little influence on the rates of singlet alkylcarbene rearrangements. The exo-selectivities observed for 1,2-shifts in rigid systems are explained by torsional and steric interactions which develop in the transition structures. Substituent effects on pericyclic reactions have been computed for several conrotatory and disrotatory electrocyclizations. The six-electron disrotatory electrocyclization of 1-substituted hexatrienes displays a strong electronic component in determining stereoselectivity, despite incredible steric interference. The eight-electron conrotatory electrocyclization transition structure of 1-substituted octatetraene has an unusual helical transition structure which does not differentiate between substituent position. The effects of solvents on the acidity differences between E and Z esters has supplemented earlier ab initio quantum mechanical results on the enhanced acidity of Meldrum's acid. Monte Carlo simulations predict a

  7. On rates and mechanisms of OH and O3 reactions with isoprene-derived hydroxy nitrates.

    Science.gov (United States)

    Lee, Lance; Teng, Alex P; Wennberg, Paul O; Crounse, John D; Cohen, Ronald C

    2014-03-06

    Eight distinct hydroxy nitrates are stable products of the first step in the atmospheric oxidation of isoprene by OH. The subsequent chemical fate of these molecules affects global and regional production of ozone and aerosol as well as the location of nitrogen deposition. We synthesized and purified 3 of the 8 isoprene hydroxy nitrate isomers: (E/Z)-2-methyl-4-nitrooxybut-2-ene-1-ol and 3-methyl-2-nitrooxybut-3-ene-1-ol. Oxidation of these molecules by OH and ozone was studied using both chemical ionization mass spectrometry and thermo-dissociation laser induced fluorescence. The OH reaction rate constants at 300 K measured relative to propene at 745 Torr are (1.1 ± 0.2) × 10(-10) cm(3) molecule(-1) s(-1) for both the E and Z isomers and (4.2 ± 0.7) × 10(-11) cm(3) molecule(-1) s(-1) for the third isomer. The ozone reaction rate constants for (E/Z)-2-methyl-4-nitrooxybut-2-ene-1-ol are (2.7 ± 0.5) × 10(-17) and (2.9 ± 0.5) × 10(-17) cm(3) molecule(-1) s(-1), respectively. 3-Methyl-2-nitrooxybut-3-ene-1-ol reacts with ozone very slowly, within the range of (2.5-5) × 10(-19) cm(3) molecule(-1) s(-1). Reaction pathways, product yields, and implications for atmospheric chemistry are discussed. A condensed mechanism suitable for use in atmospheric chemistry models is presented.

  8. Global reaction mechanism for the auto-ignition of full boiling range gasoline and kerosene fuels

    Science.gov (United States)

    Vandersickel, A.; Wright, Y. M.; Boulouchos, K.

    2013-12-01

    Compact reaction schemes capable of predicting auto-ignition are a prerequisite for the development of strategies to control and optimise homogeneous charge compression ignition (HCCI) engines. In particular for full boiling range fuels exhibiting two stage ignition a tremendous demand exists in the engine development community. The present paper therefore meticulously assesses a previous 7-step reaction scheme developed to predict auto-ignition for four hydrocarbon blends and proposes an important extension of the model constant optimisation procedure, allowing for the model to capture not only ignition delays, but also the evolutions of representative intermediates and heat release rates for a variety of full boiling range fuels. Additionally, an extensive validation of the later evolutions by means of various detailed n-heptane reaction mechanisms from literature has been presented; both for perfectly homogeneous, as well as non-premixed/stratified HCCI conditions. Finally, the models potential to simulate the auto-ignition of various full boiling range fuels is demonstrated by means of experimental shock tube data for six strongly differing fuels, containing e.g. up to 46.7% cyclo-alkanes, 20% napthalenes or complex branched aromatics such as methyl- or ethyl-napthalene. The good predictive capability observed for each of the validation cases as well as the successful parameterisation for each of the six fuels, indicate that the model could, in principle, be applied to any hydrocarbon fuel, providing suitable adjustments to the model parameters are carried out. Combined with the optimisation strategy presented, the model therefore constitutes a major step towards the inclusion of real fuel kinetics into full scale HCCI engine simulations.

  9. Thermal analysis experiment for elucidating sodium-water chemical reaction mechanism in steam generator of sodium-cooled fast reactor

    International Nuclear Information System (INIS)

    Kikuchi, Shin; Kurihara, Akikazu; Ohshima, Hiroyuki

    2012-01-01

    For the purpose of elucidating the mechanism of the sodium-water surface reaction in a steam generator of sodium-cooled fast reactors, kinetic study of the sodium (Na)-sodium hydroxide (NaOH) reaction has been carried out by using Differential Thermal Analysis (DTA) technique. The parameters, including melting points of Na and NaOH, phase transition temperature of NaOH, Na-NaOH reaction temperature, and decomposition temperature of sodium hydride (NaH) have been identified from DTA curves. Based on the measured reaction temperature, rate constant of sodium monoxide (Na 2 O) generation was obtained. Thermal analysis results indicated that Na 2 O generation at the secondary overall reaction should be considered during the sodium-water reaction. (author)

  10. Alternative interpretation of low-energy nuclear reaction processes with deuterated metals based on the Bose-Einstein condensation mechanism

    International Nuclear Information System (INIS)

    Yeong, E. Kim; Passell, Thomas O.

    2006-01-01

    Recently, a generalization of the Bose-Einstein condensation (BEC) mechanism has been made to a ground-state mixture of two different species of positively charged bosons in harmonic traps. The theory has been used to describe (D + Li) reactions in the low energy nuclear reaction (LENR) processes in condensed matter and predicts that the (D + Li) reaction rates can be larger than (D + D) reaction rates by as much as a factor of ∼ 50, implying that (D + Li) reactions may be occurring in addition to the (D + D) reactions. A survey of the existing data from LENR experiments is carried out to check the validity of the theoretical prediction. We conclude that there is compelling experimental evidence which support the theoretical prediction. New experimental tests of the theoretical prediction are suggested. (authors)

  11. Alternative Interpretation of Low-Energy Nuclear Reaction Processes with Deuterated Metals Based on the Bose-Einstein Condensation Mechanism

    Science.gov (United States)

    Kim, Yeong E.; Passell, Thomas O.

    2006-02-01

    Recently, a generalization of the Bose-Einstein condensation (BEC) mechanism has been made to a ground-state mixture of two different species of positively charged bosons in harmonic traps. The theory has been used to describe (D + Li) reactions in the low energy nuclear reaction (LENR) processes in condensed matter and predicts that the (D + Li) reaction rates can be larger than (D + D) reaction rates by as much as a factor of ~50, implying that (D + Li) reactions may be occuring in addition to the (D + D) reactions. A survey of the existing data from LENR experiments is carried out to check the validity of the theoretical prediction. We conclude that there is compelling experimental evidence which support the theoretical prediction. New experimental tests of the theoretical prediction are suggested.

  12. Alternative interpretation of low-energy nuclear reaction processes with deuterated metals based on the Bose-Einstein condensation mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Yeong, E. Kim [Department of Physics, Purdue University, West Lafayette, IN 47907 (United States); Passell, Thomas O. [TOP Consulting, PO Box 336, Palo Alto, CA 94302-0336 (United States)

    2006-07-01

    Recently, a generalization of the Bose-Einstein condensation (BEC) mechanism has been made to a ground-state mixture of two different species of positively charged bosons in harmonic traps. The theory has been used to describe (D + Li) reactions in the low energy nuclear reaction (LENR) processes in condensed matter and predicts that the (D + Li) reaction rates can be larger than (D + D) reaction rates by as much as a factor of {approx} 50, implying that (D + Li) reactions may be occurring in addition to the (D + D) reactions. A survey of the existing data from LENR experiments is carried out to check the validity of the theoretical prediction. We conclude that there is compelling experimental evidence which support the theoretical prediction. New experimental tests of the theoretical prediction are suggested. (authors)

  13. Kinetic calorimetry in the study of the mechanism of low-temperature chemical reactions

    Science.gov (United States)

    Barkalov, I. M.; Kiryukhin, D. P.

    Chemical reactions are always followed by a change in the reacting system enthalpy, hence, calorimetry as a method of enthalpy and heat capacity measuring is a universal and, sometimes, even the only possible way of studying chemical reaction kinetics. Throughout its long history, the calorimeter, having preserved the positions of the main method of thermodynamic studies, has conquered a new field of application: that of kinetic study of chemical reactions. The advantages and disadvantages of the kinetic calorimeter are now obvious. First, the advantages are: (1) the possibility of measuring the rate of a chemical reaction without any special requirements being imposed on the reaction medium (solid, viscous, multicomponent systems); (2) the high efficiency: a large volume of kinetic information in one experiment and a non-destructive character of changes; (3) the possibility of measuring directly in the field of ionizing radiation (γ-radiation, accelerated electrons) and light; and (4) recording of the chemical conversion directly at the time of its occurrence. The disadvantages of this method are: (1) the high inertia of standard calorimeter systems (τC⋍102-103S), which restricts the possibilities of studying fast processes; and (2) the complexity of the correct organization of the calorimeter experiment when the parameters of the process are changed (overheating in the sample, conversion of the process to explosive and auto wave regimens). One of the oldest and most universal methods of studying the mechanism of chemical reactions, calorimetry, is now passing through a period of turbulent development due to the advances in electronics and computerization. The wide variety of types of calorimeter set-ups and the large assortment of measurement schemes in the currently described methods complicate the experimental selection of the necessary instrument rather than facilitate it. The basic principles of the method, the types of calorimeters, and the measuring

  14. Effects of alpha-amylase reaction mechanisms on analysis of resistant-starch contents.

    Science.gov (United States)

    Moore, Samuel A; Ai, Yongfeng; Chang, Fengdan; Jane, Jay-lin

    2015-01-22

    This study aimed to understand differences in the resistant starch (RS) contents of native and modified starches obtained using two standard methods of RS content analysis: AOAC Method 991.43 and 2002.02. The largest differences were observed in native potato starch, cross-linked wheat distarch phosphate, and high-amylose corn starch stearic-acid complex (RS5) between using AOAC Method 991.43 with Bacillus licheniformis α-amylase (BL) and AOAC Method 2002.02 with porcine pancreatic α-amylase (PPA). To determine possible reasons for these differences, we hydrolyzed raw-starch granules with BL and PPA with equal activity at pH 6.9 and 37°C for up to 84 h and observed the starch granules displayed distinct morphological differences after the hydrolysis. Starches hydrolyzed by BL showed erosion on the surface of the granules; those hydrolyzed by PPA showed pitting on granule surfaces. These results suggested that enzyme reaction mechanisms, including the sizes of the binding sites and the reaction patterns of the two enzymes, contributed to the differences in the RS contents obtained using different methods of RS analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Reaction Mechanism and Distribution Behavior of Arsenic in the Bottom Blown Copper Smelting Process

    Directory of Open Access Journals (Sweden)

    Qinmeng Wang

    2017-08-01

    Full Text Available The control of arsenic, a toxic and carcinogenic element, is an important issue for all copper smelters. In this work, the reaction mechanism and distribution behavior of arsenic in the bottom blown copper smelting process (SKS process were investigated and compared to the flash smelting process. There are obvious differences of arsenic distribution in the SKS process and flash process, resulting from the differences of oxygen potentials, volatilizations, smelting temperatures, reaction intensities, and mass transfer processes. Under stable production conditions, the distributions of arsenic among matte, slag, and gas phases are 6%, 12%, and 82%, respectively. Less arsenic is reported in the gas phase with the flash process than with the SKS process. The main arsenic species in gas phase are AsS (g, AsO (g, and As2 (g. Arsenic exists in the slag predominantly as As2O3 (l, and in matte as As (l. High matte grade is harmful to the elimination of arsenic to gas. The changing of Fe/SiO2 has slight effects on the distributions of arsenic. In order to enhance the removal of arsenic from the SKS smelting system to the gas phase, low oxygen concentration, low ratios of oxygen/ore, and low matte grade should be chosen. In the SKS smelting process, no dust is recycled, and almost all dust is collected and further treated to eliminate arsenic and recover valuable metals by other process streams.

  16. Computational comparison of quantum-mechanical models for multistep direct reactions

    International Nuclear Information System (INIS)

    Koning, A.J.; Akkermans, J.M.

    1993-01-01

    We have carried out a computational comparison of all existing quantum-mechanical models for multistep direct (MSD) reactions. The various MSD models, including the so-called Feshbach-Kerman-Koonin, Tamura-Udagawa-Lenske and Nishioka-Yoshida-Weidenmueller models, have been implemented in a single computer system. All model calculations thus use the same set of parameters and the same numerical techniques; only one adjustable parameter is employed. The computational results have been compared with experimental energy spectra and angular distributions for several nuclear reactions, namely, 90 Zr(p,p') at 80 MeV, 209 Bi(p,p') at 62 MeV, and 93 Nb(n,n') at 25.7 MeV. In addition, the results have been compared with the Kalbach systematics and with semiclassical exciton model calculations. All quantum MSD models provide a good fit to the experimental data. In addition, they reproduce the systematics very well and are clearly better than semiclassical model calculations. We furthermore show that the calculated predictions do not differ very strongly between the various quantum MSD models, leading to the conclusion that the simplest MSD model (the Feshbach-Kerman-Koonin model) is adequate for the analysis of experimental data

  17. Studies on adsorption, reaction mechanisms and kinetics for photocatalytic degradation of CHD, a pharmaceutical waste.

    Science.gov (United States)

    Sarkar, Santanu; Bhattacharjee, Chiranjib; Curcio, Stefano

    2015-11-01

    The photocatalytic degradation of chlorhexidine digluconate (CHD), a disinfectant and topical antiseptic and adsorption of CHD catalyst surface in dark condition has been studied. Moreover, the value of kinetic parameters has been measured and the effect of adsorption on photocatalysis has been investigated here. Substantial removal was observed during the photocatalysis process, whereas 40% removal was possible through the adsorption route on TiO2 surface. The parametric variation has shown that alkaline pH, ambient temperature, low initial substrate concentration, high TiO2 loading were favourable, though at a certain concentration of TiO2 loading, photocatalytic degradation efficiency was found to be maximum. The adsorption study has shown good confirmation with Langmuir isotherm and during the reaction at initial stage, it followed pseudo-first-order reaction, after that Langmuir Hinshelwood model was found to be appropriate in describing the system. The present study also confirmed that there is a significant effect of adsorption on photocatalytic degradation. The possible mechanism for adsorption and photocatalysis has been shown here and process controlling step has been identified. The influences of pH and temperature have been explained with the help of surface charge distribution of reacting particles and thermodynamic point of view respectively. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Water deficit mechanisms in perennial shrubs Cerasus humilis leaves revealed by physiological and proteomic analyses.

    Science.gov (United States)

    Yin, Zepeng; Ren, Jing; Zhou, Lijuan; Sun, Lina; Wang, Jiewan; Liu, Yulong; Song, Xingshun

    2016-01-01

    Drought (Water deficit, WD) poses a serious threat to extensively economic losses of trees throughout the world. Chinese dwarf cherry ( Cerasus humilis ) is a good perennial plant for studying the physiological and sophisticated molecular network under WD. The aim of this study is to identify the effect of WD on C. humilis through physiological and global proteomics analysis and improve understanding of the WD resistance of plants. Currently, physiological parameters were applied to investigate C. humilis response to WD. Moreover, we used two-dimensional gel electrophoresis (2DE) to identify differentially expressed proteins in C. humilis leaves subjected to WD (24 d). Furthermore, we also examined the correlation between protein and transcript levels. Several physiological parameters, including relative water content and Pn were reduced by WD. In addition, the malondialdehyde (MDA), relative electrolyte leakage (REL), total soluble sugar, and proline were increased in WD-treated C. humilis . Comparative proteomic analysis revealed 46 protein spots (representing 43 unique proteins) differentially expressed in C. humilis leaves under WD. These proteins were mainly involved in photosynthesis, ROS scavenging, carbohydrate metabolism, transcription, protein synthesis, protein processing, and nitrogen and amino acid metabolisms, respectively. WD promoted the CO 2 assimilation by increase light reaction and Calvin cycle, leading to the reprogramming of carbon metabolism. Moreover, the accumulation of osmolytes (i.e., proline and total soluble sugar) and enhancement of ascorbate-glutathione cycle and glutathione peroxidase/glutathione s-transferase pathway in leaves could minimize oxidative damage of membrane and other molecules under WD. Importantly, the regulation role of carbohydrate metabolisms (e. g. glycolysis, pentose phosphate pathways, and TCA) was enhanced. These findings provide key candidate proteins for genetic improvement of perennial plants metabolism under

  19. The quantum-chemical investigation of N-cyclization reaction mechanism for epichlorohydrin aminolysis products

    Directory of Open Access Journals (Sweden)

    Andrey V. Tokar

    2014-12-01

    Full Text Available The mechanism of intramolecular cyclization for products of epichlorohydrin aminolysis by secondary amines has been investigated at ab initio level of theory. By comparative analysis of energetic characteristics, which obtained in vacuo as well as in acetonitrile solution with the trace quantities of water as an «active» solvation partner of reaction, it has been shown a decisive role of solvent, which occurs mainly at the expense of the polarizable effects for nonspecific solvation. Indeed, the addition to the substrate of one water molecule have decreased corresponding EACT values only 24.1 kJ/mol, while the appearance of acetonitrile surroundings have the same influence ~42.0 kJ/mol. The results of calculations are in good agreement with that data, which have been obtained for such type modeling previously.

  20. A coupled model of transport-reaction-mechanics with trapping. Part I - Small strain analysis

    Science.gov (United States)

    Salvadori, A.; McMeeking, R.; Grazioli, D.; Magri, M.

    2018-05-01

    A fully coupled model for mass and heat transport, mechanics, and chemical reactions with trapping is proposed. It is rooted in non-equilibrium rational thermodynamics and assumes that displacements and strains are small. Balance laws for mass, linear and angular momentum, energy, and entropy are stated. Thermodynamic restrictions are identified, based on an additive strain decomposition and on the definition of the Helmholtz free energy. Constitutive theory and chemical kinetics are studied in order to finally write the governing equations for the multi-physics problem. The field equations are solved numerically with the finite element method, stemming from a three-fields variational formulation. Three case-studies on vacancies redistribution in metals, hydrogen embrittlement, and the charge-discharge of active particles in Li-ion batteries demonstrate the features and the potential of the proposed model.

  1. NATO Advanced Research Workshop on the Mechanisms of Reactions of Organometallic Compounds with Surfaces

    CERN Document Server

    Williams, J

    1989-01-01

    A NATO Advanced Research Workshop on the "Mechanisms of Reactions of Organometallic Compounds with Surfaces" was held in St. Andrews, Scotland in June 1988. Many of the leading international researchers in this area were present at the workshop and all made oral presentations of their results. In addition, significant amounts of time were set aside for Round Table discussions, in which smaller groups considered the current status of mechanistic knowledge, identified areas of dispute or disagreement, and proposed experiments that need to be carried out to resolve such disputes so as to advance our understanding of this important research area. All the papers presented at the workshop are collected in this volume, together with summaries of the conclusions reached at the Round Table discussions. The workshop could not have taken place without financial support from NATO, and donations were also received from Associated Octel, Ltd., STC Ltd., and Epichem Ltd., for which the organisers are very grateful. The orga...

  2. A Reaction-Diffusion-Based Coding Rate Control Mechanism for Camera Sensor Networks

    Directory of Open Access Journals (Sweden)

    Naoki Wakamiya

    2010-08-01

    Full Text Available A wireless camera sensor network is useful for surveillance and monitoring for its visibility and easy deployment. However, it suffers from the limited capacity of wireless communication and a network is easily overflown with a considerable amount of video traffic. In this paper, we propose an autonomous video coding rate control mechanism where each camera sensor node can autonomously determine its coding rate in accordance with the location and velocity of target objects. For this purpose, we adopted a biological model, i.e., reaction-diffusion model, inspired by the similarity of biological spatial patterns and the spatial distribution of video coding rate. Through simulation and practical experiments, we verify the effectiveness of our proposal.

  3. A reaction-diffusion-based coding rate control mechanism for camera sensor networks.

    Science.gov (United States)

    Yamamoto, Hiroshi; Hyodo, Katsuya; Wakamiya, Naoki; Murata, Masayuki

    2010-01-01

    A wireless camera sensor network is useful for surveillance and monitoring for its visibility and easy deployment. However, it suffers from the limited capacity of wireless communication and a network is easily overflown with a considerable amount of video traffic. In this paper, we propose an autonomous video coding rate control mechanism where each camera sensor node can autonomously determine its coding rate in accordance with the location and velocity of target objects. For this purpose, we adopted a biological model, i.e., reaction-diffusion model, inspired by the similarity of biological spatial patterns and the spatial distribution of video coding rate. Through simulation and practical experiments, we verify the effectiveness of our proposal.

  4. Catapult mechanism for fast particle emission in fission and heavy ion reactions

    International Nuclear Information System (INIS)

    Maedler, P.

