The Experts below are selected from a list of 144 Experts worldwide ranked by ideXlab platform
John Ross - One of the best experts on this subject based on the ideXlab platform.
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from the determination of Complex Reaction Mechanisms to systems biology
Annual Review of Biochemistry, 2008Co-Authors: John RossAbstract:This review presents several methods of determining Complex chemical Reaction Mechanisms and their functions. One method is based on correlation functions of measured time series of concentrations of chemical species, another is on measurements of temporal responses of concentrations to various perturbations of arbitrary magnitude, the third deals with the analysis of oscillatory systems, and the fourth describes the use of genetic algorithms. All methods are applicable to chemical, biochemical, and biological Reaction systems and to genetic networks. The methods depend on the design of appropriate experiments for the whole system and corresponding theories for interpretation that lead to information on the causal chemical connectivity of species, Reaction pathways, Reaction Mechanisms, control centers in the system, and functions of the system. The first three methods require no assumption of a model or hypothesis, nor extensive calculations, unlike the interpretation of measurements made on a gene network at only one time. The methods offer advantageous approaches to systems biology.
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determination of Complex Reaction Mechanisms analysis of chemical biological and genetic networks
2005Co-Authors: John RossAbstract:We present several methods of determining, not guessing, Complex chemical Reaction Mechanisms and their functions. One method is based on the theory of correlation functions of measured time series of concentrations of chemical species; another is on measurements of temporal responses of concentrations to various perturbations of arbitrary magnitude; a third deals with the analysis of oscillatory systems; a fourth is on the use of genetic algorithms to determine functions of chemical Reaction networks. All methods are applicable to chemical, biochemical, and biological Reaction systems and to genetic networks and systems biology. The methods depend on the design of appropriate experiments on the whole system and corresponding theories for interpretation that lead to information on the causal chemical connectivity of species, on Reaction pathways, on Reaction Mechanisms, on control centers in the system, and on functions of the system. The first three methods require no assumption of a model or hypothesis, nor extensive calculations, unlike the interpretation of measurements made on a gene network at only one time.
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new approaches to the deduction of Complex Reaction Mechanisms
Accounts of Chemical Research, 2003Co-Authors: John RossAbstract:The formulation of a macroscopic Reaction mechanism, the sequence of elementary Reaction steps by which reactants are turned into products, is difficult. We review several new methods of determining the causal connectivity of chemical species, the Reaction pathway (the sequence of chemical species), and the Reaction Mechanisms of Complex Reaction systems from prescribed measurements and theories.
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nonlinear kinetics and new approaches to Complex Reaction Mechanisms
Annual Review of Physical Chemistry, 1999Co-Authors: John Ross, Marcel Ovidiu VladAbstract:▪ Abstract This paper reviews recent developments in the field of nonlinear chemical kinetics. Five topics are dealt with: (a) new approaches to Complex Reaction Mechanisms, stoichiometric network analysis, classification of chemical oscillators and formulation of their Mechanisms by deduction from experiments, and correlation metric construction of Reaction pathways from measurements; (b) thermodynamic and stochastic theory of nonequilibrium processes, the eikonal approximation, the evaluation of stochastic potentials, experimental tests of the thermodynamic and stochastic theory of relative stability, and fluctuation-dissipation relations in nonequilibrium chemical systems; (c) chemical kinetics and cellular automata and lattice gas automata; (d) theoretical approaches and experimental studies of stochastic resonance in chemical kinetics; and (e) rate processes in disordered systems, stochastic Liouville equations, stretched exponential relaxation in disordered systems, and universality classes for rate...
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toward a systematic determination of Complex Reaction Mechanisms
The Journal of Physical Chemistry, 1993Co-Authors: Tim Chevalier, Igor Schreiber, John RossAbstract:Given a Complex chemical Reaction with an unknown or a partially known mechanism, we examine the possibility of determining the essential parts of the mechanism by a number of experimental methods, all of which rely upon the experimental evaluation of the stationary-state Jacobian matrix elements (JMEs). If the response by all species to a pulse perturbation of one of the species can be measured, then it is possible to determine all of the JMEs. A different experimental method, a concentration shift experiment, relies on measuring the change of steady-state concentrations in a chemical reactor after the inflow of each species has been altered. Another technique employs the induction (or cessation) of oscillations caused by a delayed feedback imposed on an inflow species
John E Pearson - One of the best experts on this subject based on the ideXlab platform.
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on imposing detailed balance in Complex Reaction Mechanisms
Biophysical Journal, 2006Co-Authors: Jin Yang, William J Bruno, William S Hlavacek, John E PearsonAbstract:The principle of microscopic reversibility implies detailed balance—the statement that, at thermodynamic equilibrium, each individual Reaction is balanced. That is, at equilibrium each individual Reaction occurs with equal forward and backward fluxes. A Reaction system that satisfies detailed balance does not consume or dissipate free energy at thermodynamic equilibrium (1). Although Reaction systems with no closed loops (or acyclic systems) always satisfy detailed balance, most Complex Reaction schemes involve Reaction cycles, and satisfying detailed balance requires that the product of equilibrium constants around a Reaction cycle equals one. Colquhoun et al. (2) recently presented methods to impose detailed balance on Complex Reaction Mechanisms, such as ion channel kinetic schemes modeled with finite Markov chains. The methods rely on finding a fundamental cycle basis with respect to a spanning tree of a graph representing the Reaction topology. In this comment, we discuss an alternative method that balances the forward and backward fluxes of each reversible Reaction and does not require direct consideration of Reaction cycles. The method will be discussed for single molecule dynamics and mass-action kinetics. We will also discuss techniques for identifying a minimal Reaction network for imposing detailed balance.
