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In order to investigate transport properties of molecular solutions on mesoscopic scales, we use the fluctuation-dissipation theorem and velocity and noise autocorrelation to determine the diffusion constant of two simulated solutions of particles interacting through Lennard-Jones potentials. This thesis describes classical transport theories which are valid for macroscopic diffusion, and includes a discussion of the nature of the force on solute particles which are comparable in size to solvent particles (we call diffusion in this limit ‘mesoscopic diffusion’). Next, it discusses transport theories of systems in this limit, and methods of determining their diffusion constant by extracting the velocity autocorrelation of particles in simulations. Finally, it includes results from a molecular dynamics simulation with GROMACS, and the details of preparing and running a force-field dependent simulation on MATLAB. The MATLAB simulation of liquid methyl red (or, otherwise, methyl red in a solvent whose molecules have mass and size properties exactly like itself) gives a value for the diffusion constant to be 7 1 10 . This is value is significantly different from several experimentally determined diffusion coefficients of methyl red in organic solvents.
Tuli, Santona, "THE ROLE OF MOLECULAR DYNAMICS SIMULATIONS IN INVESTIGATING DIFFUSION ON MESOSCOPIC SCALES" (2013). Physics & Astronomy Honors Theses. 8.
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