    1984-01-01

    The fission processes of slabs of nuclear matter is modelled in the Hartree-Fock time dependence approximation by adding an initial collective velocity field to the static self-consistent solution. In dependence on its amplitude either large amplitude density oscillations are excited or fission occurs. The final disintegration of the slab proceeds on a time scale 10 -22 s and is characterized by a sharp peak in the actual velocity field in the region of the ''snatching'' inner low density tails. A characteristic time later a low density lump correlated with a peak in the velocity field energies in front of the fragments. These particles are called ''catapult particles''. Recent experimental results possibly provide evidence for catapult neutrons in low-energy fission. The significance of the catapult mechanism for fast particle emission in the exit channel of heavy ion reactions is discussed

  5. Influence of alkali-silica reaction on the physical, mechanical, and structural behaviour of reinforced concrete

    DEFF Research Database (Denmark)

    Barbosa, Ricardo Antonio

    Alkali-silica reaction (ASR) is one of the major concrete deterioration mechanisms in the world. Cracking in concrete structures due to ASR has been observed worldwide. In Denmark numerous concrete structures have been built with a critical amount of ASR-reactive aggregate, mostly as porous opaline...... and porous calcareous opaline flint in the fine aggregate fraction. During the last few decades, an increasing number of bridges in Denmark have been severely damaged due to ASR. In the most severe cases, the ASR-damaged bridges have been demolished and reconstructed due to uncertainty about their residual...... following features in common: (a) significant amount of ASR cracks were observed on and inside the slabs, (b) the ASR cracks were oriented parallel to the plane of the slabs, and (c) ASR occurred in the fine aggregate fraction. In this PhD study, both the compressive strength and tensile strength of drilled...

  6. The influence of the entrance channel mass asymmetry on the reaction mechanism

    International Nuclear Information System (INIS)

    Agarwal, S.; Galin, J.; Gatty, B.; Guerreau, D.; Lefort, M.; Tarrago, X.; Babinet, R.; Girard, J.

    1980-01-01

    We have tried to investigate the influence of the entrance channel mass asymmetry on the reaction mechanisms associated with heavy ion collisions. Two systems, one very much asymmetric (O + Mo) and the other one almost symmetric (Cr + Fe), were studied in detail by measuring evaporation residues, deep inelastic collision products and fission fragments. An important fraction of the fragments observed in the Cr + Fe system exhibits all the characteristics of fission fragments. The analysis of these data seems to indicate that these fission like products are most likely emitted by a long lived composite system having not reached full statistical equilibrium for all the degrees of freedom. As a consequence, the fusion cross section for this symmetric system is too low as compared to predictions based on a critical distance approach for fusion, whereas the asymmetric system (O + Mo) is well understood in terms of the same model. (orig.)

  7. Understanding the Oxygen Evolution Reaction Mechanism on CoOx using Operando Ambient-Pressure X-ray Photoelectron Spectroscopy

    International Nuclear Information System (INIS)

    Favaro, Marco; Yang, Jinhui; Nappini, Silvia; Magnano, Elena

    2017-01-01

    Photoelectrochemical water splitting is a promising approach for renewable production of hydrogen from solar energy and requires interfacing advanced water-splitting catalysts with semiconductors. Understanding the mechanism of function of such electrocatalysts at the atomic scale and under realistic working conditions is a challenging, yet important, task for advancing efficient and stable function. This is particularly true for the case of oxygen evolution catalysts and, here, we study a highly active Co 3 O 4 /Co(OH) 2 biphasic electrocatalyst on Si by means of operando ambient-pressure X-ray photoelectron spectroscopy performed at the solid/liquid electrified interface. Spectral simulation and multiplet fitting reveal that the catalyst undergoes chemical-structural transformations as a function of the applied anodic potential, with complete conversion of the Co(OH) 2 and partial conversion of the spinel Co 3 O 4 phases to CoO(OH) under precatalytic electrochemical conditions. Furthermore, we observe new spectral features in both Co 2p and O 1s core-level regions to emerge under oxygen evolution reaction conditions on CoO(OH). The operando photoelectron spectra support assignment of these newly observed features to highly active Co 4+ centers under catalytic conditions. Comparison of these results to those from a pure phase spinel Co 3 O 4 catalyst supports this interpretation and reveals that the presence of Co(OH) 2 enhances catalytic activity by promoting transformations to CoO(OH). The direct investigation of electrified interfaces presented in this work can be extended to different materials under realistic catalytic conditions, thereby providing a powerful tool for mechanism discovery and an enabling capability for catalyst design.

  8. Implicit coupling of turbulent diffusion with chemical reaction mechanisms for prognostic atmospheric dispersion models

    Energy Technology Data Exchange (ETDEWEB)

    Berlowitz, D.R.

    1996-11-01

    In the last few decades the negative impact by humans on the thin atmospheric layer enveloping the earth, the basis for life on this planet, has increased steadily. In order to halt, or at least slow down this development, the knowledge and study of these anthropogenic influence has to be increased and possible remedies have to be suggested. An important tool for these studies are computer models. With their help the atmospheric system can be approximated and the various processes, which have led to the current situation can be quantified. They also serve as an instrument to assess short or medium term strategies to reduce this human impact. However, to assure efficiency as well as accuracy, a careful analysis of the numerous processes involved in the dispersion of pollutants in the atmosphere is called for. This should help to concentrate on the essentials and also prevent excessive usage of sometimes scarce computing resources. The basis of the presented work is the EUMAC Zooming Model (ETM), and particularly the component calculating the dispersion of pollutants in the atmosphere, the model MARS. The model has two main parts: an explicit solver, where the advection and the horizontal diffusion of pollutants are calculated, and an implicit solution mechanism, allowing the joint computation of the change of concentration due to chemical reactions, coupled with the respective influence of the vertical diffusion of the species. The aim of this thesis is to determine particularly the influence of the horizontal components of the turbulent diffusion on the existing implicit solver of the model. Suggestions for a more comprehensive inclusion of the full three dimensional diffusion operator in the implicit solver are made. This is achieved by an appropriate operator splitting. A selection of numerical approaches to tighten the coupling of the diffusion processes with the calculation of the applied chemical reaction mechanisms are examined. (author) figs., tabs., refs.

  9. Theoretical study on the reaction mechanism of hydrogenation of furfural to furfuryl alcohol on Lewis acidic BEA zeolites: effects of defect structure and tetravalent metals substitution.

    Science.gov (United States)

    Injongkol, Yuwanda; Maihom, Thana; Treesukul, Piti; Sirijaraensre, Jakkapan; Boekfa, Bundet; Limtrakul, Jumras

    2017-09-13

    Furfural acquired from agricultural sources is receiving extensive attention in the petrochemical industry as it offers an alternative route to generate more valuable hydrocarbon compounds. Herein, we investigate the furfural hydrogenation to furfuryl alcohol catalyzed by Lewis acidic BEA zeolites at the molecular level by means of the M06-L density functional theory. The mechanistic pictures in the catalytic procedure are revealed. The possible reaction pathways are considered to proceed via either concerted or stepwise mechanisms. With the contribution of zeolite oxygen bridging for the H-H splitting, the rate determining step activation barrier for the stepwise mechanism is 14.7 kcal mol -1 lower than that for the concerted mechanism. The stepwise reaction therefore seems to be favored compared to the concerted one. The catalytic effect of the defect zeolite framework on the stepwise mechanism is also investigated. The activation energy for the stepwise rate-determining step over this site is significantly lower than the corresponding step over the perfect one by 14.1 kcal mol -1 . Finally, the catalytic activity of tetravalent metal centers (Sn, Ge, Zr and Hf) substituted in BEA is also preliminarily compared and it is found to follow the order of Hf > Zr > Sn > Ge based on activation energies and the reaction rate. The difference in the activation energy can be traced back to the difference in the charge transfer from the catalytic site to the adsorbed molecules.

  10. Contributions to the study of nuclear reactions mechanism induced by heavy ions on intermediate mass nuclei

    International Nuclear Information System (INIS)

    Avrigeanu, M.

    1982-01-01

    A detailed analysis is presented, based on Hauser-Feshbach statistical model calculations of the γ-ray excitation functions measured in the sup(74,76)Ge ( 12 C, xn) and sup(72,73)Ge ( 16 O,xnyp) reactions. The most usual quantities provided by the in beam γ-ray measurements such as the cross sections for the population of the final states as well as the decay scheme and the degree of alignment of these states mainly offer the means of testing models of both the reaction mechanism and nuclear properties of high excitation energies, since they concentrate information on the whole reaction process. Experimental information on sup(85,86)Sr and sup(85,86)Y, γ-decay scheme and the excitation functions for the population of the final states were obtained by sub(74,76)Ge ( 12 C,αn), n = 2-4, sup(74,76)Ge ( 14 N,xn) n = 3-5, sup(72,73)Ge ( 16 O,xnyp), x = 1-3, y=1 reactions at incident energies between 35 and 60 MW. Statistical model calculations in the Hauser-Feshbach formalism have been compared with the experimental γ-ray excitation functions. The competitive emission of neutrons, protons, alpha particles and gamma rays from the compound nucleus has been considered in the calculations. The calculations describe satisfactorily the total cross sections for the population of the 2n, 3n and 4n channels for 12 C + sup(74,76)Ge and 2n, np, 3n and 2np channels for 16 O + 72 Ge. The calculations are sensitive to the characteristics of the excited levels (such as spin values) but htis this sensitivity could be exploited with some reliability only if one makes use of a rather complete level scheme in the calculations. In the case of 2n, np, 3n and 2 np channels for 16 O+ 73 Ge one concludes on the reliability of consideration some structural aspects in the calculations

  11. Proton propagation through nuclei and the quasi-free reaction mechanism studied with (e,e'p) reactions

    International Nuclear Information System (INIS)

    Dutta, D.; Abbott, D.; Amatuni, T.A.

    1997-01-01

    Jefferson Lab experiment E91-013 measured the energy dependence of proton propagation in nuclei, using the quasi-free (e, e'p) reaction. The ratios of the experimental (e, e'p) cross-sections integrated over the quasi-free region to PWIA calculations are presented as a function of momentum transfer, (0.6 2 2 ) and target nucleus (C, Fe and Au). As a first step towards a longitudinal and transverse separation of the quasi-free cross-section, a super ratio of the measured to the calculated cross-sections at forward and backward angles is presented

  12. In vivo time-resolved microtomography reveals the mechanics of the blowfly flight motor.

    Directory of Open Access Journals (Sweden)

    Simon M Walker

    2014-03-01

    Full Text Available Dipteran flies are amongst the smallest and most agile of flying animals. Their wings are driven indirectly by large power muscles, which cause cyclical deformations of the thorax that are amplified through the intricate wing hinge. Asymmetric flight manoeuvres are controlled by 13 pairs of steering muscles acting directly on the wing articulations. Collectively the steering muscles account for <3% of total flight muscle mass, raising the question of how they can modulate the vastly greater output of the power muscles during manoeuvres. Here we present the results of a synchrotron-based study performing micrometre-resolution, time-resolved microtomography on the 145 Hz wingbeat of blowflies. These data represent the first four-dimensional visualizations of an organism's internal movements on sub-millisecond and micrometre scales. This technique allows us to visualize and measure the three-dimensional movements of five of the largest steering muscles, and to place these in the context of the deforming thoracic mechanism that the muscles actuate. Our visualizations show that the steering muscles operate through a diverse range of nonlinear mechanisms, revealing several unexpected features that could not have been identified using any other technique. The tendons of some steering muscles buckle on every wingbeat to accommodate high amplitude movements of the wing hinge. Other steering muscles absorb kinetic energy from an oscillating control linkage, which rotates at low wingbeat amplitude but translates at high wingbeat amplitude. Kinetic energy is distributed differently in these two modes of oscillation, which may play a role in asymmetric power management during flight control. Structural flexibility is known to be important to the aerodynamic efficiency of insect wings, and to the function of their indirect power muscles. We show that it is integral also to the operation of the steering muscles, and so to the functional flexibility of the

  13. In vivo time-resolved microtomography reveals the mechanics of the blowfly flight motor.

    Science.gov (United States)

    Walker, Simon M; Schwyn, Daniel A; Mokso, Rajmund; Wicklein, Martina; Müller, Tonya; Doube, Michael; Stampanoni, Marco; Krapp, Holger G; Taylor, Graham K

    2014-03-01

    Dipteran flies are amongst the smallest and most agile of flying animals. Their wings are driven indirectly by large power muscles, which cause cyclical deformations of the thorax that are amplified through the intricate wing hinge. Asymmetric flight manoeuvres are controlled by 13 pairs of steering muscles acting directly on the wing articulations. Collectively the steering muscles account for flight muscle mass, raising the question of how they can modulate the vastly greater output of the power muscles during manoeuvres. Here we present the results of a synchrotron-based study performing micrometre-resolution, time-resolved microtomography on the 145 Hz wingbeat of blowflies. These data represent the first four-dimensional visualizations of an organism's internal movements on sub-millisecond and micrometre scales. This technique allows us to visualize and measure the three-dimensional movements of five of the largest steering muscles, and to place these in the context of the deforming thoracic mechanism that the muscles actuate. Our visualizations show that the steering muscles operate through a diverse range of nonlinear mechanisms, revealing several unexpected features that could not have been identified using any other technique. The tendons of some steering muscles buckle on every wingbeat to accommodate high amplitude movements of the wing hinge. Other steering muscles absorb kinetic energy from an oscillating control linkage, which rotates at low wingbeat amplitude but translates at high wingbeat amplitude. Kinetic energy is distributed differently in these two modes of oscillation, which may play a role in asymmetric power management during flight control. Structural flexibility is known to be important to the aerodynamic efficiency of insect wings, and to the function of their indirect power muscles. We show that it is integral also to the operation of the steering muscles, and so to the functional flexibility of the insect flight motor.

  14. Load-adaptive bone remodeling simulations reveal osteoporotic microstructural and mechanical changes in whole human vertebrae.

    Science.gov (United States)

    Badilatti, Sandro D; Christen, Patrik; Parkinson, Ian; Müller, Ralph

    2016-12-08

    Osteoporosis is a major medical burden and its impact is expected to increase in our aging society. It is associated with low bone density and microstructural deterioration. Treatments are available, but the critical factor is to define individuals at risk from osteoporotic fractures. Computational simulations investigating not only changes in net bone tissue volume, but also changes in its microstructure where osteoporotic deterioration occur might help to better predict the risk of fractures. In this study, bone remodeling simulations with a mechanical feedback loop were used to predict microstructural changes due to osteoporosis and their impact on bone fragility from 50 to 80 years of age. Starting from homeostatic bone remodeling of a group of seven, mixed sex whole vertebrae, five mechanostat models mimicking different biological alterations associated with osteoporosis were developed, leading to imbalanced bone formation and resorption with a total net loss of bone tissue. A model with reduced bone formation rate and cell sensitivity led to the best match of morphometric indices compared to literature data and was chosen to predict postmenopausal osteoporotic bone loss in the whole group. Thirty years of osteoporotic bone loss were predicted with changes in morphometric indices in agreement with experimental measurements, and only showing major deviations in trabecular number and trabecular separation. In particular, although being optimized to match to the morphometric indices alone, the predicted bone loss revealed realistic changes on the organ level and on biomechanical competence. While the osteoporotic bone was able to maintain the mechanical stability to a great extent, higher fragility towards error loads was found for the osteoporotic bones. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Dissection of Ire1 functions reveals stress response mechanisms uniquely evolved in Candida glabrata.

    Directory of Open Access Journals (Sweden)

    Taiga Miyazaki

    2013-01-01

    Full Text Available Proper protein folding in the endoplasmic reticulum (ER is vital in all eukaryotes. When misfolded proteins accumulate in the ER lumen, the transmembrane kinase/endoribonuclease Ire1 initiates splicing of HAC1 mRNA to generate the bZIP transcription factor Hac1, which subsequently activates its target genes to increase the protein-folding capacity of the ER. This cellular machinery, called the unfolded protein response (UPR, is believed to be an evolutionarily conserved mechanism in eukaryotes. In this study, we comprehensively characterized mutant phenotypes of IRE1 and other related genes in the human fungal pathogen Candida glabrata. Unexpectedly, Ire1 was required for the ER stress response independently of Hac1 in this fungus. C. glabrata Ire1 did not cleave mRNAs encoding Hac1 and other bZIP transcription factors identified in the C. glabrata genome. Microarray analysis revealed that the transcriptional response to ER stress is not mediated by Ire1, but instead is dependent largely on calcineurin signaling and partially on the Slt2 MAPK pathway. The loss of Ire1 alone did not confer increased antifungal susceptibility in C. glabrata contrary to UPR-defective mutants in other fungi. Taken together, our results suggest that the canonical Ire1-Hac1 UPR is not conserved in C. glabrata. It is known in metazoans that active Ire1 nonspecifically cleaves and degrades a subset of ER-localized mRNAs to reduce the ER load. Intriguingly, this cellular response could occur in an Ire1 nuclease-dependent fashion in C. glabrata. We also uncovered the attenuated virulence of the C. glabrata Δire1 mutant in a mouse model of disseminated candidiasis. This study has unveiled the unique evolution of ER stress response mechanisms in C. glabrata.

  16. A Detailed Chemical Kinetic Reaction Mechanism for Oxidation of Four Small Alkyl Esters in Laminar Premixed Flames

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, C K; Pitz, W J; Westmoreland, P R; Dryer, F L; Chaos, M; Osswald, P; Kohse-Hoinghaus, K; Cool, T A; Wang, J; Yang, B; Hansen, N; Kasper, T

    2008-02-08

    A detailed chemical kinetic reaction mechanism has been developed for a group of four small alkyl ester fuels, consisting of methyl formate, methyl acetate, ethyl formate and ethyl acetate. This mechanism is validated by comparisons between computed results and recently measured intermediate species mole fractions in fuel-rich, low pressure, premixed laminar flames. The model development employs a principle of similarity of functional groups in constraining the H atom abstraction and unimolecular decomposition reactions in each of these fuels. As a result, the reaction mechanism and formalism for mechanism development are suitable for extension to larger oxygenated hydrocarbon fuels, together with an improved kinetic understanding of the structure and chemical kinetics of alkyl ester fuels that can be extended to biodiesel fuels. Variations in concentrations of intermediate species levels in these flames are traced to differences in the molecular structure of the fuel molecules.

  17. Magnetic isotope effect and theory of atomic orbital hybridization to predict a mechanism of chemical exchange reactions.

    Science.gov (United States)

    Epov, Vladimir N

    2011-08-07

    A novel approach is suggested to investigate the mechanisms of chemical complexation reactions based on the results of Fujii with co-workers; they have experimentally observed that several metals and metalloids demonstrate mass-independent isotope fractionation during the reactions with the DC18C6 crown ether using solvent-solvent extraction. In this manuscript, the isotope fractionation caused by the magnetic isotope effect is used to understand the mechanisms of chemical exchange reactions. Due to the rule that reactions are allowed for certain electron spin states, and forbidden for others, magnetic isotopes show chemical anomalies during these reactions. Mass-independent fractionation is suggested to take place due to the hyperfine interaction of the nuclear spin with the electron spin of the intermediate product. Moreover, the sign of the mass-independent fractionation is found to be dependent on the element and its species, which is also explained by the magnetic isotope effect. For example, highly negative mass-independent isotope fractionation of magnetic isotopes was observed for reactions of DC18C6 with SnCl(2) species and with several Ru(III) chloro-species, and highly positive for reactions of this ether with TeCl(6)(2-), and with several Cd(II) and Pd(II) species. The atomic radius of an element is also a critical parameter for the reaction with crown ether, particularly the element ions with [Kr]4d(n)5s(m) electron shell fits the best with the DC18C6 crown ring. It is demonstrated that the magnetic isotope effect in combination with the theory of orbital hybridization can help to understand the mechanism of complexation reactions. The suggested approach is also applied to explain previously published mass-independent fractionation of Hg isotopes in other types of chemical exchange reactions. This journal is © the Owner Societies 2011

  18. Influence of additives on microstructures, mechanical properties and shock-induced reaction characteristics of Al/Ni composites

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Wei; Zhang, Xianfeng, E-mail: lynx@mail.njust.edu.cn; Wu, Yang; He, Yong; Wang, Chuanting; Guo, Lei

    2015-11-05

    Granular composites containing aluminum (Al) and nickel (Ni) are typical structural energetic materials, which possess ideal combination of both mechanical properties and energy release capability. The influence of two additives, namely Teflon (PTFE) and copper (Cu), on mechanical properties and shock-induced chemical reaction (SICR) characteristics of Al/Ni material system has been investigated. Three composites, namely Al/Ni, Al/Ni/PTFE and Al/Ni/Cu with same volumetric ratio of Al powder to Ni powder, were processed by means of static pressing. Scanning electron microscopy was used to study the microstructure of the mentioned three composites. Quasi static compression tests were also conducted to determine the mechanical properties and fracture behavior of the mentioned three composites. It was shown that the additives affected both compressive strength and fracture mode of the three composites. Impact initiation experiments on the mentioned three composites were performed to determine their shock-induced chemical reaction characteristics by considering pressure histories measured in the test chamber. The experimental results showed that the additives had significant effects on critical initiation velocity, reaction rate, reaction efficiency and post-reaction behavior. - Highlights: • .Al/Ni, Al/Ni/PTFE and Al/Ni/Cu were processed by means of static pressing. • .Microstructures, mechanical properties and shock-induced reactions were studied. • .Microstructures affect both compressive strength and fracture mode. • .Impact velocity is an important factor in shock-induced chemical characteristics. • .Each additive has significant effects on energy release behavior.