Keiji Morokuma - One of the best experts on this subject based on the ideXlab platform.
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artificial force induced Reaction method for systematic determination of Complex Reaction Mechanisms
Chemical Record, 2016Co-Authors: W M C Sameera, Akhilesh K Sharma, Satoshi Maeda, Keiji MorokumaAbstract:Nowadays, computational studies are very important for the elucidation of Reaction Mechanisms and selectivity of Complex Reactions. However, traditional computational methods usually require an estimated Reaction path, mainly driven by limited experimental implications, intuition, and assumptions of stationary points. However, the artificial force induced Reaction (AFIR) method in the global Reaction route mapping (GRRM) strategy can be used for unbiased and automatic Reaction path searches for Complex Reactions. In this account, we highlight applications of the AFIR method to a variety of Reactions (organic, organometallic, enzymatic, and photochemical) of Complex molecular systems. In addition, the AFIR method has been successfully used to rationalise the origin of stereo- and regioselectivity. The AFIR method can be applied from small to large molecular systems, and will be a very useful tool for the study of Complex molecular problems in many areas of chemistry, biology, and material sciences.
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toward predicting full catalytic cycle using automatic Reaction path search method a case study on hco co 3 catalyzed hydroformylation
Journal of Chemical Theory and Computation, 2012Co-Authors: Satoshi Maeda, Keiji MorokumaAbstract:Toward systematic prediction of Reaction pathways in Complex chemical Reaction systems by quantum chemical calculations, a new automatic Reaction path search approach has been proposed on the basis of the artificial force induced Reaction (AFIR) method [J. Chem. Theory Comput.2011, 7, 2335–2345.]. We demonstrate in this Letter that this approach enabled semiautomatic determination of the full catalytic cycle of the HCo(CO)3-catalyzed hydroformylation. The search was fully systematic; no initial guess was required concerning the entire Reaction mechanism as well as each transition-state structure. This approach opens the door to nonempirical prediction of Complex Reaction Mechanisms involving multiple steps in multiple pathways, such as full cycles of catalytic Reactions.
Dean Hoffman - One of the best experts on this subject based on the ideXlab platform.
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systematic application of the principle of detailed balancing to Complex homogeneous chemical Reaction Mechanisms
Journal of Physical Chemistry A, 2019Co-Authors: David M Stanbury, Dean HoffmanAbstract:It is not uncommon for proposed Complex Reaction Mechanisms to violate the principle of detailed balancing. Here, we draw attention to three ways in which such violations can occur: reversible Reaction loops where the rate constants do not attain closure, illegal loops, and reversible steps having rate equations in the forward and reverse directions that are inconsistent with the equilibrium expressions. We present two simple methods to test whether a proposed mechanism is consistent with the first two aspects of the principle of detailed balancing. Both methods are restricted to closed homogeneous isothermal Reactions having Mechanisms that consist of stoichiometrically balanced Reaction steps. The first method is restricted to Mechanisms in which all Reaction steps are reversible; values of Δf G° are assigned to all Reaction species, equilibrium constants are then computed for all steps, and all rate constants for elementary steps are constrained by the relationship Keq = kf/ kr. The second method is applicable to Mechanisms that can consist of a series of reversible and/or irreversible Reaction steps. One first examines the subset of reversible steps to determine whether any of these steps are stoichiometrically equivalent to a combination of any of the other steps. If so, the forward and reverse rate expressions must yield equilibrium constants that are in agreement with the stoichiometric relationships. Next, the complete set of steps is examined to look for "illegal Reaction loops". Both of these procedures are performed by constructing matrices that represent the stoichiometries of the various Reaction steps and then performing row reductions to identify basis sets of loops. A method based on linear programming is described that determines whether a mechanism contains any illegal loops. These methods are applied in the analysis of several published Reaction Mechanisms.
Jin Yang - One of the best experts on this subject based on the ideXlab platform.
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on imposing detailed balance in Complex Reaction Mechanisms
Biophysical Journal, 2006Co-Authors: Jin Yang, William J Bruno, William S Hlavacek, John E PearsonAbstract:The principle of microscopic reversibility implies detailed balance—the statement that, at thermodynamic equilibrium, each individual Reaction is balanced. That is, at equilibrium each individual Reaction occurs with equal forward and backward fluxes. A Reaction system that satisfies detailed balance does not consume or dissipate free energy at thermodynamic equilibrium (1). Although Reaction systems with no closed loops (or acyclic systems) always satisfy detailed balance, most Complex Reaction schemes involve Reaction cycles, and satisfying detailed balance requires that the product of equilibrium constants around a Reaction cycle equals one. Colquhoun et al. (2) recently presented methods to impose detailed balance on Complex Reaction Mechanisms, such as ion channel kinetic schemes modeled with finite Markov chains. The methods rely on finding a fundamental cycle basis with respect to a spanning tree of a graph representing the Reaction topology. In this comment, we discuss an alternative method that balances the forward and backward fluxes of each reversible Reaction and does not require direct consideration of Reaction cycles. The method will be discussed for single molecule dynamics and mass-action kinetics. We will also discuss techniques for identifying a minimal Reaction network for imposing detailed balance.