Source Codes For Statistical Thermodynamics and Stochastic Kinetics
We make codes available for conducting simple molecular simulations and simple stochastic kinetic simulations. The codes and the underlying theories are described in the textbook "Statistical Thermodynamics and Stochastic Kinetics: An Introduction for Engineers", published by Cambridge University Press.
Here are short excerts from the book: "Statistical mechanics is a powerful and elegant theory, at whose core lie the concepts of phase space, probability distributions and partition functions. With these concepts, statistical mechanics explains physical properties, such entropy, and physical phenomena, such as irreversibility, all in terms of microscopic properties."
"The invention of digital computers ushered a new era of computational methods that numerically determine the partition function, rendering feasible the connection between microscopic Hamiltonians and thermodynamic behavior for complex systems. "
"We will present computer simulations as a natural extension of statistical mechanical theories. We will detail the methodological steps and provide a clear sequence of numerical steps, algorithms and computer codes to implement Monte Carlo and molecular dynamics simulations of simple systems."
Statistical Thermodynamic Codes
We provide codes for conducting molecular dynamics and Monte Carlo simulations. The simulated systems are of monoatomic Lennard-Jones particles. Molecular dynamics simulations are conducted with moldyn in the NVE ensemble. Monte Carlo simulations are conducted with mmc-codes in the NVT ensemble.
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Stochastic Kinetic Codes
We provide codes for conducting stochastic and hybrid simulations of reacting networks away from the thermodynamic limit. The codes come in two flavors: one with a MATLAB GUI for setting up the reaction networks and another one with a MS Windows GUI for setting up the networks. The algorithm is the same in both for simulating the reaction networks and is based on the open source code Hybrid Stochastic Simulations for Supercomputers (Hy3S is available on hysss.sourceforge.net). The MS Windows version has evolved from the open source project SynBioSS (www.synbioss.org).
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