  19. Influence of additives on microstructures, mechanical properties and shock-induced reaction characteristics of Al/Ni composites

    International Nuclear Information System (INIS)

    Xiong, Wei; Zhang, Xianfeng; Wu, Yang; He, Yong; Wang, Chuanting; Guo, Lei

    2015-01-01

    Granular composites containing aluminum (Al) and nickel (Ni) are typical structural energetic materials, which possess ideal combination of both mechanical properties and energy release capability. The influence of two additives, namely Teflon (PTFE) and copper (Cu), on mechanical properties and shock-induced chemical reaction (SICR) characteristics of Al/Ni material system has been investigated. Three composites, namely Al/Ni, Al/Ni/PTFE and Al/Ni/Cu with same volumetric ratio of Al powder to Ni powder, were processed by means of static pressing. Scanning electron microscopy was used to study the microstructure of the mentioned three composites. Quasi static compression tests were also conducted to determine the mechanical properties and fracture behavior of the mentioned three composites. It was shown that the additives affected both compressive strength and fracture mode of the three composites. Impact initiation experiments on the mentioned three composites were performed to determine their shock-induced chemical reaction characteristics by considering pressure histories measured in the test chamber. The experimental results showed that the additives had significant effects on critical initiation velocity, reaction rate, reaction efficiency and post-reaction behavior. - Highlights: • .Al/Ni, Al/Ni/PTFE and Al/Ni/Cu were processed by means of static pressing. • .Microstructures, mechanical properties and shock-induced reactions were studied. • .Microstructures affect both compressive strength and fracture mode. • .Impact velocity is an important factor in shock-induced chemical characteristics. • .Each additive has significant effects on energy release behavior

  20. Reaction and nucleation mechanisms of copper electrodeposition on disposable pencil graphite electrode

    Energy Technology Data Exchange (ETDEWEB)

    Majidi, M.R. [Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, 29th Bahman Bolvard, Tabriz 51664 (Iran, Islamic Republic of)], E-mail: sr.majidi@gmail.com; Asadpour-Zeynali, K.; Hafezi, B. [Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, 29th Bahman Bolvard, Tabriz 51664 (Iran, Islamic Republic of)

    2009-01-01

    The reaction and nucleation mechanism of copper electrodeposition on disposable pencil graphite electrode (PGE) in acidic sulphate solution were investigated using cyclic voltammetry (CV) and chronoamperometry (CA) techniques, respectively. Electrochemical experiments were followed by morphological studies with scanning electron microscopy (SEM). The effect of some experimental parameters, namely copper concentration, pH, scan rate, background electrolyte, deposition potential, and conditioning surface of the electrode were described. At the surface of PGE, Cu{sup 2+} ions were reduced at -250 mV vs. SCE. It was found that electrodeposition of copper is affected by rough surface of PGE. The nucleation mechanisms were examined by fitting the experimental CA data into Scharifker-Hills nucleation models. The nuclei population densities were also determined by means of two common fitting models developed for three-dimensional nucleation and growth (Scharifker-Mostany and Mirkin-Nilov-Herrman-Tarallo). It was found that deposition potential and background electrolyte affect the distribution of the deposited copper. The morphology of the deposited copper is affected by background electrolyte.

  1. Inducer expulsion in Streptococcus pyogenes: properties and mechanism of the efflux reaction

    International Nuclear Information System (INIS)

    Sutrina, S.L.; Reizer, J.; Saier, M.H Jr.

    1988-01-01

    Expulsion of preaccumulated methyl-β-D-thiogalactoside-phosphate (TMG-P) from Streptococcus pyogenes is a two-step process comprising intracellular dephosphorylation of TMG-P followed by rapid efflux of the intracellularly formed free galactoside. The present study identifies the mechanism and the order and characterizes the temperature dependency of the efflux step. Unidirectional efflux of the intracellularly formed [ 14 C]TMG was only slightly affected when measured in the presence of unlabeled TMG (25 to 400 mM) in the extracellular medium. In contrast, pronounced inhibition of net efflux was observed in the presence of relatively low concentrations (1 to 16 mM) of extracellular [ 14 C]TMG. Since net efflux was nearly arrested when the external concentration of [ 14 C]TMG approached the intracellular concentration of this sugar, we propose that a facilitated diffusion mechanism is responsible for efflux and equilibration of TMG between the intracellular and extracellular milieus. The exit reaction was markedly dependent upon temperature, exhibited a high energy of activation (23 kcal [ca. 96 kJ] per mol), and followed first-order kinetics, indicating that the permease mediating this efflux was not saturated under the conditions of expulsion employed

  2. Patterned biofilm formation reveals a mechanism for structural heterogeneity in bacterial biofilms.

    Science.gov (United States)

    Gu, Huan; Hou, Shuyu; Yongyat, Chanokpon; De Tore, Suzanne; Ren, Dacheng

    2013-09-03

    Bacterial biofilms are ubiquitous and are the major cause of chronic infections in humans and persistent biofouling in industry. Despite the significance of bacterial biofilms, the mechanism of biofilm formation and associated drug tolerance is still not fully understood. A major challenge in biofilm research is the intrinsic heterogeneity in the biofilm structure, which leads to temporal and spatial variation in cell density and gene expression. To understand and control such structural heterogeneity, surfaces with patterned functional alkanthiols were used in this study to obtain Escherichia coli cell clusters with systematically varied cluster size and distance between clusters. The results from quantitative imaging analysis revealed an interesting phenomenon in which multicellular connections can be formed between cell clusters depending on the size of interacting clusters and the distance between them. In addition, significant differences in patterned biofilm formation were observed between wild-type E. coli RP437 and some of its isogenic mutants, indicating that certain cellular and genetic factors are involved in interactions among cell clusters. In particular, autoinducer-2-mediated quorum sensing was found to be important. Collectively, these results provide missing information that links cell-to-cell signaling and interaction among cell clusters to the structural organization of bacterial biofilms.

  3. Crystal structure of the Haemophilus influenzae Hap adhesin reveals an intercellular oligomerization mechanism for bacterial aggregation

    Science.gov (United States)

    Meng, Guoyu; Spahich, Nicole; Kenjale, Roma; Waksman, Gabriel; St Geme, Joseph W

    2011-01-01

    Bacterial biofilms are complex microbial communities that are common in nature and are being recognized increasingly as an important determinant of bacterial virulence. However, the structural determinants of bacterial aggregation and eventual biofilm formation have been poorly defined. In Gram-negative bacteria, a major subgroup of extracellular proteins called self-associating autotransporters (SAATs) can mediate cell–cell adhesion and facilitate biofilm formation. In this study, we used the Haemophilus influenzae Hap autotransporter as a prototype SAAT to understand how bacteria associate with each other. The crystal structure of the H. influenzae HapS passenger domain (harbouring the SAAT domain) was determined to 2.2 Å by X-ray crystallography, revealing an unprecedented intercellular oligomerization mechanism for cell–cell interaction. The C-terminal SAAT domain folds into a triangular-prism-like structure that can mediate Hap–Hap dimerization and higher degrees of multimerization through its F1–F2 edge and F2 face. The intercellular multimerization can give rise to massive buried surfaces that are required for overcoming the repulsive force between cells, leading to bacterial cell–cell interaction and formation of complex microcolonies. PMID:21841773

  4. Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor

    KAUST Repository

    Bagchi, Samik

    2016-06-20

    Granules enriched with anammox bacteria are essential in enhancing the treatment of ammonia-rich wastewater, but little is known about how anammox bacteria grow and multiply inside granules. Here, we combined metatranscriptomics, quantitative PCR and 16S rRNA gene sequencing to study the changes in community composition, metabolic gene content and gene expression in a granular anammox reactor with the objective of understanding the molecular mechanism of anammox growth and multiplication that led to formation of large granules. Size distribution analysis revealed the spatial distribution of granules in which large granules having higher abundance of anammox bacteria (genus Brocadia) dominated the bottom biomass. Metatranscriptomics analysis detected all the essential transcripts for anammox metabolism. During the later stage of reactor operation, higher expression of ammonia and nitrite transport proteins and key metabolic enzymes mainly in the bottom large granules facilitated anammox bacteria activity. The high activity resulted in higher growth and multiplication of anammox bacteria and expanded the size of the granules. This conceptual model for large granule formation proposed here may assist in the future design of anammox processes for mainstream wastewater treatment.

  5. mRNA-Seq Reveals Novel Molecular Mechanisms and a Robust Fingerprint in Graves' Disease

    Science.gov (United States)

    Sachidanandam, Ravi; Morshed, Syed; Latif, Rauf; Shi, Ruijin; Davies, Terry F.

    2014-01-01

    Context: The immune response in autoimmune thyroid disease has been shown to occur primarily within the thyroid gland in which the most abundant antigens can be found. A variety of capture molecules are known to be expressed by thyroid epithelial cells and serve to attract and help retain an intrathyroidal immune infiltrate. Objective: To explore the entire repertoire of expressed genes in human thyroid tissue, we have deep sequenced the transcriptome (referred to as mRNA-Seq). Design and Patients: We applied mRNA-Seq to thyroid tissue from nine patients with Graves' disease subjected to total thyroidectomy and compared the data with 12 samples of normal thyroid tissue obtained from patients having a thyroid nodule removed. The expression for each gene was calculated from the sequencing data by taking the median of the coverage across the length of the gene. The expression levels were quantile normalized and a gene signature was derived from these. Results: On comparison of expression levels in tissues derived from Graves' patients and controls, there was clear evidence for overexpression of the antigen presentation pathway consisting of HLA and associated genes. We also found a robust disease signature and discovered active innate and adaptive immune signaling networks. Conclusions: These data reveal an active immune defense system in Graves' disease, which involves novel molecular mechanisms in its pathogenesis and development. PMID:24971664

  6. Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles

    Directory of Open Access Journals (Sweden)

    Cassandra Collins

    2017-09-01

    Full Text Available Armillaria mellea is a major plant pathogen. Yet, the strategies the organism uses to infect susceptible species, degrade lignocellulose and other plant material and protect itself against plant defences and its own glycodegradative arsenal are largely unknown. Here, we use a combination of gel and MS-based proteomics to profile A. mellea under conditions of oxidative stress and changes in growth matrix. 2-DE and LC-MS/MS were used to investigate the response of A. mellea to H2O2 and menadione/FeCl3 exposure, respectively. Several proteins were detected with altered abundance in response to H2O2, but not menadione/FeCl3 (i.e., valosin-containing protein, indicating distinct responses to these different forms of oxidative stress. One protein, cobalamin-independent methionine synthase, demonstrated a common response in both conditions, which may be a marker for a more general stress response mechanism. Further changes to the A. mellea proteome were investigated using MS-based proteomics, which identified changes to putative secondary metabolism (SM enzymes upon growth in agar compared to liquid cultures. Metabolomic analyses revealed distinct profiles, highlighting the effect of growth matrix on SM production. This establishes robust methods by which to utilize comparative proteomics to characterize this important phytopathogen.

  7. The gating mechanism of the human aquaporin 5 revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Lorant Janosi

    Full Text Available Aquaporins are protein channels located across the cell membrane with the role of conducting water or other small sugar alcohol molecules (aquaglyceroporins. The high-resolution X-ray structure of the human aquaporin 5 (HsAQP5 shows that HsAQP5, as all the other known aquaporins, exhibits tetrameric structure. By means of molecular dynamics simulations we analyzed the role of spontaneous fluctuations on the structural behavior of the human AQP5. We found that different conformations within the tetramer lead to a distribution of monomeric channel structures, which can be characterized as open or closed. The switch between the two states of a channel is a tap-like mechanism at the cytoplasmic end which regulates the water passage through the pore. The channel is closed by a translation of the His67 residue inside the pore. Moreover, water permeation rate calculations revealed that the selectivity filter, located at the other end of the channel, regulates the flow rate of water molecules when the channel is open, by locally modifying the orientation of His173. Furthermore, the calculated permeation rates of a fully open channel are in good agreement with the reported experimental value.

  8. Mechanism of crack healing at room temperature revealed by atomistic simulations

    International Nuclear Information System (INIS)

    Li, J.; Fang, Q.H.; Liu, B.; Liu, Y.; Liu, Y.W.; Wen, P.H.

    2015-01-01

    Three dimensional molecular dynamics (MD) simulations are systematically carried out to reveal the mechanism of the crack healing at room temperature, in terms of the dislocation shielding and the atomic diffusion to control the crack closure, in a copper (Cu) plate suffering from a shear loading. The results show that the process of the crack healing is actualized through the dislocation emission at a crack tip accompanied with intrinsic stacking faults ribbon forming in the crack tip wake, the dislocation slipping in the matrix and the dislocation annihilation in the free surface. Dislocation included stress compressing the crack tip is examined from the MD simulations and the analytical models, and then the crack closes rapidly due to the assistance of the atomic diffusion induced by the thermal activation when the crack opening displacement is less than a threshold value. This phenomenon is very different from the previous results for the crack propagation under the external load applied because of the crack healing (advancing) largely dependent on the crystallographic orientations of crack and the directions of external loading. Furthermore, based on the energy characteristic and considering the crack size effect, a theoretical model is established to predict the relationships between the crack size and the shear stress which qualitatively agree well with that obtained in the MD simulations

  9. Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model.

    Science.gov (United States)

    Zeng, Xiaojun; Zhang, Liyun; Xiao, Xiuchan; Jiang, Yuanyuan; Guo, Yanzhi; Yu, Xinyan; Pu, Xuemei; Li, Menglong

    2016-04-05

    Thrombin-binding aptamer (TBA) with the sequence 5'GGTTGGTGTGGTTGG3' could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the structural stability of G-quadruplex has not been satisfactorily elucidated on experiments so far. Herein, we studied the unfolding pathway of TBA by a combination of molecular dynamics simulation (MD) and Markov State Model (MSM). Our results revealed that the unfolding of TBA is not a simple two-state process but proceeds along multiple pathways with multistate intermediates. One high flux confirms some observations from NMR experiment. Another high flux exhibits a different and simpler unfolding pathway with less intermediates. Two important intermediate states were identified. One is similar to the G-triplex reported in the folding of G-quadruplex, but lack of H-bonding between guanines in the upper plane. More importantly, another intermediate state acting as a connector to link the folding region and the unfolding one, was the first time identified, which exhibits higher population and stability than the G-triplex-like intermediate. These results will provide valuable information for extending our understanding the folding landscape of G-quadruplex formation.

  10. Large-scale analysis by SAGE reveals new mechanisms of v-erbA oncogene action

    Directory of Open Access Journals (Sweden)

    Faure Claudine

    2007-10-01

    Full Text Available Abstract Background: The v-erbA oncogene, carried by the Avian Erythroblastosis Virus, derives from the c-erbAα proto-oncogene that encodes the nuclear receptor for triiodothyronine (T3R. v-ErbA transforms erythroid progenitors in vitro by blocking their differentiation, supposedly by interference with T3R and RAR (Retinoic Acid Receptor. However, v-ErbA target genes involved in its transforming activity still remain to be identified. Results: By using Serial Analysis of Gene Expression (SAGE, we identified 110 genes deregulated by v-ErbA and potentially implicated in the transformation process. Bioinformatic analysis of promoter sequence and transcriptional assays point out a potential role of c-Myb in the v-ErbA effect. Furthermore, grouping of newly identified target genes by function revealed both expected (chromatin/transcription and unexpected (protein metabolism functions potentially deregulated by v-ErbA. We then focused our study on 15 of the new v-ErbA target genes and demonstrated by real time PCR that in majority their expression was activated neither by T3, nor RA, nor during differentiation. This was unexpected based upon the previously known role of v-ErbA. Conclusion: This paper suggests the involvement of a wealth of new unanticipated mechanisms of v-ErbA action.

  11. Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions

    International Nuclear Information System (INIS)

    Eibl, Clarissa; Hessenberger, Manuel; Wenger, Julia; Brandstetter, Hans

    2014-01-01

    Pyrin domains (PYDs) recruit downstream effector molecules in NLR signalling. A specific charge-relay system suggests a the formation of a signalling complex involving a PYD dimer. The cytosolic tripartite NLR receptors serve as important signalling platforms in innate immunity. While the C-terminal domains act as sensor and activation modules, the N-terminal death-like domain, e.g. the CARD or pyrin domain, is thought to recruit downstream effector molecules by homotypic interactions. Such homotypic complexes have been determined for all members of the death-domain superfamily except for pyrin domains. Here, crystal structures of human NLRP14 pyrin-domain variants are reported. The wild-type protein as well as the clinical D86V mutant reveal an unexpected rearrangement of the C-terminal helix α6, resulting in an extended α5/6 stem-helix. This reordering mediates a novel symmetric pyrin-domain dimerization mode. The conformational switching is controlled by a charge-relay system with a drastic impact on protein stability. How the identified charge relay allows classification of NLRP receptors with respect to distinct recruitment mechanisms is discussed

  12. Floral reversion mechanism in longan (Dimocarpus longan Lour.) revealed by proteomic and anatomic analyses.

    Science.gov (United States)

    You, Xiangrong; Wang, Lingxia; Liang, Wenyu; Gai, Yonghong; Wang, Xiaoyan; Chen, Wei

    2012-02-02

    Two-dimensional gel electrophoresis (2-DE) was used to analyze the proteins related to floral reversion in Dimocarpus longan Lour. Proteins were extracted from buds undergoing the normal process of flowering and from those undergoing floral reversion in three developing stages in D. longan. Differentially expressed proteins were identified from the gels after 2-DE analysis, which were confirmed using matrix-assisted laser desorption/ionization-time of flying-mass spectroscopy and protein database search. A total of 39 proteins, including 18 up-regulated and 21 down-regulated proteins, were classified into different categories, such as energy and substance metabolism, protein translation, secondary metabolism, phytohormone, cytoskeleton structure, regulation, and stress tolerance. Among these, the largest functional class was associated with primary metabolism. Down-regulated proteins were involved in photosynthesis, transcription, and translation, whereas up-regulated proteins were involved in respiration. Decreased flavonoid synthesis and up-regulated GA20ox might be involved in the floral reversion process. Up-regulated 14-3-3 proteins played a role in the regulation of floral reversion in D. longan by responding to abiotic stress. Observations via transmission electron microscopy revealed the ultrastructure changes in shedding buds undergoing floral reversion. Overall, the results provided insights into the molecular basis for the floral reversion mechanism in D. longan. Copyright © 2011 Elsevier B.V. All rights reserved.

  13. Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum.

    Science.gov (United States)

    Kenyon, Amy; Gavriouchkina, Daria; Zorman, Jernej; Napolitani, Giorgio; Cerundolo, Vincenzo; Sauka-Spengler, Tatjana

    2017-07-26

    The mechanisms governing neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilise biotagging, a novel genome-wide profiling approach based on cell type-specific in vivo biotinylation in zebrafish to analyse the initial response of neutrophils to Mycobacterium marinum, a close genetic relative of M. tuberculosis used to model tuberculosis. Differential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, NLRC3 ortholog (wu: fb15h11) and il1β. Crispr/Cas9-mediated knockout of caspase b, which acts by proteolytic processing of il1β, results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterial infection, thus impairing granuloma development. We also show that a number of immediate early response genes (IEGs) are responsible for orchestrating the initial neutrophil response to mycobacterial infection. Further perturbation of the IEGs exposes egr3 as a key transcriptional regulator controlling il1β transcription.

  14. Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Samuel Hertig

    2016-06-01

    Full Text Available Molecular dynamics (MD simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.

  15. Simulation mechanisms of low energy nuclear reaction using super flow energy external fields

    International Nuclear Information System (INIS)

    Gareev, F.A.; Zhidkova, I.E.; ); Ratis, Yu.I.

