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Full-Text Articles in Biological and Chemical Physics
Genetic Programming For Multitimescale Modeling, Kumara Sastry, Duane D. Johnson, David E. Goldberg, Pascal Bellon
Genetic Programming For Multitimescale Modeling, Kumara Sastry, Duane D. Johnson, David E. Goldberg, Pascal Bellon
Duane D. Johnson
A bottleneck for multitimescale thermally activated dynamics is the computation of the potential energy surface. We explore the use of genetic programming (GP) to symbolically regress a mapping of the saddle-point barriers from only a few calculated points via molecular dynamics, thereby avoiding explicit calculation of all barriers. The GP-regressed barrier function enables use of kinetic Monte Carlo to simulate real-time kinetics (seconds to hours) based upon realistic atomic interactions. To illustrate the concept, we apply a GP regression to vacancy-assisted migration on a surface of a concentrated binary alloy (from both quantum and empirical potentials) and predict the diffusion …
Unbiased Density Functional Solutions Of Freezing In Binary Mixtures Of Hard Or Soft Spheres, M. Valera, R. F. Bielby, F. J. Pinksi, Duane D. Johnson
Unbiased Density Functional Solutions Of Freezing In Binary Mixtures Of Hard Or Soft Spheres, M. Valera, R. F. Bielby, F. J. Pinksi, Duane D. Johnson
Duane D. Johnson
various size ratios, σ2/σ1, using density functional theory. The Grand Potential is minimized using an unbiased, discrete, real-space mesh that does not constrain the shape of the density, and, in many cases, leads to solutions qualitatively different from those using Gaussians and plane-waves. Besides the usual face-centered-cubic solid-solution phase for σ2/σ1≈1.0, we find a sublattice-melt phase for σ2/σ1=0.85–0.5 (where the small-sphere density is nonlocalized and multi-peaked) and the NaCl phase for σ2/σ1=0.45–0.35 (when the small-sphere density again sharpens). For a range of size ratios of soft sphere mixtures, we could not find stable nonuniform solutions. Preliminary calculations within a Modified-Weighted …
Spatial Variation Of A Short-Lived Intermediate Chemical Species In A Couette Reactor, R. Dennis Vigil, Q. Ouyang, Harry L. Swinney
Spatial Variation Of A Short-Lived Intermediate Chemical Species In A Couette Reactor, R. Dennis Vigil, Q. Ouyang, Harry L. Swinney
R. Dennis Vigil
We have conducted experiments and simulations of the spatial variation of a short-lived intermediate species (triiodide) in the autocatalytic oxidation of arsenite by iodate in a reactor that is essentially one dimensional-the Couette reactor. (This reactor consists of two concentric cylinders with the inner one rotating and the outer one at rest; reagents are continuously fed and removed at each end in such a way that there is no net axial flux and there are opposing arsenite and iodate gradients.) The predictions ?f a one-dim~ns~onal . reaction-diffusion model which has no adjustable parameters, are In good qualItative (and, In some …