Vlachos Group Github Code Base

*Click the title of the file to download.


Reaction rate calculation and unit conversion
A pdf summary of our methodology calculating reaction rates as well as converting units in our reaction engineering research.


Multiscale sensitivity analysis MATLAB code, Example file 1 2 3
MATLAB scripts for simulating a model chemical reaction system with two time scales. Sensitivity analysis is built into the algorithm. Files are separated into 4 portions. Extract the MSA code at a desired path, and extract example files in example_data folder in the desired path.
A. Hashemi, M. Nunez, P. Plechac, and D. G. Vlachos, Stochastic Averaging and Sensitivity Analysis for Two Scale Reaction Networks, Journal of Chemical Physics 144, 074104 (2016).
FORTRAN files for likelihood ration sensitivity analysis in Zacros
Fortran files which introduce parametric sensitivity analysis capabilities into the Zacros kinetic Monte Carlo code available at
M. Nunez, and D. G. Vlachos, Steady State Likelihood Ratio Sensitivity Analysis for Stiff Kinetic Monte Carlo Simulations, Journal of Chemical Physics 142(4), 7 (2015).
Group additivity for furanic compounds on Pd(111)
Download the R.I.N.G and Matlab codes for fast estimation of therochemical properties of furanic compounds on Pd(111) using group additivity. Instruction included as a pdf file.
V. Vorotnikov, S. Wang and D. G. Vlachos, Group Additivity for Estimating Thermochemical Properties of Furanic Compounds on Pd(111), Ind. Eng. Chem. Res. 53(30), 11929-11938 (2014)
Stochastic Simulation Code
Download the windows executable codes for the binomial and Poisson τ-leap for a well-mixed system, and MATLAB codes that generates necessary inputs for the executable software.
Chatterjee, D. G. Vlachos and M. A. Katsoulakis, Binomial distribution based t-leap accelerated stochastic simulation, Journal of Chemical Physics 122, 0241121-0241126 (2005).

Supplementary Information