    2005-01-01

    Full text: The review of possible stimulation mechanisms of the LENR (low energy nuclear reactions) is represented. We have concluded that transamination of nuclei at low energies and excess heat are possible in the framework of the modern physical theory - the universal resonance synchronization principle and based on its different enhancement mechanisms of reaction rates are responsible for these processes. The excitation nd ionization of atom may play role as trigger for LERN. Investigation of this phenomenon requires knowledge of different branches if science: nuclear and atomic physics, chemistry and electrochemistry, condensed matter and solid state physics. The results of this research field can provide a new source of energy, substances and technologies. The puzzle of poor re-productivity of experimental data in due ti the fact LENR occurs in open systems and it is extremely sensitive to parameters of external fields and systems. Classical re-productivity principle should be reconsidered for LENR experiments. Poor re-productivity and unexpected results do not means that the experiment is wrong. Our main conclusion: LENR may be understand in terms of the modern theory without any violation of the basic physics. 2) Weak and electromagnetic interactions may show the strong influence of the surrounding conditions on the nuclear processes. 3) Universal resonance synchronization principle is a key issue to make a bridge between various scales of interactions and it is responsible for self-organization of hierarchical systems independent of substances, fields and interactions. We bring some arguments in favor of the mechanism - order based on order - declared by Schroedinger in fundamental problem of contemporary science. 4) The universal resonance synchronization principle became a fruitful interdisciplinary science of general laws of self-organized processes in different branches of physics because it is consequence of the energy conservation law and resonance

  16. Effect of the Ti/B4C mole ratio on the reaction products and reaction mechanism in an Al–Ti–B4C powder mixture

    International Nuclear Information System (INIS)

    Zhang, Jingjing; Lee, Jung-Moo; Cho, Young-Hee; Kim, Su-Hyeon; Yu, Huashun

    2014-01-01

    The effect of the Ti/B 4 C mole ratio on the fabrication behavior of Al composites is investigated using Al–Ti–B 4 C powder mixtures as reactants. The quick spontaneous infiltration (QSI) process combined with the combustion reaction and DTA analysis were used. According to the thermodynamic predictions, which are verified in the experimental results, TiB 2 is formed in all the samples whereas TiC is only formed in reactants with a Ti/B 4 C mole ratio of more than two. The C atoms from the reacted B 4 C do not move into TiC but instead they move into Al 3 BC or Al 4 C 3 when the Ti/B 4 C mole ratio is less than two. In addition, the reaction mechanism with a Ti/B 4 C mole ratio of 0.75 is investigated extensively. - Highlights: • The critical role of the Ti/B 4 C mole ratio on the reaction products of Al–Ti–B 4 C was studied using experiments. • The experimental results are also supported by thermodynamic calculations presented in this paper. • The reaction mechanism with a Ti/B 4 C mole ratio of 0.75 is investigated extensively

  17. Reaction mechanism and thermal stability study on cathode materials for rechargeable lithium ion batteries

    Science.gov (United States)

    Fang, Jin

    Olivine-type lithium iron phosphate has been a very promising cathode material since it was proposed by Padhi in 1997, low-cost, environmental friendly and stable structure ensure the commercialization of LiFePO 4. In LiFePO4, during charge and discharge process, Li ions are transferred between two phases, Li-poor LialphaFePO 4 and Li-rich Li1-betaFePO4, which implies a significant energy barrier for the new phase nucleation and interface growth, contrary to the fast reaction kinetics experimentally observed. The understanding of the lithiation and delithiation mechanism of this material has spurred a lot of research interests. Many theory models have been proposed to explain the reaction mechanism of LiFePO4, among them, the single phase model claims that the reaction goes through a metastable single phase, and the over potential required to form this single phase is about 30mV, so we studied the driving force to transport lithium ions between Lialpha FePO4 and Li1-betaFePO4 phases and compared the particle sizes effect. Experiment results shows that, the nano-sized (30nm) LiFePO4 has wider solid solution range, lower solid solution formation temperature and faster kinetics than normal LiFePO4 (150nm). Also a 20mV over potential was observed in both samples, either after relaxing the FePO4/LiFePO4 system to equilibrium or transport lithium from one side to the other side, the experiment result is corresponding to theoretical calculation; indicates the reaction might go through single-phase reaction mechanism. The energy and power density of lithium ion battery largely depend on cathode materials. Mn substituted LiFePO4 has a higher voltage than LiFePO4, which results a higher theoretical energy density. Safety issue is one of the most important criterions for batteries, since cathode materials need to maintain stable structure during hundreds of charge and discharge cycles and ranges of application conditions. We have reported that iron-rich compound o-Fe1-yMnyPO4

  18. The Atmospherically Important Reaction of Hydroxyl Radicals with Methyl Nitrate: A Theoretical Study Involving the Calculation of Reaction Mechanisms, Enthalpies, Activation Energies, and Rate Coefficients.

    Science.gov (United States)

    Ng, Maggie; Mok, Daniel K W; Lee, Edmond P F; Dyke, John M

    2017-09-07

    A theoretical study, involving the calculation of reaction enthalpies, activation energies, mechanisms, and rate coefficients, was made of the reaction of hydroxyl radicals with methyl nitrate, an important process for methyl nitrate removal in the earth's atmosphere. Four reaction channels were considered: formation of H 2 O + CH 2 ONO 2 , CH 3 OOH + NO 2 , CH 3 OH + NO 3 , and CH 3 O + HNO 3 . For all channels, geometry optimization and frequency calculations were performed at the M06-2X/6-31+G** level, while relative energies were improved at the UCCSD(T*)-F12/CBS level. The major channel is found to be the H abstraction channel, to give the products H 2 O + CH 2 ONO 2 . The reaction enthalpy (ΔH 298 K RX ) of this channel is computed as -17.90 kcal mol -1 . Although the other reaction channels are also exothermic, their reaction barriers are high (>24 kcal mol -1 ), and therefore these reactions do not contribute to the overall rate coefficient in the temperature range considered (200-400 K). Pathways via three transition states were identified for the H abstraction channel. Rate coefficients were calculated for these pathways at various levels of variational transition state theory including tunneling. The results obtained are used to distinguish between two sets of experimental rate coefficients, measured in the temperature range of 200-400 K, one of which is approximately an order of magnitude greater than the other. This comparison, as well as the temperature dependence of the computed rate coefficients, shows that the lower experimental values are favored. The implications of the results to atmospheric chemistry are discussed.

  19. Mechanically activated SHS reaction in the Fe-Al system: in-situ time resolved diffraction using synchrotron radiation

    International Nuclear Information System (INIS)

    Gaffet, E.; Charlot, F.; Klein, D.; Bernard, F.; Niepce, J.C.

    1998-01-01

    The mechanical activation self propagating high temperature synthesis (M.A.S.H.S.) processing is a new way to produce nanocrystalline iron aluminide intermetallic compounds. This process is maily the combination of two steps; in the one hand, a mechanical activation where the Fe - Al powder mixture was milled during a short time at given energy and frequency of shocks and in the other hand, a self propagating high temperature synthesis (S.H.S.) reaction, for which the exothermicity of the Fe + Al reaction is used. This fast propagated MASHS reaction has been in-situ investigated using the time resolved X-ray diffraction (TRXRD) using a X-ray synchrotron beam and an infrared thermography camera, allowing the coupling of the materials structure and the temperature field. The effects of the initial mean compositions, of the milling conditions as well as of the compaction parameters on the MASHS reaction are reported. (orig.)

  20. Theoretical investigation of the mechanism of tritiated methane dehydrogenation reaction using nickel-based catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Liang; Li, Jiamao; Deng, Bing; Yang, Yong; Wang, Heyi [Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621900 (China); Li, Weiyi [School of Physics and Chemistry, Xihua University, Chengdu 610065 (China); Li, Shuo, E-mail: lishuo@cqut.edu.cn [School of Chemical Engineering, Chongqing University of Technology, Chongqing 400054 (China); Tan, Zhaoyi, E-mail: tanzhaoyi@caep.cn [Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621900 (China)

    2015-06-15

    Graphical abstract: - Highlights: • Four-step dehydrogenation of CT{sub 4} catalyzed by Ni to form Ni–C by releasing T{sub 2}. • The process of Ni + CT{sub 4} → NiCT{sub 2} + T{sub 2} is more achievable than that of NiCT{sub 2} → NiC + T{sub 2}. • TNiCT → T{sub 2}NiC step is the RDS with the rate constant of k = 2.8 × 10{sup 13} exp(−313,136/RT). • The hydrogen isotope effect value of k{sub H}/k{sub T} is 2.94, and k{sub D}/k{sub T} is 1.39. • CH{sub 4} and CD{sub 4} dehydrogenations are likely to occur, accompanied by the CT{sub 4} cracking. - Abstract: The mechanism of tritiated methane dehydrogenation reaction catalyzed by nickel-based catalyst was investigated in detail by density functional theory (DFT) at the B3LYP/[6-311++G(d, p), SDD] level. The computational results indicated that the dehydrogenation of tritiated methane is endothermic. The decomposition of tritiated methane catalyzed by Ni to form Ni-based carbon (Ni–C) after a four-step dehydrogenation companied with releasing tritium. After the first and second dehydrogenation steps, Ni + CT{sub 4} formed NiCT{sub 2}. After the third and fourth dehydrogenation steps, NiCT{sub 2} formed NiC. The first and second steps of dehydrogenation occurred on both the singlet and triplet states, and the lowest energy route is Ni + CT{sub 4} → {sup 1}COM → {sup 1}TS1 → {sup 3}IM1 → {sup 3}TS2 → {sup 3}IM2. The third and fourth steps of dehydrogenation occurred on both the singlet and quintet states, and the minimum energy reaction pathway appeared to be IM3 → {sup 1}TS4 → {sup 5}IM4 → {sup 5}TS5 → {sup 5}IM5 → {sup 5}pro + T{sub 2}. The fourth step of dehydrogenation TNiCT → T{sub 2}NiC was the rate-determining step of the entire reaction with the rate constant of k{sub 2} = 2.8 × 10{sup 13} exp(−313,136/RT) (in cm{sup 3} mol{sup −1} s{sup −1}), and its activation energy barrier was calculated to be 51.8 kcal/mol. The Ni-catalyzed CH{sub 4} and CD{sub 4} cracking

  1. Structure of Hordeum vulgare NADPH-dependent thioredoxin reductase 2. Unwinding the reaction mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Kirkensgaard, Kristine G. [Carlsberg Laboratory (Denmark); Enzyme and Protein Chemistry, Department of Systems BioIogy, Technical University of Denmark (Denmark); Hägglund, Per; Finnie, Christine; Svensson, Birte [Enzyme and Protein Chemistry, Department of Systems BioIogy, Technical University of Denmark (Denmark); Henriksen, Anette, E-mail: anette@crc.dk [Carlsberg Laboratory (Denmark)

    2009-09-01

    The first crystal structure of a cereal NTR, a protein involved in seed development and germination, has been determined. The structure is in a conformation that excludes NADPH binding and indicates that a domain reorientation facilitated by Trx binding precedes NADPH binding in the reaction mechanism. Thioredoxins (Trxs) are protein disulfide reductases that regulate the intracellular redox environment and are important for seed germination in plants. Trxs are in turn regulated by NADPH-dependent thioredoxin reductases (NTRs), which provide reducing equivalents to Trx using NADPH to recycle Trxs to the active form. Here, the first crystal structure of a cereal NTR, HvNTR2 from Hordeum vulgare (barley), is presented, which is also the first structure of a monocot plant NTR. The structure was determined at 2.6 Å resolution and refined to an R{sub cryst} of 19.0% and an R{sub free} of 23.8%. The dimeric protein is structurally similar to the structures of AtNTR-B from Arabidopsis thaliana and other known low-molecular-weight NTRs. However, the relative position of the two NTR cofactor-binding domains, the FAD and the NADPH domains, is not the same. The NADPH domain is rotated by 25° and bent by a 38% closure relative to the FAD domain in comparison with AtNTR-B. The structure may represent an intermediate between the two conformations described previously: the flavin-oxidizing (FO) and the flavin-reducing (FR) conformations. Here, analysis of interdomain contacts as well as phylogenetic studies lead to the proposal of a new reaction scheme in which NTR–Trx interactions mediate the FO to FR transformation.

  2. Structure of Hordeum vulgare NADPH-dependent thioredoxin reductase 2. Unwinding the reaction mechanism

    International Nuclear Information System (INIS)

    Kirkensgaard, Kristine G.; Hägglund, Per; Finnie, Christine; Svensson, Birte; Henriksen, Anette

    2009-01-01

    The first crystal structure of a cereal NTR, a protein involved in seed development and germination, has been determined. The structure is in a conformation that excludes NADPH binding and indicates that a domain reorientation facilitated by Trx binding precedes NADPH binding in the reaction mechanism. Thioredoxins (Trxs) are protein disulfide reductases that regulate the intracellular redox environment and are important for seed germination in plants. Trxs are in turn regulated by NADPH-dependent thioredoxin reductases (NTRs), which provide reducing equivalents to Trx using NADPH to recycle Trxs to the active form. Here, the first crystal structure of a cereal NTR, HvNTR2 from Hordeum vulgare (barley), is presented, which is also the first structure of a monocot plant NTR. The structure was determined at 2.6 Å resolution and refined to an R cryst of 19.0% and an R free of 23.8%. The dimeric protein is structurally similar to the structures of AtNTR-B from Arabidopsis thaliana and other known low-molecular-weight NTRs. However, the relative position of the two NTR cofactor-binding domains, the FAD and the NADPH domains, is not the same. The NADPH domain is rotated by 25° and bent by a 38% closure relative to the FAD domain in comparison with AtNTR-B. The structure may represent an intermediate between the two conformations described previously: the flavin-oxidizing (FO) and the flavin-reducing (FR) conformations. Here, analysis of interdomain contacts as well as phylogenetic studies lead to the proposal of a new reaction scheme in which NTR–Trx interactions mediate the FO to FR transformation

  3. Study of a new mechanism of reaction between heavy ions: the quasi-fission

    International Nuclear Information System (INIS)

    Ngo, Christian.

    1975-01-01

    A new type of deep inelastic reaction between two heavy ions (quasi-fission) has been discovered and studied when the product Z 1 Z 2 between the two ion atomic numbers is greater than or approximately equal to 1500. This mechanism is mainly binary, the total kinetic energy of the products is the one expected for a binary fission giving the same products, most of the products have masses very close to the initial masses, the angular distribution of the light products is peaked slightly forwards the projectile grazing angle (when the bombarding energy is not too much above the interaction barrier), at last, the total cross section for this process is a large part of the total reaction cross section. These results have been interpreted on the one hand using a static model and on the other hand using a dynamic model. An interaction potential between the two heavy ions has been derived using the energy density formalism within the framework of the sudden approximation. It has been shown that the nuclear part satisfies a scaling law which allows to factorize it in one term which depends on the two ion masses and another term which is independent of the system (universal function). Using the critical distance notion, the static calculations reproduce the quasi-fission cross sections. With regards to the dynamical calculations, the previously described potential has been introduced within the framework of Deubler and Dietrich's model. It is a classical dynamical calculation including dissipative terms. The vibration degrees of freedom of each ion have been explicitely taken into account. This calculation nicely reproduces both the energy loss in the relative motion, the focusing effect of the angular distribution, and the quasi-fission cross sections [fr

  4. The Reaction Mechanism of Claisen Rearrangement Obtained by Transition State Spectroscopy and Single Direct-Dynamics Trajectory

    Directory of Open Access Journals (Sweden)

    Takayoshi Kobayashi

    2013-02-01

    Full Text Available Chemical bond breaking and formation during chemical reactions can be observed using “transition state spectroscopy”. Comparing the measurement result of the transition state spectroscopy with the simulation result of single direct-dynamics trajectory, we have elucidated the reaction dynamics of Claisen rearrangement of allyl vinyl ether. Observed the reaction of the neat sample liquid, we have estimated the time constants of transformation from straight-chain structure to aromatic-like six-membered ring structure forming the C1-C6 bond. The result clarifies that the reaction proceeds via three steps taking longer time than expected from the gas phase calculation. This finding provides new hypothesis and discussions, helping the development of the field of reaction mechanism analysis.

  5. Influence of the initial grain size of silicon on microstructure and mechanical properties of reaction-sintered silicon nitride

    International Nuclear Information System (INIS)

    Heinrich, J.

    1977-01-01

    The influence of the initial grain size of the silicon powder on the microstructure and the resulting mechanical properties are studied. The smaller the grain size of the silicon powders used, the higher will be the degree of reaction at the beginning of the nitridation reaction and the higher the amount of α-modification in the fully nitridated samples. Moreover, the nitrification time can be considerably shortened when fine-grained silicon powders ( [de

  6. Directed evolution and in silico analysis of reaction centre proteins reveal molecular signatures of photosynthesis adaptation to radiation pressure.

    Directory of Open Access Journals (Sweden)

    Giuseppina Rea

    2011-01-01

    Full Text Available Evolutionary mechanisms adopted by the photosynthetic apparatus to modifications in the Earth's atmosphere on a geological time-scale remain a focus of intense research. The photosynthetic machinery has had to cope with continuously changing environmental conditions and particularly with the complex ionizing radiation emitted by solar flares. The photosynthetic D1 protein, being the site of electron tunneling-mediated charge separation and solar energy transduction, is a hot spot for the generation of radiation-induced radical injuries. We explored the possibility to produce D1 variants tolerant to ionizing radiation in Chlamydomonas reinhardtii and clarified the effect of radiation-induced oxidative damage on the photosynthetic proteins evolution. In vitro directed evolution strategies targeted at the D1 protein were adopted to create libraries of chlamydomonas random mutants, subsequently selected by exposures to radical-generating proton or neutron sources. The common trend observed in the D1 aminoacidic substitutions was the replacement of less polar by more polar amino acids. The applied selection pressure forced replacement of residues more sensitive to oxidative damage with less sensitive ones, suggesting that ionizing radiation may have been one of the driving forces in the evolution of the eukaryotic photosynthetic apparatus. A set of the identified aminoacidic substitutions, close to the secondary plastoquinone binding niche and oxygen evolving complex, were introduced by site-directed mutagenesis in un-transformed strains, and their sensitivity to free radicals attack analyzed. Mutants displayed reduced electron transport efficiency in physiological conditions, and increased photosynthetic performance stability and oxygen evolution capacity in stressful high-light conditions. Finally, comparative in silico analyses of D1 aminoacidic sequences of organisms differently located in the evolution chain, revealed a higher ratio of residues

  7. Asymmetric Horner-Wadsworth-Emmons Reactions with meso-Dialdehydes: Scope, Mechanism, and Synthetic Applications

    DEFF Research Database (Denmark)

    Rein, Tobias; Vares, Lauri; Kawasaki, Ikuo

    1999-01-01

    Asymmetric Homer-Wadsworth-Emmons reactions between chiral phosphonate reagents and various meso-dialdehydes have been investigated. A mechanistic model useful for rationalizing the experimentally observed stereoselectivities is presented. Furthermore; strategies for applying these reactions...

  8. Atomic force microscopy reveals multiple patterns of antenna organization in purple bacteria: implications for energy transduction mechanisms and membrane modeling.

    Science.gov (United States)

    Sturgis, James N; Niederman, Robert A

    2008-01-01

    Recent topographs of the intracytoplasmic membrane (ICM) of purple bacteria obtained by atomic force microscopy (AFM) have provided the first surface views of the native architecture of a multicomponent biological membrane at submolecular resolution, representing an important landmark in structural biology. A variety of species-dependent, closely packed arrangements of light-harvesting (LH) complexes was revealed: the most highly organized was found in Rhodobacter sphaeroides in which the peripheral LH2 antenna was seen either in large clusters or in fixed rows interspersed among ordered arrays of dimeric LH1-reaction center (RC) core complexes. A more random organization was observed in other species containing both the LH1 and LH2 complexes, as typified by Rhododspirillum photometricum with randomly packed monomeric LH1-RC core complexes intermingled with large, paracrystalline domains of LH2 antenna. Surprisingly, no structures that could be identified as the ATP synthase or cytochrome bc (1) complexes were observed, which may reflect their localization at ICM vesicle poles or in curved membrane areas, out of view from the flat regions imaged by AFM. This possible arrangement of energy transducing complexes has required a reassessment of energy tranduction mechanisms which place the cytochrome bc (1) complex in close association with the RC. Instead, more plausible proposals must account for the movement of quinone redox species over considerable membrane distances on appropriate time scales. AFM, together with atomic resolution structures are also providing the basis for molecular modeling of the ICM that is leading to an improved picture of the supramolecular organization of photosynthetic complexes, as well as the forces that drive their segregation into distinct domains.

