### Reaction rates, chaos theory and molecular dynamics

My doctoral thesis at Yale was focused on the use of chaos theory to understand chemical reaction dynamics at the molecular level. This work was directed by Nelson De Leon and was executed collaboratively with M.A. Mehta, based on earlier work by De Leon with C.C. Marston and A.O. de Almeida. The image above illustrates the phase space dynamics of the DeLeon-Berne Hamiltonian, showing the first graphical numerical reconstruction of what we originally called "cylindrical manifolds." It was created by Mehta, and was subsequently edited a bit under my direction by F. Torres.

This early work on cylindrical manifolds in phase space has impacted the fields of aerospace engineering, the celestial three-body problem, and space mission design. A recent paper (click here) shows how the theory can be extended to time-dependent Hamiltonians as well. See below for several publications.

The dynamics of the De Leon-Berne Hamiltonian may be explored interactively online. See M. Hammond and N. De Leon, "Double Well Reaction Dynamics," Link To Wolfram

, Published May 11, 2012.In a separate project, more recently we have worked collaboratively with Song Ling in a study of semiclassical limits for molecular dynamics (see below).

References:

(1) S. Ling and R.Q. Topper, invited book chapter, *On the zero point energy difficulty of quasiclassical trajectory simulations*, in ** Handbook of Computational Chemistry Research**, C. T. Collett and C. D. Robson, Eds., Nova Science Publishers, Hauppauge, NY, pp. 467-476

**(2010).**ISBN: 978-1-60741-047-8 . Preprint.

(2) R.Q. Topper, *Visualizing molecular phase space: Non–statistical effects in reaction dynamics, *invited article, in *Reviews in Computational Chemistry***10**, pp. 101-176, K.B. Lipkowitz and D.B. Boyd, Eds., VCH Publishers, New York **(1997)**. This is a review article and includes some of the content that was intended for III. in the series below (which never saw print due to battles with the referees over I and II). See also references therein. A preview is available on Google Books. Photocopy available on request. Link

(3) N. De Leon, M.A. Mehta, and R.Q. Topper, *Cylindrical manifolds in phase space as mediators of chemical reaction dynamics and kinetics I. Theory,*** Journal of Chemical Physics 94**, 8310

**(1991)**. PDF

(4) N. De Leon, M.A. Mehta, and R.Q. Topper, *Cylindrical manifolds in phase space as mediators of chemical reaction dynamics and kinetics II. Numerical considerations and applications to molecular models with two degrees of freedom, Journal of Chemical Physics*

**94**, 8329

**(1991)**. PDF