The dynamics calculations employ VTST methods discussed above, and spectroscopic applications involve a new vertical excitation model. Many enzymatic reactions involve proton and hydride transfer, but until recently techniques for simulating the dynamics of these processes were usually based entirely in classical mechanics. We are working on a number of initiatives for including quantum effects in biological simulations. This includes tunneling, zero point effects, and the effect of quantization on thermally averaged quantities. We have shown that proton transfers catalyzed by enolase and hydride transfer catalyzed by liver alcohol dehydrogenase are dominated by quantum mechanical events, and that these can be well modeled by semiclassical dynamics methods developed in our group.
Further development are applications are underway.
An important application of solvation modeling is the calculation of the partitioning of organic and biological molecules between aqueous and cell membranes. This has an important effect on bioavailability of drugs. We are developing and applying new molecular modeling methods that make such calculations more accurate. Our research in this area focuses on computational studies of nanoparticle growth and dynamics. We are concerned with the development and implementation of new methods for modeling and simulation of nanoparticles and their elementary processes, including nucleation, deposition, and surface reactions.