  9. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

    Science.gov (United States)

    Almonacid, Daniel E; Yera, Emmanuel R; Mitchell, John B O; Babbitt, Patricia C

    2010-03-12

    Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine

  10. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

    Directory of Open Access Journals (Sweden)

    Daniel E Almonacid

    2010-03-01

    Full Text Available Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3 show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1 catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56% suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to

  11. Quantitative ligand and receptor binding studies reveal the mechanism of interleukin-36 (IL-36) pathway activation.

    Science.gov (United States)

    Zhou, Li; Todorovic, Viktor; Kakavas, Steve; Sielaff, Bernhard; Medina, Limary; Wang, Leyu; Sadhukhan, Ramkrishna; Stockmann, Henning; Richardson, Paul L; DiGiammarino, Enrico; Sun, Chaohong; Scott, Victoria

    2018-01-12

    IL-36 cytokines signal through the IL-36 receptor (IL-36R) and a shared subunit, IL-1RAcP (IL-1 receptor accessory protein). The activation mechanism for the IL-36 pathway is proposed to be similar to that of IL-1 in that an IL-36R agonist (IL-36α, IL-36β, or IL-36γ) forms a binary complex with IL-36R, which then recruits IL-1RAcP. Recent studies have shown that IL-36R interacts with IL-1RAcP even in the absence of an agonist. To elucidate the IL-36 activation mechanism, we considered all possible binding events for IL-36 ligands/receptors and examined these events in direct binding assays. Our results indicated that the agonists bind the IL-36R extracellular domain with micromolar affinity but do not detectably bind IL-1RAcP. Using surface plasmon resonance (SPR), we found that IL-1RAcP also does not bind IL-36R when no agonist is present. In the presence of IL-36α, however, IL-1RAcP bound IL-36R strongly. These results suggested that the main pathway to the IL-36R·IL-36α·IL-1RAcP ternary complex is through the IL-36R·IL-36α binary complex, which recruits IL-1RAcP. We could not measure the binding affinity of IL-36R to IL-1RAcP directly, so we engineered a fragment crystallizable-linked construct to induce IL-36R·IL-1RAcP heterodimerization and predicted the binding affinity during a complete thermodynamic cycle to be 74 μm The SPR analysis also indicated that the IL-36R antagonist IL-36Ra binds IL-36R with higher affinity and a much slower off rate than the IL-36R agonists, shedding light on IL-36 pathway inhibition. Our results reveal the landscape of IL-36 ligand and receptor interactions, improving our understanding of IL-36 pathway activation and inhibition. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. The Role of Various Stressors in the Trigger Mechanism of Raynaud's Disease (Hemorheological and Vascular Reactions

    Directory of Open Access Journals (Sweden)

    Mantskava M.M.

    2014-05-01

    Full Text Available The emergence and spread of stress reactions are provided by the blood circulation system. In its turn, the adequacy of blood circulation depends on the hemorheological and vascular mechanisms. The changeability of their properties appears to be the basis of the increasing of stress stages. From the viewpoint of biophysical reactions, any change and movement occur with the expenditure and accumulation of energy. Higher level of adaptation energy waste and secondary level take place, when a small stressor entails a small expenditure. There is a maximum possible rate of adaptive energy consumption and at this maximum the organism cannot cope with any additional stimulus. At the same time adaptive and stress diseases develop. Let’s consider the duration and manifestation of Raynaud's disease from the perspective of adaptation diseases and diseases of the third grade, which appears to be the cause of the double stress effect - cold and emotional- physical and psychic. Total of 97 patients with Raynaud's disease were examined. For a new vision of the problem it was necessary to find out how the streessors of various nature impact the hemoreheological status and vascular resistance. For this purpose all the patients were examined for a resistance index of resistive arteries of the hand and the indices of erythrocyte aggregation and deformability. The patients were divided into four subgroups. The first subgroup – the patients after chilblain, the second subgroup – the patients with psychic strerssor, the third subgroup – the patients with prolonged chronic stress, and the fourth subgroup – the patients without the differentiation of the stressors. According to the obtained results, it is obvious that at cold and emotional stress (I and II subgroups the hemorheological and vascular parameters are changed. However, this change (hemorheological and vascular is more pronounced at chronic emotional stress (III subgroup as compared both to the

  13. Informal payments and the quality of health care: Mechanisms revealed by Tanzanian health workers.

    Science.gov (United States)

    Mæstad, Ottar; Mwisongo, Aziza

    2011-02-01

    Informal payments for health services are common in many transitional and developing countries. The aim of this paper is to investigate the nature of informal payments in the health sector of Tanzania and to identify mechanisms through which informal payments may affect the quality of health care. Our focus is on the effect of informal payments on health worker behaviours, in particular the interpersonal dynamics among health workers at their workplaces. We organised eight focus groups with 58 health workers representing different cadres and levels of care in one rural and one urban district in Tanzania. We found that health workers at all levels receive informal payments in a number of different contexts. Health workers sometimes share the payments received, but only partially, and more rarely within the cadre than across cadres. Our findings indicate that health workers are involved in 'rent-seeking' activities, such as creating artificial shortages and deliberately lowering the quality of service, in order to extract extra payments from patients or to bargain for a higher share of the payments received by their colleagues. The discussions revealed that many health workers think that the distribution of informal payments is grossly unfair. The findings suggest that informal payments can impact negatively on the quality of health care through rent-seeking behaviours and through frustrations created by the unfair allocation of payments. Interestingly, the presence of corruption may also induce non-corrupt workers to reduce the quality of care. Positive impacts can occur because informal payments may induce health workers to increase their efforts, and maybe more so if there is competition among health workers about receiving the payments. Moreover, informal payments add to health workers' incomes and might thus contribute to retention of health workers within the health sector. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  14. Epitope mapping for monoclonal antibody reveals the activation mechanism for αVβ3 integrin.

    Directory of Open Access Journals (Sweden)

    Tetsuji Kamata

    Full Text Available Epitopes for a panel of anti-αVβ3 monoclonal antibodies (mAbs were investigated to explore the activation mechanism of αVβ3 integrin. Experiments utilizing αV/αIIb domain-swapping chimeras revealed that among the nine mAbs tested, five recognized the ligand-binding β-propeller domain and four recognized the thigh domain, which is the upper leg of the αV chain. Interestingly, the four mAbs included function-blocking as well as non-functional mAbs, although they bound at a distance from the ligand-binding site. The epitopes for these four mAbs were further determined using human-to-mouse αV chimeras. Among the four, P3G8 recognized an amino acid residue, Ser-528, located on the side of the thigh domain, while AMF-7, M9, and P2W7 all recognized a common epitope, Ser-462, that was located close to the α-genu, where integrin makes a sharp bend in the crystal structure. Fibrinogen binding studies for cells expressing wild-type αVβ3 confirmed that AMF-7, M9, and P2W7 were inhibitory, while P3G8 was non-functional. However, these mAbs were all unable to block binding when αVβ3 was constrained in its extended conformation. These results suggest that AMF-7, M9, and P2W7 block ligand binding allosterically by stabilizing the angle of the bend in the bent conformation. Thus, a switchblade-like movement of the integrin leg is indispensable for the affinity regulation of αVβ3 integrin.

  15. Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs.

    Directory of Open Access Journals (Sweden)

    Dimitar V Pachov

    2015-07-01

    Full Text Available Proteins perform their function or interact with partners by exchanging between conformational substates on a wide range of spatiotemporal scales. Structurally characterizing these exchanges is challenging, both experimentally and computationally. Large, diffusional motions are often on timescales that are difficult to access with molecular dynamics simulations, especially for large proteins and their complexes. The low frequency modes of normal mode analysis (NMA report on molecular fluctuations associated with biological activity. However, NMA is limited to a second order expansion about a minimum of the potential energy function, which limits opportunities to observe diffusional motions. By contrast, kino-geometric conformational sampling (KGS permits large perturbations while maintaining the exact geometry of explicit conformational constraints, such as hydrogen bonds. Here, we extend KGS and show that a conformational ensemble of the α subunit Gαs of heterotrimeric stimulatory protein Gs exhibits structural features implicated in its activation pathway. Activation of protein Gs by G protein-coupled receptors (GPCRs is associated with GDP release and large conformational changes of its α-helical domain. Our method reveals a coupled α-helical domain opening motion while, simultaneously, Gαs helix α5 samples an activated conformation. These motions are moderated in the activated state. The motion centers on a dynamic hub near the nucleotide-binding site of Gαs, and radiates to helix α4. We find that comparative NMA-based ensembles underestimate the amplitudes of the motion. Additionally, the ensembles fall short in predicting the accepted direction of the full activation pathway. Taken together, our findings suggest that nullspace sampling with explicit, holonomic constraints yields ensembles that illuminate molecular mechanisms involved in GDP release and protein Gs activation, and further establish conformational coupling between key

  16. Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl.

    Science.gov (United States)

    Kuechler, Erich R; York, Darrin M

    2014-02-07

    The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

  17. The Mechanical and Reaction Behavior of PTFE/Al/Fe2O3 under Impact and Quasi-Static Compression

    Directory of Open Access Journals (Sweden)

    Jun-yi Huang

    2017-01-01

    Full Text Available Quasi-static compression and drop-weight test were used to characterize the mechanical and reaction behavior of PTFE/Al/Fe2O3 composites. Two kinds of PTFE/Al/Fe2O3 composites were prepared with different mass of PTFE, and the reaction phenomenon and stress-strain curves were recorded; the residuals after reaction were analyzed by X-ray diffraction (XRD. The results showed that, under quasi-static compression condition, the strength of the materials is increased (from 37.1 Mpa to 77.2 Mpa with the increase of PTFE, and the reaction phenomenon occurred only in materials with high PTFE content. XRD analysis showed that the reaction between Al and Fe2O3 was not triggered with identical experimental conditions. In drop-weight tests, PTFE/Al/Fe2O3 specimens with low PTFE content were found to be more insensitive by high-speed photography, and a High Temperature Metal Slag Spray (HTMSS phenomenon was observed in both kinds of PTFE/Al/Fe2O3 composites, indicating the existence of thermite reaction, which was confirmed by XRD. In PTFE/Al/Fe2O3 system, the reaction between PTFE and Al precedes the reaction between Al and Fe2O3.

  18. Ageing mechanisms in chickpea seeds: Relationship of sugar hydrolysis and lipid peroxidation with Amadori and Millard reactions

    Directory of Open Access Journals (Sweden)

    mahdi shaaban

    2017-05-01

    Full Text Available This experiment was performed in order to study on ageing mechanisms of chickpea seeds (Cicer arietinum L. in natural storage and accelerated ageing conditions in seed laboratory of Gorgan Agricultural Science and Natural Resources, Gorgan, Iran at 2015. Experiment was in completely randomized design arrangement with four replications. Treatments were 2 and 4 years natural storage and 1-5 days of accelerated ageing with control treatment. The results showed that with increasing of natural storage and accelerated ageing duration, germination percentage was decreased. Increasing of ageing duration decreased soluble sugars, non-reducing sugars and soluble proteins but lipid peroxidation, reducing sugars, protein carbonylation and Amadori and Millard reaction were increased. In natural storage condition lipid peroxidation was more than sugar hydrolysis but in accelerated ageing condition sugar hydrolysis was more than lipid peroxidation. These results show that the main reason of Amadori and Millard reaction in chickpea seeds in natural storage condition is lipid peroxidation and in accelerated ageing condition is sugar hydrolysis. Also, the results showed that Amadori reaction in natural storage condition was more than Amadori reaction and in accelerated ageing condition Millard reaction was more than Amadori reaction. The results of the present study showed that sever Millard reaction after Amadori reaction induced higher damage on seed and results to more decrease of seed viability and reduce of seed germination percentage in accelerated ageing than natural storage.

  19. Fundamental mechanisms and reactions in non-catalytic subcritical hydrothermal processes: A review.

    Science.gov (United States)

    Yousefifar, Azadeh; Baroutian, Saeid; Farid, Mohammed M; Gapes, Daniel J; Young, Brent R

    2017-10-15

    The management and disposal of solid waste is of increasing concern across the globe. Hydrothermal processing of sludge has been suggested as a promising solution to deal with the considerable amounts of sludge produced worldwide. Such a process not only degrades organic compounds and reduces waste volume, but also provides an opportunity to recover valuable substances. Hydrothermal processing comprises two main sub-processes: wet oxidation (WO) and thermal hydrolysis (TH), in which the formation of various free radicals results in the production of different intermediates. Volatile fatty acids (VFAs), especially acetic acid, are usually the main intermediates which remain as a by-product of the process. This paper aims to review the fundamental mechanism for hydrothermal processing of sludge, and the formation of different free radicals and intermediates therein. In addition, the proposed kinetic models for the two processes (WO and TH) from the literature are reviewed and the advantages and disadvantages of each model are outlined. The effect of mass transfer as a critical component of the design and development of the processes, which has been neglected in most of these proposed models, is also reviewed, and the effect of influencing parameters on the processes' controlling step (reaction or mass transfer) is discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Fragment molecular orbital study on electron tunneling mechanisms in bacterial photosynthetic reaction center.

    Science.gov (United States)

    Kitoh-Nishioka, Hirotaka; Ando, Koji

    2012-11-01

    The tunneling mechanisms of electron transfers (ETs) in photosynthetic reaction center of Blastochloris viridis are studied by the ab initio fragment molecular orbital (FMO) method combined with the generalized Mulliken-Hush (GMH) and the bridge Green function (GF) calculations of the electronic coupling T(DA) and the tunneling current method for the ET pathway analysis at the fragment-based resolution. For the ET from batctriopheophytin (H(L)) to menaquinone (MQ), a major tunneling current through Trp M250 and a minor back flow via Ala M215, Ala M216, and His M217 are quantified. For the ET from MQ to ubiquinone, the major tunneling pathway via the nonheme Fe(2+) and His L190 is identified as well as minor pathway via His M217 and small back flows involving His L230, Glu M232, and His M264. At the given molecular structure from X-ray experiment, the spin state of the Fe(2+) ion, its replacement by Zn(2+), or its removal are found to affect the T(DA) value by factors within 2.2. The calculated T(DA) values, together with experimentally estimated values of the driving force and the reorganization energy, give the ET rates in reasonable agreement with experiments.

  1. Analyzing General Chemistry Texts' Treatment of Rates of Change Concepts in Reaction Kinetics Reveals Missing Conceptual Links

    Science.gov (United States)

    Seethaler, Sherry; Czworkowski, John; Wynn, Lynda

    2018-01-01

    Change over time is a crosscutting theme in the sciences that is pivotal to reaction kinetics, an anchoring concept in undergraduate chemistry, and students' struggles with rates of change are well-documented. Informed by the education scholarship in chemistry, physics, and mathematics, a research team with members from complementary disciplinary…

  2. Processing Mechanisms in Hearing-Impaired Listeners: Evidence from Reaction Times and Sentence Interpretation.

    Science.gov (United States)

    Carroll, Rebecca; Uslar, Verena; Brand, Thomas; Ruigendijk, Esther

    The authors aimed to determine whether hearing impairment affects sentence comprehension beyond phoneme or word recognition (i.e., on the sentence level), and to distinguish grammatically induced processing difficulties in structurally complex sentences from perceptual difficulties associated with listening to degraded speech. Effects of hearing impairment or speech in noise were expected to reflect hearer-specific speech recognition difficulties. Any additional processing time caused by the sustained perceptual challenges across the sentence may either be independent of or interact with top-down processing mechanisms associated with grammatical sentence structure. Forty-nine participants listened to canonical subject-initial or noncanonical object-initial sentences that were presented either in quiet or in noise. Twenty-four participants had mild-to-moderate hearing impairment and received hearing-loss-specific amplification. Twenty-five participants were age-matched peers with normal hearing status. Reaction times were measured on-line at syntactically critical processing points as well as two control points to capture differences in processing mechanisms. An off-line comprehension task served as an additional indicator of sentence (mis)interpretation, and enforced syntactic processing. The authors found general effects of hearing impairment and speech in noise that negatively affected perceptual processing, and an effect of word order, where complex grammar locally caused processing difficulties for the noncanonical sentence structure. Listeners with hearing impairment were hardly affected by noise at the beginning of the sentence, but were affected markedly toward the end of the sentence, indicating a sustained perceptual effect of speech recognition. Comprehension of sentences with noncanonical word order was negatively affected by degraded signals even after sentence presentation. Hearing impairment adds perceptual processing load during sentence processing

  3. Comparative analysis of alfalfa (Medicago sativa L.) leaf transcriptomes reveals genotype-specific salt tolerance mechanisms.

    Science.gov (United States)

    Lei, Yunting; Xu, Yuxing; Hettenhausen, Christian; Lu, Chengkai; Shen, Guojing; Zhang, Cuiping; Li, Jing; Song, Juan; Lin, Honghui; Wu, Jianqiang

    2018-02-15

    Soil salinity is an important factor affecting growth, development, and productivity of almost all land plants, including the forage crop alfalfa (Medicago sativa). However, little is known about how alfalfa responds and adapts to salt stress, particularly among different salt-tolerant cultivars. Among seven alfalfa cultivars, we found that Zhongmu-1 (ZM) is relatively salt-tolerant and Xingjiang Daye (XJ) is salt-sensitive. Compared to XJ, ZM showed slower growth under low-salt conditions, but exhibited stronger tolerance to salt stress. RNA-seq analysis revealed 2237 and 1125 differentially expressed genes (DEGs) between ZM and XJ in the presence and absence of salt stress, among which many genes are involved in stress-related pathways. After salt treatment, compared with the controls, the number of DEGs in XJ (19373) was about four times of that in ZM (4833). We also detected specific differential gene expression patterns: In response to salt stress, compared with XJ, ZM maintained relatively more stable expression levels of genes related to the ROS and Ca 2+ pathways, phytohormone biosynthesis, and Na + /K + transport. Notably, several salt resistance-associated genes always showed greater levels of expression in ZM than in XJ, including a transcription factor. Consistent with the suppression of plant growth resulting from salt stress, the expression of numerous photosynthesis- and growth hormone-related genes decreased more dramatically in XJ than in ZM. By contrast, the expression levels of photosynthetic genes were lower in ZM under low-salt conditions. Compared with XJ, ZM is a salt-tolerant alfalfa cultivar possessing specific regulatory mechanisms conferring exceptional salt tolerance, likely by maintaining high transcript levels of abiotic and biotic stress resistance-related genes. Our results suggest that maintaining this specific physiological status and/or plant adaptation to salt stress most likely arises by inhibition of plant growth in ZM through

  4. Mechanisms of chemical vapor generation by aqueous tetrahydridoborate. Recent developments toward the definition of a more general reaction model

    Science.gov (United States)

    D'Ulivo, Alessandro

    2016-05-01

    A reaction model describing the reactivity of metal and semimetal species with aqueous tetrahydridoborate (THB) has been drawn taking into account the mechanism of chemical vapor generation (CVG) of hydrides, recent evidences on the mechanism of interference and formation of byproducts in arsane generation, and other evidences in the field of the synthesis of nanoparticles and catalytic hydrolysis of THB by metal nanoparticles. The new "non-analytical" reaction model is of more general validity than the previously described "analytical" reaction model for CVG. The non-analytical model is valid for reaction of a single analyte with THB and for conditions approaching those typically encountered in the synthesis of nanoparticles and macroprecipitates. It reduces to the previously proposed analytical model under conditions typically employed in CVG for trace analysis (analyte below the μM level, borane/analyte ≫ 103 mol/mol, no interference). The non-analytical reaction model is not able to explain all the interference effects observed in CVG, which can be achieved only by assuming the interaction among the species of reaction pathways of different analytical substrates. The reunification of CVG, the synthesis of nanoparticles by aqueous THB and the catalytic hydrolysis of THB inside a common frame contribute to rationalization of the complex reactivity of aqueous THB with metal and semimetal species.

  5. Transcriptome analysis reveals differences in mechanisms regulating cessation of luteal function in pregnant and non-pregnant dogs.

    Science.gov (United States)

    Zatta, Sophie; Rehrauer, Hubert; Gram, Aykut; Boos, Alois; Kowalewski, Mariusz Pawel

    2017-09-27

    In the domestic dog, corpora lutea (CL) are the only source of progesterone (P4), both in pregnant and non-pregnant cycles because there is no placental steroidogenesis. The absence of an endogenous luteolysin in absence of pregnancy results in long-lasting physiological pseudopregnancy, strongly contrasting with the acute luteolysis observed prepartum. The underlying biological mechanisms and the involvement of P4 signalling remain, however, not fully understood. Therefore, here, next-generation sequencing (RNA-Seq) was performed on CL from the late luteal phase and compared with normally luteolyzing CL collected at the prepartum P4 decrease. The contrast "luteal regression over luteolysis" yielded 1595 differentially expressed genes (DEG). The CL in late luteal regression were predominantly associated with functional terms linked to extracellular matrix (p = 5.52e-05). Other terms related to transcriptional activity (p = 2.45e-04), and steroid hormone signalling (p = 2.29e-04), which were more highly represented in late regression than during luteolysis. The prepartum luteolysis was associated with immune inflammatory responses (p = 2.87e-14), including acute-phase reaction (p = 4.10e-06). Immune system-related events were also more highly represented in CL derived from normal luteolysis (p = 7.02e-04), compared with those from dogs in which luteolysis was induced with an antigestagen (1480 DEG in total). Additionally, the withdrawal of P4 at mid-gestation resulted in 92 DEG; over-represented terms enriched in antigestagen-treated dogs were related to the inflammatory response (p = 0.005) or response to IL1 (p = 7.29e-05). Terms related to proliferation, e.g., centrosome organization (p = 0.002) and steroid metabolic processes (p = 0.001), prevailed at mid-gestation. Thereby, our results revealed the nature of luteotropic effects of P4 within canine CL. It appears that, even though they result in diminished steroidogenic output, the effect of

  6. The (3He,α) reaction mechanism. A study of the angular momentum transfer

    International Nuclear Information System (INIS)

    Guttormsen, M.; Bergholt, L.; Ingebretsen, F.; Loevhoeiden, G.; Messelt, S.; Rekstad, J.; Tveter, T.S.; Helstrup, H.; Thorsteinsen, T.F.

