Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates

An efficient simulation algorithm for chemical kinetic systems with disparate rates is proposed. This new algorithm is quite general, and it amounts to a simple and seamless modification of the classical stochastic simulation algorithm (SSA), also known as the Gillespie [J. Comput. Phys. 22, 403 (1976); J. Phys. Chem. 81, 2340 (1977)] algorithm. The basic idea is to use an outer SSA to simulate the slow processes with rates computed from an inner SSA which simulates the fast reactions. Averaging theorems for Markov processes can be used to identify the fast and slow variables in the system as well as the effective dynamics over the slow time scale, even though the algorithm itself does not rely on such information. This nested SSA can be easily generalized to systems with more than two separated time scales. Convergence and efficiency of the algorithm are discussed using the established error estimates and illustrated through examples.     

Comment on "Quasirelativistic theory equivalent to fully relativistic theory" [J. Chem. Phys. 123, 241102 (2005)

The connection between the exact quasirelativistic approach developed in the title reference [W. Kutzelnigg and W. Liu, J. Chem. Phys. 123, 241102 (2005)] and the method of elimination of the small component in matrix form developed previously by Dyall is explicitly worked out. An equation that links Hermitian and non-Hermitian formulations of the exact quasirelativistic theory is derived. Besides establishing a kinship between the existing formulations, the proposed equation can be employed for the derivation of new formulations of the exact quasirelativistic theory.     

Comment on "Dynamic ion association in aqueous solutions of sulfate" [J. Chem. Phys. 123, 034508 (2005)

The "dynamic exchange" model of ion association proposed by Watanabe and Hamaguchi, [J. Chem. Phys.123, 034508 (2005)] for aqueous solutions of MgSO4 is shown to be inconsistent with the extensive information available from Raman, relaxation, and thermodynamic studies, all of which can be explained by the Eigen equilibrium model.     

Comment on "MMM1D: A method for calculating electrostatic interactions in one-dimensional periodic geometries" [J. Chem. Phys. 123, 144103 (2005)

This comment gives an alternative derivation of the MMM1D method reported by Arnold and Holm [J. Chem. Phys.123, 144103 (2005)]. Moreover, several errors in expressions presented in the cited paper are identified.     

Comment on "Revised electron affinity of SF6 from kinetic data" [J. Chem. Phys. 136, 121102 (2012)

The adiabatic electron affinity (AEA) of SF(6) has been calculated near the relativistic CCSDT(Q) basis set limit. Our best theoretical value (1.0340 ±?0.03 eV) is in excellent agreement with the recently revised experimental value of 1.03?±?0.05 eV reported by Troe et al. [J. Chem. Phys. 136, 121102 (2012)]. While our best nonrelativistic, clamped-nuclei, valence CCSD(T) basis set limit value of 0.9058 eV is in good accord with the previously reported CCSD(T)/CBS values, to obtain an accurate AEA, several additional contributions need to be taken into account. The most important one is scalar-relativistic effects (0.0839 eV), followed by inner-shell correlation (0.0216 eV) and post-CCSD(T) correlation effects (0.0248 eV), the latter almost entirely due to connected quadruple excitations. The diagonal Born-Oppenheimer correction is an order of magnitude less important at -0.0022 eV.