Quantum simulation of enzyme catalysis

Separating the dynamics of variables that evolve on different timescales is a common assumption in exploring complex systems, and a great deal of progress has been made in understanding chemical systems by treating independently the fast processes of an activated chemical species from the slower processes that proceed activation. Protein motion underlies all biocatalytic reactions, and understanding the nature of this motion is central to understanding how enzymes catalyze reactions with such specificity and such rate enhancement. This understanding is challenged by evidence of breakdowns in the separability of timescales of dynamics in the active site form motions of the solvating protein. Quantum simulation methods that bridge these timescales by simultaneously evolving quantum and classical degrees of freedom provide an important method on which to explore this breakdown. In the following dissertation, three problems of enzyme catalysis are explored through quantum simulation.

Pulsed neutron measurements in two adjacent finite media

The pulsed neutron technique has been used to investigate the decay of thermal neutrons in two adjacent water-borated water finite media. Experiments were performed with a 6x6x6 inches cubic assembly divided in two halves by a thin membrane and filled with pure distilled water on one side and borated water on the other side.

The fundamental decay constant was measured versus the boric acid concentration in the poisoned medium. The experimental results showed good agreement with the predictions of the time dependent diffusion model. It was assumed that the addition of boric acid increases the absorption cross section of the poisoned medium without affecting its diffusion properties: In these conditions, space-energy separability and the concept of an “effective” buckling as derived from diffusion theory were introduced. Their validity was supported by the experimental results.

Measurements were performed with the absorption cross section of the poisoned medium increasing gradually up to 16 times its initial value. Extensive use of the IBM 7090-7094 Computing facility was made to analyze properly the decay data (Frantic Code). Attention was given to the count loss correction scheme and the handling of the statistics involved. Fitting of the experimental results into the analytical form predicted by the diffusion model led to

Ʃ_av = 4721 sec^-1 (±150)

D_o = 35972 cm²sec^-1 (±800) for water at 21˚C

C (given) = 3420 cm⁴sec^-1

These values, when compared with published data, show that the diffusion model is adequate in describing the experiment.