    1994-01-01

    The γ-rays emitted after the 163 Dy( 3 He,αxn) reactions at E( 3 He) = 45 MeV have been measured. The transferred angular momentum in the reaction is deduced from the side-feeding γ-intensities of the ground bands in the residual 162-x Dy isotopes. With decreasing α-energy the average spin transfer increases from similar 5h to similar 11h. The ( 3 He,α) reaction at these energies is dominated by direct processes. Even at the highest spin transfer the contribution from the compound reaction channel is negligible. ((orig.))

  7. Reactions of phenols and alcohols over thoria: mechanism of ether formation

    International Nuclear Information System (INIS)

    Karuppannasamy, S.; Narayanan, K.; Pillai, C.N.

    1980-01-01

    The dehydration of phenols and alkylation of phenols by alcohols over thoria were studied at 400 to 500 0 C and atmospheric pressure. Phenol and cresols, when dehydrated gave diaryl ethers as main products. With para-substituted phenols such as p-methoxy, p-t-butyl, p-chloro, and p-nitrophenol no ether formation was noticed. All the reactions were accompanied by considerable amount of coke formation. Alkylation of phenols by alcohols gave a mixture of O- and C-alkylated products under the same reaction conditions. O-alkylation and C-alkylation are parallel reactions. The mechanistic aspects of the reactions are discussed. 3 figures, 3 tables

  8. Degradation of quinoline by wet oxidation - kinetic aspects and reaction mechanisms

    DEFF Research Database (Denmark)

    Thomsen, A.B.

    1998-01-01

    The high temperature, high pressure wet oxidation reaction of quinoline has been studied as a function of initial concentration, pH and temperature. At neutral to acidic pH, it is effective in the oxidation of quinoline at 240 degrees C and above, whereas under alkaline conditions the reaction...... is markedly slowed down. The results indicate that the reaction is an auto-catalysed, free radical chain reaction transforming 99% of quinoline to other substances. Of the quinoline. 30-50% was oxidised to CO2 and H2O depending on the initial concentration. Wet oxidation of deuterium-labelled quinoline...

  9. Kinetic study on S_NAr reactions of 1-(Y-Substituted-phenoxy)-2,4-dinitrobenzenes with azide ion: Effect of changing nucleophile from hydroxide to zzide ion on reaction mechanism and reactivity

    International Nuclear Information System (INIS)

    Seo, Hyeon Ok; Kim, Min Young; Han, So Yeop; Um, Ik Hwan

    2015-01-01

    Second-order rate constants (k_N_3_−) for SNAr reactions of 1-(Y-substituted-phenoxy)-2,4-dinitrobenzenes (2a–2h) with math formula in 80 mol % H_2O/20 mol % DMSO at 25.0 ± 0.1 °C have been measured spectrophotometrically. The Brønsted-type plot is linear with β"l"g = −0.38. The Hammett plots correlated with math formula and math formula constants exhibit highly scattered points. In contrast, the Yukawa–Tsuno plot results in an excellent linear correlation with ρ_Y = 1.02 and r = 0.51, indicating that a negative charge develops partially on the O atom of the leaving Y-substituted-phenoxy moiety in the transition state. Accordingly, the reactions have been concluded to proceed through a stepwise mechanism, in which expulsion of the leaving group occurs in the rate-determining step. Comparison of k_N_3_− with the k_O_H_− values reported previously for the corresponding reactions with OH"− has revealed that math formula is only 6- to 26-fold less reactive than OH"− toward substrates 2a–2h, although the former is over 11 pK_a units less basic than the latter. Solvation and polarizability effects have been suggested to be responsible for the unusual reactivity shown by math formula and OH"−. Effects of changing nucleophile from OH"− to N_3"− on reaction mechanism and reactivity are discussed in detail

  10. Double-lock ratchet mechanism revealing the role of  SER-344 in FoF1 ATP synthase

    KAUST Repository

    Beke-Somfai, T.

    2011-03-07

    In a majority of living organisms, FoF1 ATP synthase performs the fundamental process of ATP synthesis. Despite the simple net reaction formula, ADP+Pi→ATP+H2O, the detailed step-by-step mechanism of the reaction yet remains to be resolved owing to the complexity of this multisubunit enzyme. Based on quantum mechanical computations using recent high resolution X-ray structures, we propose that during ATP synthesis the enzyme first prepares the inorganic phosphate for the γP-OADP bond-forming step via a double-proton transfer. At this step, the highly conserved αS344 side chain plays a catalytic role. The reaction thereafter progresses through another transition state (TS) having a planar ion configuration to finally form ATP. These two TSs are concluded crucial for ATP synthesis. Using stepwise scans and several models of the nucleotide-bound active site, some of the most important conformational changes were traced toward direction of synthesis. Interestingly, as the active site geometry progresses toward the ATP-favoring tight binding site, at both of these TSs, a dramatic increase in barrier heights is observed for the reverse direction, i.e., hydrolysis of ATP. This change could indicate a "ratchet" mechanism for the enzyme to ensure efficacy of ATP synthesis by shifting residue conformation and thus locking access to the crucial TSs.

  11. Kinetics and mechanism of the gas-phase reaction of Cl atoms and OH radicals with fluorobenzene at 296 K

    DEFF Research Database (Denmark)

    Andersen, Mads Peter Sulbæk; Nielsen, Ole John; Hurley, MD

    2002-01-01

    Smog chamber/FTIR techniques were used to study the kinetics and mechanism of the reaction of Cl atoms and OH radicals with fluorobenzene, C6H5F, in 700 Torr of N-2 or air diluent at 296 K. Reaction of Cl atoms with C6H5F proceeds via two pathways: H-atom abstraction to give HCl and the C6H4F...... with Cl atoms via a mechanism which, at least in part, leads neither to production of C6H5Cl nor to reformation of C6H5F. As the steady-state Cl atom concentration is increased, the fraction of the C6H5F-Cl adduct undergoing reaction with Cl atoms increases causing an increase in the effective rate...

  12. The influence of the “cage effect” on the mechanism of reversible bimolecular multistage chemical reactions in solutions

    International Nuclear Information System (INIS)

    Doktorov, Alexander B.

    2015-01-01

    Manifestations of the “cage effect” at the encounters of reactants are theoretically treated by the example of multistage reactions in liquid solutions including bimolecular exchange reactions as elementary stages. It is shown that consistent consideration of quasi-stationary kinetics of multistage reactions (possible only in the framework of the encounter theory) for reactions proceeding near reactants contact can be made on the basis of the concepts of a “cage complex.” Though mathematically such a consideration is more complicated, it is more clear from the standpoint of chemical notions. It is established that the presence of the “cage effect” leads to some important effects not inherent in reactions in gases or those in solutions proceeding in the kinetic regime, such as the appearance of new transition channels of reactant transformation that cannot be caused by elementary event of chemical conversion for the given mechanism of reaction. This results in that, for example, rate constant values of multistage reaction defined by standard kinetic equations of formal chemical kinetics from experimentally measured kinetics can differ essentially from real values of these constants

  13. The influence of the "cage effect" on the mechanism of reversible bimolecular multistage chemical reactions in solutions.

    Science.gov (United States)

    Doktorov, Alexander B

    2015-08-21

    Manifestations of the "cage effect" at the encounters of reactants are theoretically treated by the example of multistage reactions in liquid solutions including bimolecular exchange reactions as elementary stages. It is shown that consistent consideration of quasi-stationary kinetics of multistage reactions (possible only in the framework of the encounter theory) for reactions proceeding near reactants contact can be made on the basis of the concepts of a "cage complex." Though mathematically such a consideration is more complicated, it is more clear from the standpoint of chemical notions. It is established that the presence of the "cage effect" leads to some important effects not inherent in reactions in gases or those in solutions proceeding in the kinetic regime, such as the appearance of new transition channels of reactant transformation that cannot be caused by elementary event of chemical conversion for the given mechanism of reaction. This results in that, for example, rate constant values of multistage reaction defined by standard kinetic equations of formal chemical kinetics from experimentally measured kinetics can differ essentially from real values of these constants.

  14. The influence of the “cage effect” on the mechanism of reversible bimolecular multistage chemical reactions in solutions

    Energy Technology Data Exchange (ETDEWEB)

    Doktorov, Alexander B., E-mail: doktorov@kinetics.nsc.ru [Voevodsky Institute of Chemical Kinetics & Combustion, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia and Novosibirsk State University, Novosibirsk 630090 (Russian Federation)

    2015-08-21

    Manifestations of the “cage effect” at the encounters of reactants are theoretically treated by the example of multistage reactions in liquid solutions including bimolecular exchange reactions as elementary stages. It is shown that consistent consideration of quasi-stationary kinetics of multistage reactions (possible only in the framework of the encounter theory) for reactions proceeding near reactants contact can be made on the basis of the concepts of a “cage complex.” Though mathematically such a consideration is more complicated, it is more clear from the standpoint of chemical notions. It is established that the presence of the “cage effect” leads to some important effects not inherent in reactions in gases or those in solutions proceeding in the kinetic regime, such as the appearance of new transition channels of reactant transformation that cannot be caused by elementary event of chemical conversion for the given mechanism of reaction. This results in that, for example, rate constant values of multistage reaction defined by standard kinetic equations of formal chemical kinetics from experimentally measured kinetics can differ essentially from real values of these constants.

  15. [Biomechanical significance of the acetabular roof and its reaction to mechanical injury].

    Science.gov (United States)

    Domazet, N; Starović, D; Nedeljković, R

    1999-01-01

    The introduction of morphometry into the quantitative analysis of the bone system and functional adaptation of acetabulum to mechanical damages and injuries enabled a relatively simple and acceptable examination of morphological acetabular changes in patients with damaged hip joints. Measurements of the depth and form of acetabulum can be done by radiological methods, computerized tomography and ultrasound (1-9). The aim of the study was to obtain data on the behaviour of acetabular roof, the so-called "eyebrow", by morphometric analyses during different mechanical injuries. Clinical studies of the effect of different loads on acetabular roof were carried out in 741 patients. Radiographic findings of 400 men and 341 women were analysed. The control group was composed of 148 patients with normal hip joints. Average age of the patients was 54.7 years and that of control subjects 52.0 years. Data processing was done for all examined patients. On the basis of our measurements the average size of female "eyebrow" ranged from 24.8 mm to 31.5 mm with standard deviation of 0.93 and in men from 29.4 mm to 40.3 mm with standard deviation of 1.54. The average size in the whole population was 32.1 mm with standard deviation of 15.61. Statistical analyses revealed high correlation coefficients between the age and "eyebrow" size in men (r = 0.124; p 0.05). The examination of the size of collodiaphysial angle and length of "eyebrow" revealed that "eyebrow" length was in inverse proportion to the size of collodiaphysial angle (r = 0.113; p 0.05) and female (r = 0.005; p > 0.05) patients. The "eyebrow" length was proportionally dependent on the size of the shortened extremity in all examined subjects. This dependence was statistically significant both in female (r = 0.208; p < 0.05) and male (r = 0.193; p < 0.05) patients. The study revealed that fossa acetabuli was forward and downward laterally directed. The size, form and cross-section of acetabulum changed during different

  16. Analysis of mechanism of complex chemical reaction taking radiation chemical purification of gases from impurities as an example

    International Nuclear Information System (INIS)

    Gerasimov, G.Ya.; Makarov, V.N.

    1997-01-01

    Algorithm of selecting optimal mechanism of complex chemical reaction, enabling to reduce the number of its stages, is suggested. Main steps of constructing the kinetic model of the medium are considered, taking the radiation chemical purification (using fast electron radiation) of gases (N 2 , CO 2 , O 2 and others) from impurities as an example. 17 refs., 3 figs., 2 tabs

  17. Grain rotation and lattice deformation during photoinduced chemical reactions revealed by in situ X-ray nanodiffraction.

    Science.gov (United States)

    Huang, Zhifeng; Bartels, Matthias; Xu, Rui; Osterhoff, Markus; Kalbfleisch, Sebastian; Sprung, Michael; Suzuki, Akihiro; Takahashi, Yukio; Blanton, Thomas N; Salditt, Tim; Miao, Jianwei

    2015-07-01

    In situ X-ray diffraction (XRD) and transmission electron microscopy (TEM) have been used to investigate many physical science phenomena, ranging from phase transitions, chemical reactions and crystal growth to grain boundary dynamics. A major limitation of in situ XRD and TEM is a compromise that has to be made between spatial and temporal resolution. Here, we report the development of in situ X-ray nanodiffraction to measure high-resolution diffraction patterns from single grains with up to 5 ms temporal resolution. We observed, for the first time, grain rotation and lattice deformation in chemical reactions induced by X-ray photons: Br(-) + hv → Br + e(-) and e(-) + Ag(+) → Ag(0). The grain rotation and lattice deformation associated with the chemical reactions were quantified to be as fast as 3.25 rad s(-1) and as large as 0.5 Å, respectively. The ability to measure high-resolution diffraction patterns from individual grains with a temporal resolution of several milliseconds is expected to find broad applications in materials science, physics, chemistry and nanoscience.

  18. Reaction Mechanisms and Structural and Physicochemical Properties of Caffeic Acid Grafted Chitosan Synthesized in Ascorbic Acid and Hydroxyl Peroxide Redox System.

    Science.gov (United States)

    Liu, Jun; Pu, Huimin; Chen, Chong; Liu, Yunpeng; Bai, Ruyu; Kan, Juan; Jin, Changhai

    2018-01-10

    The ascorbic acid (AA) and hydroxyl peroxide (H 2 O 2 ) redox pair induced free radical grafting reaction is a promising approach to conjugate phenolic groups with chitosan (CS). In order to reveal the exact mechanisms of the AA/H 2 O 2 redox pair induced grafting reaction, free radicals generated in the AA/H 2 O 2 redox system were compared with hydroxyl radical ( • OH) produced in the Fe 2+ /H 2 O 2 redox system. Moreover, the structural and physicochemical properties of caffeic acid grafted CS (CA-g-CS) synthesized in these two redox systems were compared. Results showed that only ascorbate radical (Asc •- ) was produced in the AA/H 2 O 2 system. The reaction between Asc •- and CS produced novel carbon-centered radicals, whereas no new free radicals were detected when • OH reacted with CS. Thin layer chromatography, UV-vis, Fourier transform infrared, and nuclear magnetic resonance spectroscopic analyses all confirmed that CA was successfully grafted onto CS through Asc •- . However, CA could be hardly grafted onto CS via • OH. CA-g-CS synthesized through Asc •- exhibited lower thermal stability and crystallinity than the reaction product obtained through • OH. For the first time, our results demonstrated that the synthesis of CA-g-CS in the AA/H 2 O 2 redox system was mediated by Asc •- rather than • OH.

  19. Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor

    KAUST Repository

    Bagchi, Samik; Lamendella, Regina; Strutt, Steven; Van Loosdrecht, Mark C. M.; Saikaly, Pascal

    2016-01-01

    to formation of large granules. Size distribution analysis revealed the spatial distribution of granules in which large granules having higher abundance of anammox bacteria (genus Brocadia) dominated the bottom biomass. Metatranscriptomics analysis detected all

  20. Kinetics and mechanism of ligand-exchange reactions of Cd(II) chelates

    Energy Technology Data Exchange (ETDEWEB)

    Nivorozhkin, L.E.; Kalabin, G.A.; Nivorozhkin, A.L.; Valeev, R.B.; Minkin, V.I.

    1987-03-01

    Tetrahedral Cd(II) bis(5-thio(or seleno)pyrazole-4-carboxaldiminates) of types II and III have been synthesized for the first time. The kinetics of the degenerate ligand exchange and enantiomerization of the complexes obtained have been studied by dynamic /sup 111/Cd, /sup 77/Se, and /sup 1/H (s = 1/2) NMR. The rate of intramolecular enantiomerization (k = 1/tau) is more than an order of magnitude greater than the corresponding values for processes of degenerate ligand exchange (a second-order reaction) determined from the dynamics of the averaging of the /sup 111/Cd-/sup 77/Se and /sup 111/Cd-N=CH spin-spin coupling constants. The cleavage and formation processes of the Cd-Se and Cd-N bonds are isoenergetic (..delta.. G/sub 298//sup not equal to/ = 14.4 kcal/mole for chelate II with X = Se and R = CH/sub 2/C/sub 6/H/sub 5/). The free energies of activation of degenerate ligand exchange determined form the dynamics of the averaging of the /sup 111/Cd N=CH spin-spin coupling constant increase from 12.7 to 17.9 kcal/mole along the following series for R: C/sub 2/H/sub 5/ < Ar < CH/sub 2/C/sub 6/H/sub 5/ < t-C/sub 4/H/sub 9/ < cyclo-C/sub 6/H/sub 11/. Replacement of the sulfur atom in the chelate ring by selenium results in increases in the rates of ligand exchange. A mechanism of degenerate ligand exchange has been proposed.

  1. Kinetics and reaction mechanism for aminolysis of benzyl 4-pyridyl carbonate in H2O: Effect of modification of nucleofuge from 2-pyridyl oxide to 4-pyridyl oxide on reactivity and reaction mechanism

    International Nuclear Information System (INIS)

    Kang, Ji Sun; Um, Ikhwan

    2012-01-01

    Pseudo-first-order rate constants k amine have been measured spectrophotometrically for the reactions of benzyl 4-pyridyl carbonate 6 with a series of alicyclic secondary amines in H 2 O at 25.0.deg.C. The plots of k amine vs. [amine] curve upward, indicating that the reactions proceed through a stepwise mechanism with two intermediates, a zwitterionic tetrahedral intermediate T ± and its deprotonated form T - . This contrasts to the report that the corresponding reactions of benzyl 2-pyridyl carbonate 5 proceed through a forced concerted pathway. The k amine values for the reactions of 6 have been dissected into the second-order rate constant Kk 2 and the third order rate constant Kk 3 . The Brφnsted-type plots are linear with β nuc = 0.94 and 1.18 for Kk 2 and Kk 3 , respectively. The Kk 2 for the reaction of 6 is smaller than the second-order rate constant k N for the corresponding reaction of 5, although 4-pyridyl oxide in 6 is less basic and a better nucleofuge than 2-pyridyl oxide in 5

  2. Mechanism of Cytochrome P450 17A1-Catalyzed Hydroxylase and Lyase Reactions

    DEFF Research Database (Denmark)

    Bonomo, Silvia; Jorgensen, Flemming Steen; Olsen, Lars

    2017-01-01

    Cytochrome P450 17A1 (CYP17A1) catalyzes C17 hydroxylation of pregnenolone and progesterone and the subsequent C17–C20 bond cleavage (lyase reaction) to form androgen precursors. Compound I (Cpd I) and peroxo anion (POA) are the heme-reactive species underlying the two reactions. We have characte...... the concept that the selectivity of the steroidogenic CYPs is ruled by direct interactions with the enzyme, in contrast to the selectivity of drug-metabolizing CYPs, where the reactivity of the substrates dominates....... characterized the reaction path for both the hydroxylase and lyase reactions using density functional theory (DFT) calculations and the enzyme–substrate interactions by molecular dynamics (MD) simulations. Activation barriers for positions subject to hydroxylase reaction have values close to each other and span...

  3. Kinetics and mechanisms of reactions of CF, CHF, and CF2 radicals

    International Nuclear Information System (INIS)

    Hsu, D.S.Y.; Umstead, M.E.; Lin, M.C.

    1978-01-01

    This chapter reviews briefly methods for the production of CF, CHF and CF 2 , and inmore detail, the reactions of these interesting and important radicals. Although a considerable, but not extensive, amount of work has been done on the reactions of CF 2 , little of the chemistry of CF and CHF is known. This chapter also includes the preliminary results of some experiments carried out in this Laboratory on the dynamics of some of the reactions involving these radicals. These results were largely arrived at through investigations of the degree of vibrational excitation of the HF and CO reaction products, determined by HF and CO laser emission and CO laser resonance absorption measurements. The coverage of this review is restricted to the gas phase chemistry of these radicals, and does not include their addition reactions to olefins

  4. A multi-level quantum mechanics and molecular mechanics study of SN2 reaction at nitrogen: NH2Cl + OH(-) in aqueous solution.

    Science.gov (United States)

    Lv, Jing; Zhang, Jingxue; Wang, Dunyou

    2016-02-17

    We employed a multi-level quantum mechanics and molecular mechanics approach to study the reaction NH2Cl + OH(-) in aqueous solution. The multi-level quantum method (including the DFT method with both the B3LYP and M06-2X exchange-correlation functionals and the CCSD(T) method, and both methods with the aug-cc-pVDZ basis set) was used to treat the quantum reaction region in different stages of the calculation in order to obtain an accurate potential of mean force. The obtained free energy activation barriers at the DFT/MM level of theory yielded a big difference of 21.8 kcal mol(-1) with the B3LYP functional and 27.4 kcal mol(-1) with the M06-2X functional respectively. Nonetheless, the barrier heights become very close when shifted from DFT to CCSD(T): 22.4 kcal mol(-1) and 22.9 kcal mol(-1) at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM levels of theory, respectively. The free reaction energy obtained using CCSD(T)(M06-2X)/MM shows an excellent agreement with the one calculated using the available gas-phase data. Aqueous solution plays a significant role in shaping the reaction profile. In total, the water solution contributes 13.3 kcal mol(-1) and 14.6 kcal mol(-1) to the free energy barrier heights at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM respectively. The title reaction at nitrogen is a faster reaction than the corresponding reaction at carbon, CH3Cl + OH(-).

