01741nas a2200181 4500008004100000022001400041245011500055210006900170260007600239300001200315490000700327520100800334653002601342653002701368100002001395700001701415856012701432 2012 eng d a0192-865100aNew approximate method for the stochastic simulation of chemical systems: the representative reaction approach0 aNew approximate method for the stochastic simulation of chemical aCOMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USAbWILEY-BLACKWELLcJAN a276-2850 v333 a

We have developed two new approximate methods for stochastically simulating chemical systems. The methods are based on the idea of representing all the reactions in the chemical system by a single reaction, i.e., by the representative reaction approach (RRA). Discussed in the article are the concepts underlying the new methods along with flowchart with all the steps required for their implementation. It is shown that the two RRA methods {with the reaction \$ 2A \textbackslashrightarrow B \$ as the representative reaction (RR)} perform creditably with regard to accuracy and computational efficiency, in comparison to the exact stochastic simulation algorithm (SSA) developed by Gillespie and are able to successfully reproduce at least the first two moments of the probability distribution of each species in the systems studied. As such, the RRA methods represent a promising new approach for stochastically simulating chemical systems. (C) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012

10aapproximate algorithm10aStochastic simulations1 aKadam, Shantanu1 aVanka, Kumar uhttps://library.ncl.res.in/content/new-approximate-method-stochastic-simulation-chemical-systems-representative-reaction-001119nas a2200169 4500008004100000022001400041245009500055210006900150260007100219300001200290490000700302520045700309100002400766700002000790700001700810856012200827 2012 eng d a0020-166900aTheoretical study of metal-metal cooperativity in the homogeneous water gas shift reaction0 aTheoretical study of metalmetal cooperativity in the homogeneous a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcJAN a377-3850 v513 a

The possibility of metal-metal cooperativity in improving the yield of the homogeneous water gas shift reaction (WGSR) has been investigated through full quantum mechanical density functional theory calculations. The calculations indicate that bimetallic catalysts would be likely to be more highly active than mononuclear metal-based catalysts for the WGSR. The results have implications for the design of improved WGSR catalysts in the future.

1 aKuriakose, Nishamol1 aKadam, Shantanu1 aVanka, Kumar uhttps://library.ncl.res.in/content/theoretical-study-metal-metal-cooperativity-homogeneous-water-gas-shift-reaction-002217nas a2200241 4500008004100000022001400041245014100055210006900196260006700265300001200332490000700344520126700351653002401618653002701642653002401669653002401693653002601717653003701743653002701780100002001807700001701827856013101844 2013 eng d a0192-865100aSolving the problem of negative populations in approximate accelerated stochastic simulations using the representative reaction approach0 aSolving the problem of negative populations in approximate accel a111 RIVER ST, HOBOKEN 07030-5774, NJ USAbWILEY-BLACKWELLcFEB a394-4040 v343 a

Methods based on the stochastic formulation of chemical kinetics have the potential to accurately reproduce the dynamical behavior of various biochemical systems of interest. However, the computational expense makes them impractical for the study of real systems. Attempts to render these methods practical have led to the development of accelerated methods, where the reaction numbers are modeled by Poisson random numbers. However, for certain systems, such methods give rise to physically unrealistic negative numbers for species populations. The methods which make use of binomial variables, in place of Poisson random numbers, have since become popular, and have been partially successful in addressing this problem. In this manuscript, the development of two new computational methods, based on the representative reaction approach (RRA), has been discussed. The new methods endeavor to solve the problem of negative numbers, by making use of tools like the stochastic simulation algorithm and the binomial method, in conjunction with the RRA. It is found that these newly developed methods perform better than other binomial methods used for stochastic simulations, in resolving the problem of negative populations. (C) 2012 Wiley Periodicals, Inc.

10aapproximate methods10abinomial distributions10aGillespie algorithm10aKinetic Monte Carlo10aPoisson distributions10arepresentative reaction approach10aStochastic simulations1 aKadam, Shantanu1 aVanka, Kumar uhttps://library.ncl.res.in/content/solving-problem-negative-populations-approximate-accelerated-stochastic-simulations-using-001787nas a2200157 4500008004100000022001400041245011900055210006900174260011000243300001600353490000600369520108900375100002001464700001701484856012801501 2014 eng d a2046-206900aAccounting of noise to solve the problem of negative populations in approximate accelerated stochastic simulations0 aAccounting of noise to solve the problem of negative populations aTHOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLANDbROYAL SOC CHEMISTRYcOCT a58127-581360 v43 a

The advent of different approximate accelerated stochastic simulation methods has helped considerably in reducing the computational load of the exact simulation algorithms. However, along with the reduction in the computational load comes the risk of driving the molecular numbers to the regime of negative numbers during the simulations. Over the years, various methods have been developed in order to solve the problem by using different strategies. Some methods have employed binomial numbers to model the reactions, while others have tried the partitioning of the reaction network. In this manuscript, we have proposed a new approach where the noise inherent in the choice of the number of firings of a given reaction during a time step is taken into account. This idea of noise accounting is used in conjunction with the accelerated stochastic method: the Representative Reaction Approach (RRA). It is found that the new method is successful at solving the problem of negative numbers, and compares very favorably with other state-of-the-art stochastic simulation methods.

1 aKadam, Shantanu1 aVanka, Kumar uhttps://library.ncl.res.in/content/accounting-noise-solve-problem-negative-populations-approximate-accelerated-stochastic-0