  5. Kinetic Study on Nucleophilic Substitution Reactions of 4-Chloro-2-nitrophenyl X-Substituted-benzoates with Cyclic Secondary Amines: Effect of Substituent X on Reactivity and Reaction Mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Jeon, Seong Hoon; Kim, Hyun Soo; Han, Young Joon [Sejong Science High School, Seoul (Korea, Republic of); Kim, Minyoung; Um, Ikhwan [Ewha Woman' s Univ., Seoul (Korea, Republic of)

    2013-10-15

    Second-order rate constants (k{sub N}) have been measured spectrophotometrically for the reactions of 4-chloro-2-nitrophenyl X-substituted-benzoates (1a-1h) with a series of cyclic secondary amines in 80 mol % H{sub 2}O/20 mol % DMSO at 25.0 ± 0.1 .deg. C. The Hammett plot for the reactions of 1a-1h with piperidine consists of two intersecting straight lines, while the Yukawa-Tsuno plot exhibits an excellent linear correlation with ρ{sub X} = 1.25 and r = 0.58, indicating that the nonlinear Hammett plot is not due to a change in the rate-determining step (RDS) but is caused by ground-state stabilization through resonance interactions for substrates possessing an electron-withdrawing group in the benzoyl moiety. The Brφnsted-type plot for the reactions of 4-chloro-2-nitrophenyl benzoate (1d) with a series of cyclic secondary amines curves downward with β{sub 2} = 0.85, β{sub 1} = 0.24, and pK{sub a}{sup o} = 10.5, implying that a change in RDS occurs from the k{sub 2} step to the k{sub 1} process as the pK{sub a} of the conjugate acid of the amine exceeds 10.5. Dissection of k{sub N} into the microscopic rate constants k{sub 1} and k{sub 2}/k{sub -1} ratio associated with the reaction of 1d reveals that k{sub 2} is dependent on the amine basicity, which is contrary to generally held views.

  6. Photocatalytic Removal of Dye and Reaction Mechanism Analysis over Y2O3 Composite Nanomaterials

    Directory of Open Access Journals (Sweden)

    Guo Xiaohui

    2017-01-01

    Full Text Available Y2O3 supported photocatalysts MOx (M = Fe, Ti and Bi/Y2O3 were synthesized by hydrothermal and deposition-precipitation method and used in photocatalytic degradation of xylenol orange and rhodamine B under UV light irradiation. The crystalline structure and optical properties were well characterized by XRD and UV-vis DRS. The results of XRD revealed that the MOx/Y2O3 were composed of Fe2O3, TiO2, Bi0.8Y1.2O3 and Y2O3. The UV-vis DRS showed that MOx/Y2O3 photocatalysts exhibited stronger absorption in ultraviolet, and the absorption edge shifted to visible light region significantly. The photocatalytic experiments indicated that MOx/Y2O3 photocatalysts showed better activity for photodegradation of xylenol orange than rhodamine B. Moreover, the role of Y2O3 and the mechanism of photocatalysis is proposed.

  7. A coupled mechanical-chemical model for reflecting the influence of stress on oxidation reactions in thermal barrier coating

    Science.gov (United States)

    Chen, Lin; Yueming, Li

    2018-06-01

    In this paper, a coupled mechanical-chemical model is established based on the thermodynamic framework, in which the contribution of chemical expansion to free energy is introduced. The stress-dependent chemical potential equilibrium at the gas-solid interface and the stress gradient-dependent diffusion equation as well as a so-called generalized force which is conjugate to the oxidation rate are derived from the proposed model, which could reflect the influence of stresses on the oxidation reaction. Based on the proposed coupled mechanical-chemical model, a user element subroutine is developed in ABAQUS. The numerical simulation of the high temperature oxidation in the thermal barrier coating is carried out to verify the accuracy of the proposed model, and then the influence of stresses on the oxidation reaction is investigated. In thermally grown oxide, the considerable stresses would be induced by permanent volumetric swelling during the oxidation. The stresses play an important role in the chemical potential equilibrium at the gas-solid interface and strongly affect the oxidation reaction. The gradient of the stresses, however, only occurs in the extremely thin oxidation front layer, which plays a very limited role in the oxidation reaction. The generalized force could be divided into the stress-dependent and the stress-independent parts. Comparing with the stress-independent part, the stress-dependent part is smaller, which has little influence on oxidation reaction.

  8. On the existence of and mechanism for microwave-specific reaction rate enhancement.

    Science.gov (United States)

    Dudley, Gregory B; Richert, Ranko; Stiegman, A E

    2015-04-01

    The use of microwave radiation to drive chemical reactions has become ubiquitous in almost all fields of chemistry. In all of these areas it is principally due to rapid and convenient heating resulting in significantly higher rates of reaction, with other advantages including enhanced product selectivity and control of materials properties. Although microwave heating continues to grow as an enabling technology, fundamental research into the nature of microwave heating has not grown at the same rate. In the case of chemical reactions run in homogeneous solution, particularly synthetic organic reactions, there is considerable controversy over the origins of rate enhancement, with a fundamental question being whether there exist microwave-specific effects, distinct from what can be attained under conventional convective heating, that can accelerate a reaction rate. In this Perspective, we discuss unique aspects of microwave heating of molecules in solution and discuss the origin and nature of microwave-specific effects arising from the process of "selective heating" of reactants in solution. Integral to this discussion is work from the field of dielectric relaxation spectroscopy, which provides a model for selective heating by Debye relaxation processes. The Perspective also includes a critical discussion of hypotheses of non-thermal effects (alternatively classified here as resonant processes) and an outline of specific reaction parameters for chemical systems in which microwave-specific Debye relaxation processes can result in observable reaction rate enhancement.

  9. Insight into the Reaction Mechanism of Graphene Oxide with Oxidative Free Radical

    Institute of Scientific and Technical Information of China (English)

    ZHOU Xuejiao; XU Liangyou

    2017-01-01

    Graphene oxide(GO),as an important derivative of graphene,could be considered as a super aromatic molecule decorated with a range of reactive oxygen-containing groups on its surface,which endows graphene high reactivity with other molecules.In our previous work,we demonstrated that GO sheets were cut into small pieces(graphene quantum dots,GQDs) by oxidative free radicals(hydroxyl radical HO or oxygen radical [O]) under UV irradiation.It is notable that reactions involving free radicals are influenced by reaction conditions pronouncedly.However,researches on details about reactions of GO with free radicals have not been reported thus far.In this work,the effects of different factors on the photo-Fenton reaction of GO were studied.It is demonstrated that the reaction rate is closely related to the concentration of free radicals.It is speculated that through the optimization of reaction conditions,the reaction of graphene with free radicals could carry out efficiently for further applications.

  10. Dual transcriptomics reveals co-evolutionary mechanisms of intestinal parasite infections in blue mussels Mytilus edulis

    NARCIS (Netherlands)

    Feis, M.E.; John, U.; Lokmer, A.; Luttikhuizen, P.C.; Wegner, K.M.

    2018-01-01

    On theoretical grounds, antagonistic co-evolution between hosts and their parasitesshould be a widespread phenomenon but only received little empirical support sofar. Consequently, the underlying molecular mechanisms and evolutionary stepsremain elusive, especially in nonmodel systems. Here, we

  11. A role of TRPA1 in mechanical hyperalgesia is revealed by pharmacological inhibition

    Directory of Open Access Journals (Sweden)

    Huynh Truc

    2007-12-01

    Full Text Available Abstract Mechanical hyperalgesia is a clinically-relevant form of pain sensitization that develops through largely unknown mechanisms. TRPA1, a Transient Receptor Potential ion channel, is a sensor of pungent chemicals that may play a role in acute noxious mechanosensation and cold thermosensation. We have developed a specific small molecule TRPA1 inhibitor (AP18 that can reduce cinnameldehyde-induced nociception in vivo. Interestingly, AP18 is capable of reversing CFA-induced mechanical hyperalgesia in mice. Although TRPA1-deficient mice develop normal CFA-induced hyperalgeisa, AP18 is ineffective in the knockout mice, consistent with an on-target mechanism. Therefore, TRPA1 plays a role in sensitization of nociception, and that compensation in TRPA1-deficient mice masks this requirement.

  12. Quantum mechanics. An epistemological revolution that is revealed in the description of micro-states

    International Nuclear Information System (INIS)

    Mugur-Schachter, M.

    2009-01-01

    The author deals with the issue of why quantum mechanics is so difficult to understand. The answer is identified here: the quantum formalism includes the principles of a radical revolution in epistemology. The development of these principles has led to an entire re-shaping of how to generate knowledge in sciences. It is a description of what lays behind quantum mechanics in terms of conceptualization. (A.C.)

  13. Nuclear excitations and reaction mechanisms. Progress report, 1 November 1979-30 September 1980

    International Nuclear Information System (INIS)

    1980-01-01

    Among the topics investigated were the following: photon scattering and consistency condition between seagull quadrupole terms and the absorption sum rule; Raman scattering to negative-parity states; nonlocal terms due to exchange and retardation effects in charge-transfer reactions; consistency and meaning of various approximate channel coupling array equations; derivation of equations used in empirical nuclear reaction analyses; multicluster, n-particle scattering theory; converged molecular bound state calculations; consistency of approximate channel coupling array equations; derivations of equations used in empirical nuclear reaction analyses; and WKB-type approximation in angular momenta for central potentials. References to publications are given

  14. Active Tension Network model reveals an exotic mechanical state realized in epithelial tissues

    Science.gov (United States)

    Noll, Nicholas; Mani, Madhav; Heemskerk, Idse; Streicha, Sebastian; Shraiman, Boris

    Mechanical interactions play a crucial role in epithelial morphogenesis, yet understanding the complex mechanisms through which stress and deformation affect cell behavior remains an open problem. Here we formulate and analyze the Active Tension Network (ATN) model, which assumes that mechanical balance of cells is dominated by cortical tension and introduces tension dependent active remodeling of the cortex. We find that ATNs exhibit unusual mechanical properties: i) ATN behaves as a fluid at short times, but at long times it supports external tension, like a solid; ii) its mechanical equilibrium state has extensive degeneracy associated with a discrete conformal - ''isogonal'' - deformation of cells. ATN model predicts a constraint on equilibrium cell geometry, which we demonstrate to hold in certain epithelial tissues. We further show that isogonal modes are observed in a fruit fly embryo, accounting for the striking variability of apical area of ventral cells and helping understand the early phase of gastrulation. Living matter realizes new and exotic mechanical states, understanding which helps understand biological phenomena.

  15. Reaction Mechanisms of the Atomic Layer Deposition of Tin Oxide Thin Films Using Tributyltin Ethoxide and Ozone.

    Science.gov (United States)

    Nanayakkara, Charith E; Liu, Guo; Vega, Abraham; Dezelah, Charles L; Kanjolia, Ravindra K; Chabal, Yves J

    2017-06-20

    Uniform and conformal deposition of tin oxide thin films is important for several applications in electronics, gas sensing, and transparent conducting electrodes. Thermal atomic layer deposition (ALD) is often best suited for these applications, but its implementation requires a mechanistic understanding of the initial nucleation and subsequent ALD processes. To this end, in situ FTIR and ex situ XPS have been used to explore the ALD of tin oxide films using tributyltin ethoxide and ozone on an OH-terminated, SiO 2 -passivated Si(111) substrate. Direct chemisorption of tributyltin ethoxide on surface OH groups and clear evidence that subsequent ligand exchange are obtained, providing mechanistic insight. Upon ozone pulse, the butyl groups react with ozone, forming surface carbonate and formate. The subsequent tributyltin ethoxide pulse removes the carbonate and formate features with the appearance of the bands for CH stretching and bending modes of the precursor butyl ligands. This ligand-exchange behavior is repeated for subsequent cycles, as is characteristic of ALD processes, and is clearly observed for deposition temperatures of 200 and 300 °C. On the basis of the in situ vibrational data, a reaction mechanism for the ALD process of tributyltin ethoxide and ozone is presented, whereby ligands are fully eliminated. Complementary ex situ XPS depth profiles confirm that the bulk of the films is carbon-free, that is, formate and carbonate are not incorporated into the film during the deposition process, and that good-quality SnO x films are produced. Furthermore, the process was scaled up in a cross-flow reactor at 225 °C, which allowed the determination of the growth rate (0.62 Å/cycle) and confirmed a self-limiting ALD growth at 225 and 268 °C. An analysis of the temperature-dependence data reveals that growth rate increases linearly between 200 and 300 °C.

  16. Mechanical stimulated reaction of metal/polymer mixed powders; Kinzoku/kobunshi kongo funmatsu no kikaiteki reiki hanno

    Energy Technology Data Exchange (ETDEWEB)

    Tobita, M.; Sakakibara, A.; Takemoto, Y. [Okayama University, Okayama (Japan). Faculty of Engineering; Iwabu, H. [Kurare Co. Ltd., Osaka (Japan)

    1999-12-15

    Mechanical grinding (MG) with mechanically stimulated reaction was performed on metal/polymer mixed powders. The starting materials used in this study were the metals of Mg, Ti and Mg{sub 2}Ni powders, arid polymer of PTFE, PVC and PE powders. The MG process was investigated using XRD, IR, SEM and TEM. According to XRD results, magnesium fluoride (MgF{sub 2}, TiF{sub 2}) and chloride (MgCl{sub 2}) were detected from MG products of the Mg/PTFE, Ti/PTFE and Mg/PVC blending systems, respectively. Explosive reaction was found during MG of both Mg/PTFE and Ti/PTFE. It was also confirmed by XRD results that the production of MgF{sub 2} had already been formed just before the explosive reaction in Mg/PTFE system. It was found from IR analysis that C-C single bond in the polymers, not only both in PTFE and PVC but also in PE, changed to double bond C=C. Hydrogen produced due to decomposition of PE on blending Mg{sub 2}Ni/PE was absorbed into C-Mg{sub 2}Ni-H as amorphous solutes. These mechanically stimulated reaction was powerful method for decomposition of engineering plastics. (author)

  17. Exploring reaction mechanisms and their competition in 58Ni+48Ca collisions at E = 25 AMeV

    Directory of Open Access Journals (Sweden)

    Francalanza L.

    2014-03-01

    Full Text Available Latest results concerning the study of central collisions in 58Ni+48Ca reactions at Elab(Ni=25 AMeV are presented. The experimental data, collected with the CHIMERA 4π device, have been analyzed in order to investigate the competition among different reaction mechanisms for central collisions in the Fermi energy domain. The method adopted to perform the centrality selection refers to the global variable “flow angle”, that is related to the event shape in momentum space, as it is determined by the eigenvectors of the experimental kinetic-energy tensor. The main features of the reaction products were explored by using different constraints on some of the relevant observables, such as mass and velocity distributions and their correlations. Much emphasis was devoted to the competition between fusion-evaporation processes with subsequent identification of a heavy residue and a prompt multifragmentation mechanism. The reaction mechanism was simulated in the framework of transport theories (dynamical stochastic BNV calculations, followed by sequential SIMON code and further comparison with dynamical calculations from transport model (QMD, CoMD are in progress. Moreover, an extension of this study taking into account for the light particles has been envisaged.

  18. Study of the mechanism of Pb + Au reaction at 29 A.MeV; Etude du mecanisme de la reaction Pb + Au a 29 A.MeV

    Energy Technology Data Exchange (ETDEWEB)

    Aboufirassi, M

    1994-07-01

    The aim of this thesis is to demonstrate the binary character of Pb + Au reaction at 29 A.MeV and to study the decay modes of very excited nuclei produced. The experiment set up was performed at the GANIL in the scattering chamber NAUTILUS. It was composed by multi detectors of fragments (Z {>=}8) and multi detectors of light charged particles. (Z<8). The analysis of events which lead to detection of more then 80 % of both total charge and total parallel momentum proved that two body final state is still present at this incident energy. This mechanism is similar to the mechanism of heavy ion reaction at low bombarding energy. We have shown that complete damping occurred leading to excitation energy as high as 6 Me V/u. The decay modes of deep inelastic products are evaporation residue or binary fission or multifragmentation. Analysing the fission products, we have estimated the aligned spin of deep inelastic products (45 h). Finally, the study of light charged particles detected with fission fragments has demonstrated that these particles are emitted essentially before fission. The temperature value of hot nuclei emitted at foreword angle is deduced of light particle spectra. (author). 59 refs.

  19. Mechanism of ternary breakup in the reaction 197Au+197Au at 15A MeV

    International Nuclear Information System (INIS)

    Tian Junlong; Wu Xizhen; Li Zhuxia; Zhao Kai; Zhang Yingxun; Li Xian; Yan Shiwei

    2010-01-01

    The mechanism of the ternary breakup of the very heavy system 197 Au+ 197 Au at an energy of 15A MeV has been studied by using the improved quantum molecular dynamics model. The calculation results reproduce the characteristic features in ternary breakup events explored in a series of experiments; i.e., the masses of three fragments are comparable in size and the very fast, nearly collinear breakup of the colliding system is dominant in the ternary breakup events. Further, the evolution of the time scales of different ternary reaction modes and the behavior of mass distributions of three fragments with impact parameters are studied. The time evolution of the configurations of the composite reaction systems is also studied. We find that for most of the ternary breakup events with the features found in the experiments, the configuration of the composite system has two-preformed-neck shape. The study shows that those ternary breakup events having the characteristic features found in the experiments happen at relatively small impact parameter reactions, but not at peripheral reactions. The ternary breakup reaction at peripheral reactions belongs to binary breakup with a neck emission.

  20. Phi-value analysis of a linear, sequential reaction mechanism: theory and application to ion channel gating.

    Science.gov (United States)

    Zhou, Yu; Pearson, John E; Auerbach, Anthony

    2005-12-01

    We derive the analytical form of a rate-equilibrium free-energy relationship (with slope Phi) for a bounded, linear chain of coupled reactions having arbitrary connecting rate constants. The results confirm previous simulation studies showing that Phi-values reflect the position of the perturbed reaction within the chain, with reactions occurring earlier in the sequence producing higher Phi-values than those occurring later in the sequence. The derivation includes an expression for the transmission coefficients of the overall reaction based on the rate constants of an arbitrary, discrete, finite Markov chain. The results indicate that experimental Phi-values can be used to calculate the relative heights of the energy barriers between intermediate states of the chain but provide no information about the energies of the wells along the reaction path. Application of the equations to the case of diliganded acetylcholine receptor channel gating suggests that the transition-state ensemble for this reaction is nearly flat. Although this mechanism accounts for many of the basic features of diliganded and unliganded acetylcholine receptor channel gating, the experimental rate-equilibrium free-energy relationships appear to be more linear than those predicted by the theory.

  1. Evaluation of reaction mechanisms and the kinetic parameters for the transesterification of castor oil by liquid enzymes

    DEFF Research Database (Denmark)

    Andrade, Thalles Allan; Errico, Massimiliano; Christensen, Knud Villy

    2017-01-01

    of the transesterification of castor oil with methanol using the enzyme Eversa® Transform as catalyst were investigated. Reactions were carried out for 8 hours at 35 °C with: an alcohol-to-oil molar ratio equal to 6:1, a 5 wt% of liquid enzyme solution and addition of 5 wt% of water by weight of castor oil. From...... methanolysis rates of glycerides obtained, indicated that transesterification dominates over hydrolysis. The mechanism among the four models proposed that gave the best fit could be simplified, eliminating the kinetic parameters with negligible effects on the reaction rates. This model was able to fit...

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

    Science.gov (United States)

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

    2018-05-01

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

  3. Mechanical properties of ultra thin metallic films revealed by synchrotron techniques

    Energy Technology Data Exchange (ETDEWEB)

    Gruber, Patric Alfons

    2007-07-20

    A prerequisite for the study of the scaling behavior of mechanical properties of ultra thin films is a suitable testing technique. Therefore synchrotron-based in situ testing techniques were developed and optimized in order to characterize the stress evolution in ultra thin metallic films on compliant polymer substrates during isothermal tensile tests. Experimental procedures for polycrystalline as well as single crystalline films were established. These techniques were used to systematically investigate the influence of microstructure, film thickness (20 to 1000 nm) and temperature (-150 to 200 C) on the mechanical properties. Passivated and unpassivated Au and Cu films as well as single crystalline Au films on polyimide substrates were tested. Special care was also dedicated to the microstructural characterization of the samples which was very important for the correct interpretation of the results of the mechanical tests. Down to a film thickness of about 100 to 200 nm the yield strength increased for all film systems (passivated and unpassivated) and microstructures (polycrystalline and singlecrystalline). The influence of different interfaces was smaller than expected. This could be explained by a dislocation source model based on the nucleation of perfect dislocations. For polycrystalline films the film thickness as well as the grain size distribution had to be considered. For smaller film thicknesses the increase in flow stress was weaker and the deformation behavior changed because the nucleation of perfect dislocations became unfavorable. Instead, the film materials used alternative mechanisms to relieve the high stresses. For regular and homogeneous deformation the total strain was accommodated by the nucleation and motion of partial dislocations. If the deformation was localized due to initial cracks in a brittle interlayer or local delamination, dislocation plasticity was not effective enough to relieve the stress concentration and the films showed

  4. Immediate and delayed reactions to radiocontrast media: is there an allergic mechanism?

    Science.gov (United States)

    Brockow, Knut

    2009-08-01

    Radiocontrast media can cause immediate (1 hour) and nonimmediate (>1 hour) hypersensitivity reactions that remain unpredictable and a cause of concern for radiologists and cardiologists. Immediate hypersensitivity reactions resemble anaphylaxis, whereas nonimmediate ones clinically are predominated by exanthemas. Increasing evidence indicates that immediate reactions and nonimmediate skin exanthemas may be allergic reactions involving either contrast media-reactive IgE or T cells, respectively. Skin testing is a useful tool for the diagnosis of contrast media allergy. It may have an important role in the selection of a safe product in previous reactors, although validation data are still lacking. In vitro tests to search for contrast media-specific cell activation are currently under investigation.

  5. High Electrocatalytic Response of a Mechanically Enhanced NbC Nanocomposite Electrode Towards Hydrogen Evolution Reaction

    KAUST Repository

    Coy, Emerson; Yate, Luis; Valencia, Drochss P; Aperador, Willian; Siuzdak, Katarzyna; Torruella, Pau; Azanza, Eduardo; Estrade, Sonia; Iatsunskyi, Igor; Peiró , Francesca; Zhang, Xixiang; Tejada, Javier; Ziolo, Ronald F.

    2017-01-01

    Resistant and efficient electrocatalysts for hydrogen evolution reaction (HER) are desired to replace scarce and commercially expensive platinum electrodes. Thin film electrodes of metal-carbides are a promising alternative due to their reduced

  6. Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution.

    Science.gov (United States)

    Renata, Hans; Wang, Z Jane; Arnold, Frances H

    2015-03-09

    High selectivity and exquisite control over the outcome of reactions entice chemists to use biocatalysts in organic synthesis. However, many useful reactions are not accessible because they are not in nature's known repertoire. In this Review, we outline an evolutionary approach to engineering enzymes to catalyze reactions not found in nature. We begin with examples of how nature has discovered new catalytic functions and how such evolutionary progression has been recapitulated in the laboratory starting from extant enzymes. We then examine non-native enzyme activities that have been exploited for chemical synthesis, with an emphasis on reactions that do not have natural counterparts. Non-natural activities can be improved by directed evolution, thus mimicking the process used by nature to create new catalysts. Finally, we describe the discovery of non-native catalytic functions that may provide future opportunities for the expansion of the enzyme universe. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Generalization of the Activated Complex Theory of Reaction Rates. I. Quantum Mechanical Treatment

    Science.gov (United States)

    Marcus, R. A.

    1964-01-01

    In its usual form activated complex theory assumes a quasi-equilibrium between reactants and activated complex, a separable reaction coordinate, a Cartesian reaction coordinate, and an absence of interaction of rotation with internal motion in the complex. In the present paper a rate expression is derived without introducing the Cartesian assumption. The expression bears a formal resemblance to the usual one and reduces to it when the added assumptions of the latter are introduced.

  8. Bite of the cats: relationships between functional integration and mechanical performance as revealed by mandible geometry.

    Science.gov (United States)

    Piras, Paolo; Maiorino, Leonardo; Teresi, Luciano; Meloro, Carlo; Lucci, Federico; Kotsakis, Tassos; Raia, Pasquale

    2013-11-01

    Cat-like carnivorous mammals represent a relatively homogeneous group of species whose morphology appears constrained by exclusive adaptations for meat eating. We present the most comprehensive data set of extant and extinct cat-like species to test for evolutionary transformations in size, shape and mechanical performance, that is, von Mises stress and surface traction, of the mandible. Size and shape were both quantified by means of geometric morphometrics, whereas mechanical performance was assessed applying finite element models to 2D geometry of the mandible. Additionally, we present the first almost complete composite phylogeny of cat-like carnivorans for which well-preserved mandibles are known, including representatives of 35 extant and 59 extinct species of Felidae, Nimravidae, and Barbourofelidae. This phylogeny was used to test morphological differentiation, allometry, and covariation of mandible parts within and among clades. After taking phylogeny into account, we found that both allometry and mechanical variables exhibit a significant impact on mandible shape. We also tested whether mechanical performance was linked to morphological integration. Mechanical stress at the coronoid process is higher in sabertoothed cats than in any other clade. This is strongly related to the high degree of covariation within modules of sabertooths mandibles. We found significant correlation between integration at the clade level and per-clade averaged stress values, on both original data and by partialling out interclade allometry from shapes when calculating integration. This suggests a strong interaction between natural selection and the evolution of developmental and functional modules at the clade level.

  9. Non-equilibrium statistical mechanical approach for describing heavy ion reactions

    International Nuclear Information System (INIS)

    Sventek, J.S.

    1979-01-01

    With the availability of heavy-ion projectiles (A > 4) at low to intermediate energies (4 < E/A < 10), products showing various stages of relaxation for certain macroscopic variables (center-of-mass energy, orbital angular momentum, etc.) were produced in various reactions. The distributions for these macroscopic variables showed a correlation between the stage of relaxation reached and the net amount of mass transfer which had occurred in the reaction. There was also evidence that there was an asymmetry in the number of net transfers necessary for complete relaxation between stripping ad pickup reactions. A model for describing the time-evolution of these reactions has been formulated, the keystone of which is a master-equation approach for describing the time-dependence of the mass-asymmetry. This, coupled with deterministic equations of motion for the other macroscopic coordinates in the reaction lead to calculated distributions which provide an excellent qualitative description of these reactions, and, in some cases, quantitatively reproduce the experimental data quite well

  10. Kinetics and mechanisms of photoinduced electron-transfer reaction of zinc myoglobin

    International Nuclear Information System (INIS)

    Tsukahara, Keiichi; Asami, Satoko; Okada, Mihoko; Sakurai, Takeshi.

    1994-01-01

    Photoinduced electron transfer (ET) between zinc myoglobin (ZnPPMb) and a variety of quenchers, such as hexacyanoferrate(III)([Fe(CN) 6 ] 3- ) and hexaammineruthenium(III)(Ru(NH 3 ) 6 ] 3+ ions, cationic viologens, copper(II) protein (stellacyanin), and metmyoglobins, has been studied in aqueous degassed solutions. The excited triplet state of ZnPPMb( * ZnPPMb) was quenched by [Fe(CN) 6 ] 3- in a self-associated complex. Both quenching rate constant and formation constant of the self-associated complex decrease with increasing ionic strengths. The thermal backward ET reaction for this system was not observed; it is most likely that the backward ET step is much faster than the quenching reaction. All of the cationic quenchers examined in this work did not form a self-associated complex with * ZnPPMb, and the intermolecular quenching occurred. The thermal backward ET reaction was observed for these cationic quenchers. Not only photoinduced ET but also thermal backward ET reactions were insensitive to the driving force of the reactions, suggesting that the reactions are controlled by conformational changes in ZnPPMb. The quenching rate constants increase with increasing ionic strength for the cationic quenchers. The effects of poly-L-lysine hydrochloride, sodium poly-L-glutamate, and sodium cyclo-hexaphosphate were also examined. The active site of the * ZnPPMb toward both anionic and cationic quenchers is assumed to be the positively charged site near the heme pocket. (author)

  11. Understanding the mechanisms of solid-water reactions through analysis of surface topography.

    Science.gov (United States)

    Bandstra, Joel Z; Brantley, Susan L

    2015-12-01

    The topography of a reactive surface contains information about the reactions that form or modify the surface and, therefore, it should be possible to characterize reactivity using topography parameters such as surface area, roughness, or fractal dimension. As a test of this idea, we consider a two-dimensional (2D) lattice model for crystal dissolution and examine a suite of topography parameters to determine which may be useful for predicting rates and mechanisms of dissolution. The model is based on the assumption that the reactivity of a surface site decreases with the number of nearest neighbors. We show that the steady-state surface topography in our model system is a function of, at most, two variables: the ratio of the rate of loss of sites with two neighbors versus three neighbors (d(2)/d(3)) and the ratio of the rate of loss of sites with one neighbor versus three neighbors (d(1)/d(3)). This means that relative rates can be determined from two parameters characterizing the topography of a surface provided that the two parameters are independent of one another. It also means that absolute rates cannot be determined from measurements of surface topography alone. To identify independent sets of topography parameters, we simulated surfaces from a broad range of d(1)/d(3) and d(2)/d(3) and computed a suite of common topography parameters for each surface. Our results indicate that the fractal dimension D and the average spacing between steps, E[s], can serve to uniquely determine d(1)/d(3) and d(2)/d(3) provided that sufficiently strong correlations exist between the steps. Sufficiently strong correlations exist in our model system when D>1.5 (which corresponds to D>2.5 for real 3D reactive surfaces). When steps are uncorrelated, surface topography becomes independent of step retreat rate and D is equal to 1.5. Under these conditions, measures of surface topography are not independent and any single topography parameter contains all of the available mechanistic

  12. Reaction mechanism of ethylene glycol decomposition on Pt model catalysts: A density functional theory study

    International Nuclear Information System (INIS)

    Lv, Cun-Qin; Yang, Bo; Pang, Xian-Yong; Wang, Gui-Chang

    2016-01-01

    Highlights: • DFT calculations were performed to study the ethylene glycol decomposition on Pt. • The final products are CO and H_2 on Pt(111), (100) and (211). • Ethylene glycol decomposition on Pt(111) undergoes via initial O−H bond scission and followed by C−H bond cleavage. • Ethylene glycol decomposition proceeds via initial O−H bond scission and followed by O−H bond cleavage on Pt(100)/(211). - Abstract: Understanding and controlling bond beak sequence is important in catalytic processes. The DFT-GGA method combined with slab model was performed to study the ethylene glycol decomposition on various Pt model catalysts such as close-packed Pt(111), stepped Pt(211) and a more open one, Pt(100). Calculation results show that the adsorption energies of ethylene glycol and other decomposition species depend on the coordination number of surface atom, that is, low coordination number correspond to high adsorption energy. Moreover, it was found that final products of ethylene glycol decomposition are CO and H_2 on all model catalysts, but the reaction mechanism varies: On Pt(111), the first step is O−H bond scission, followed by C−H bond cleavage, namely C_2H_6O_2 → HOCH_2CH_2O + H → HOCH_2CHO + 2H→ HOCH_2CO +3H → OCH_2CO + 4H → OCHCO + 5H → CO + HCO + 5H → 2CO + 6H→ 2CO + 3H_2; On Pt(211) and Pt(100), however, it is a second O−H bond cleavage that follows the initial O−H bond scission, that is, C_2H_6O_2 → HOCH_2CH_2O + H → OCH_2CH_2O + 2H → OCHCH_2O + 3H → OCHCHO + 4H → 2HCO + 4H → 2CO + 6H → 2CO + 3H_2  on Pt(211), and C_2H_6O_2 →HOCH_2CH_2O+ H → OCH_2CH_2O + 2H→OCHCH_2O+3H→OCCH_2O+4H→CO+H_2CO+4H→CO+HCO+5H→2CO+6H→2CO+3H_2 on Pt(100) For the catalytic order of ethylene glycol to form H_2, it may be determined based on the rate-controlling step, and it is Pt(111) > Pt(211) > Pt(100).

  13. Effects of neutral sodium hydrogen phosphate on setting reaction and mechanical strength of hydroxyapatite putty.

    Science.gov (United States)

    Ishikawa, K; Miyamoto, Y; Takechi, M; Ueyama, Y; Suzuki, K; Nagayama, M; Matsumura, T

    1999-03-05

    The setting reaction and mechanical strength in terms of diametral tensile strength (DTS) of hydroxyapatite (HAP) putty made of tetracalcium phosphate, dicalcium phosphate anhydrous, and neutral sodium hydrogen phosphate (Na1.8H1.2PO4) solution containing 8 wt % sodium alginate were evaluated as a function of the Na1.8H1.2PO4 concentration. In one condition, HAP putty was placed in an incubator kept at 37 degrees C and 100% relative humidity. In the other condition, immediately after mixing HAP putty was immersed in serum kept at 37 degrees C. Longer setting times and lower DTS values were observed when HAP putty was immersed in serum regardless of the Na1.8H1.2PO4 concentration. The setting times of the HAP putty in both conditions became shorter with an increase in the Na1. 8H1.2PO4 concentration, reaching approximately 7-13 min when the Na1. 8H1.2PO4 concentration was 0.6 mol/L or higher. The DTS value of HAP putty was relatively constant (10 MPa) regardless of the Na1.8H1. 2PO4 concentration (0.2-1.0 mol/L) when HAP putty was kept in an incubator. In contrast, when HAP putty was immersed in serum, the DTS value was dependent on the Na1.8H1.2PO4 concentration. It increased with the Na1.8H1.2PO4 concentration and reached approximately 5 MPa when the Na1.8H1.2PO4 concentration was 0.6 mol/L, after which it showed a relatively constant DTS value. We therefore would recommend a HAP putty that uses 0.6 mol/L Na1.8H1. 2PO4 since at that concentration the putty's setting time (approximately 10 min) is proper for clinical use and it shows good DTS value (approximately 5 MPa) even when it is immersed in serum immediately after mixing. Copyright 1999 John Wiley & Sons, Inc.

  14. Theoretical study of coupling mechanisms between oxygen diffusion, chemical reaction, mechanical stresses in a solid-gas reactive system

    International Nuclear Information System (INIS)

    Creton, N.; Optasanu, V.; Montesin, T.; Garruchet, S.

    2008-01-01

    This paper offers a study of oxygen dissolution into a solid, and its consequences on the mechanical behaviour of the material. In fact, mechanical strains strongly influence the oxidation processes and may be, in some materials, responsible for cracking. To realize this study, mechanical considerations are introduced into the classical diffusion laws. Simulations were made for the particular case of uranium dioxide, which undergoes the chemical fragmentation. According to our simulations, the hypothesis of a compression stress field into the oxidised UO 2 compound near the internal interface is consistent with some oxidation mechanisms of oxidation experimentally observed. More generally, this work will be extended to the simulation to an oxide layer growth on a metallic substrate. (authors)

  15. Kinetics and mechanisms of iron redox reactions in silicate melts: The effects of temperature and alkali cations

    Energy Technology Data Exchange (ETDEWEB)

    Magnien, V.; Pinet, O. [CEA VALRHO, SCDV/LEBV, F-30207 Bagnols Sur Ceze, (France); Magnien, V.; Neuville, D. R.; Roux, J.; Richet, P. [IPGP, CNRS, Physique des Mineraux et Magmas, F-75252 Paris 05, (France); Cormier, L. [Univ Paris 06, IMPMC, F-75015 Paris, (France); Hazemann, J. L. [CNRS, Inst Neel, F-38043 Grenoble, (France); De Ligny, D. [Univ Lyon 1, LMLC, CNRS, UMR 5620, F-69622 Villeurbanne, (France); Pascarelli, S. [European Synchrotron Radiat Facil, F-38043 Grenoble, (France); Vickridge, I. [Univ Paris 06, INSP, F-75015 Paris, (France)

    2008-07-01

    The kinetics and the mechanisms of iron redox reactions in molten Fe-bearing pyroxene compositions have been investigated by Raman spectroscopy and X-ray absorption Near Edge Structure (XANES) experiments at the iron K-edge. The former experiments have been made only near the glass transition whereas the latter have also been performed from about 1300 to 2100 K. The same kinetics are observed with both techniques. They are described by characteristic times that depend primarily on temperature and not on the initial redox state. At high temperatures, where both kinds of reactions could be investigated, these times are similar for oxidation and reduction. From these characteristic times we have calculated as a function of temperature and composition a parameter termed effective redox diffusivity. For a given melt, the diffusivities follow two distinct Arrhenius laws, which indicate that the mechanisms of the redox reaction are not the same near the glass transition and at high temperatures. As is now well established, diffusion of divalent cations is the dominant mechanism at low temperatures but the enhanced kinetics observed for alkali-bearing melts indicate that Li{sup +} and Na{sup +} also participate in ionic transport. At super-liquidus temperatures, in contrast, diffusion of oxygen represents the dominant mechanism. (authors)

  16. The mechanics of bacterial cluster formation on plant leaf surfaces as revealed by bioreporter technology

    NARCIS (Netherlands)

    Tecon, R.; Leveau, J.H.J.

    2012-01-01

    Bacteria that colonize the leaves of terrestrial plants often occur in clusters whose size varies from a few to thousands of cells. For the formation of such bacterial clusters, two non-mutually exclusive but very different mechanisms may be proposed: aggregation of multiple cells or clonal

  17. Fungicidal mechanisms of cathelicidins LL-37 and CATH-2 revealed by live-cell imaging

    NARCIS (Netherlands)

    Ordonez Alvarez, Soledad; Amarullah, Ilham H; Wubbolts, Richard W; Veldhuizen, Edwin J A; Haagsman, Henk P

    2014-01-01

    Antifungal mechanisms of action of two cathelicidins, chicken CATH-2 and human LL-37, were studied and compared with the mode of action of the salivary peptide histatin 5 (Hst5). Candida albicans was used as a model organism for fungal pathogens. Analysis by live-cell imaging showed that the

  18. Aromatic C-Nitroso Compounds and Their Dimers: A Model for Probing the Reaction Mechanisms in Crystalline Molecular Solids

    Directory of Open Access Journals (Sweden)

    Ivana Biljan

    2017-12-01

    Full Text Available This review is focused on the dimerization and dissociation of aromatic C-nitroso compounds and their dimers, the reactions that could be used as a convenient model for studying the thermal organic solid-state reaction mechanisms. This molecular model is simple because it includes formation or breaking of only one covalent bond between two nitrogen atoms. The crystalline molecular solids of nitroso dimers (azodioxides dissociate by photolysis under the cryogenic conditions, and re-dimerize by slow warming. The thermal re-dimerization reaction is examined under the different topotactic conditions in crystals: disordering, surface defects, and phase transformations. Depending on the conditions, and on the molecular structure, aromatic C-nitroso compounds can associate to form one-dimensional polymeric structures and are able to self-assemble on gold surfaces.

  19. Ex vivo stretch reveals altered mechanical properties of isolated dystrophin-deficient hearts.

    Directory of Open Access Journals (Sweden)

    Matthew S Barnabei

    Full Text Available Duchenne muscular dystrophy (DMD is a progressive and fatal disease of muscle wasting caused by loss of the cytoskeletal protein dystrophin. In the heart, DMD results in progressive cardiomyopathy and dilation of the left ventricle through mechanisms that are not fully understood. Previous reports have shown that loss of dystrophin causes sarcolemmal instability and reduced mechanical compliance of isolated cardiac myocytes. To expand upon these findings, here we have subjected the left ventricles of dystrophin-deficient mdx hearts to mechanical stretch. Unexpectedly, isolated mdx hearts showed increased left ventricular (LV compliance compared to controls during stretch as LV volume was increased above normal end diastolic volume. During LV chamber distention, sarcomere lengths increased similarly in mdx and WT hearts despite greater excursions in volume of mdx hearts. This suggests that the mechanical properties of the intact heart cannot be modeled as a simple extrapolation of findings in single cardiac myocytes. To explain these findings, a model is proposed in which disruption of the dystrophin-glycoprotein complex perturbs cell-extracellular matrix contacts and promotes the apparent slippage of myocytes past each other during LV distension. In comparison, similar increases in LV compliance were obtained in isolated hearts from β-sarcoglycan-null and laminin-α(2 mutant mice, but not in dysferlin-null mice, suggesting that increased whole-organ compliance in mdx mice is a specific effect of disrupted cell-extracellular matrix contacts and not a general consequence of cardiomyopathy via membrane defect processes. Collectively, these findings suggest a novel and cell-death independent mechanism for the progressive pathological LV dilation that occurs in DMD.

  20. Reaction mechanism and nuclear correlations study by low energy pion double charge exchange

    International Nuclear Information System (INIS)

    Weinfeld, Z.

    1993-06-01

    In pion double-charge-exchange (DCX) reactions, a positive (negative) pion is incident on a nucleus and a negative (positive) pion emerges. These reactions are of fundamental interest since the process must involve at least two nucleons in order to conserve charge. Although two nucleon processes are present in many reactions they are usually masked by the dominant single nucleon processes. DCX is unique in that respect since it is a two nucleon process in lowest order and thus may be sensitive to two-nucleon correlations. Measurements of low energy pion double-charge-exchange reactions to the double-isobaric-analog-state (DIAS) and ground-state (GS) of the residual nucleus provide new means for studying nucleon-nucleon correlations in nuclei. At low energies (T π 7/2 shell at energies ranging from 25 to 65 MeV. Cross sections were measured on 42,44,48 Ca, 46,50 Ti and 54 Fe. The calcium isotopes make a good set of nuclei on which to study the effects of correlations in DCX reactions