Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.

Local structures predicted from protein sequences are used extensively in every aspect of modeling and prediction of protein structure and function. For more than 50 years, they have been predicted at a low-resolution coarse-grained level (e.g.

Quantum dynamics study of the dissociative photodetachment of HOCO-.

Six-dimensional wave packet calculations are carried out to study the behavior of HOCO subsequent to the photodetachment of an electron from the negative anion, HOCO-. It is possible to form stable and/or long-lived HOCO complexes, as well as the dissociative products OH+CO and H+CO2. A variety of observables are determined: the electron kinetic energy (eKE) distributions associated with the OH+CO and H+CO2 channels, the correlated eKE and product translational energy distribution for the OH+CO channel, and product branching ratios.

Hybrid Prefactor Semiclassical Initial Value Series Representation of the Quantum Propagator.

One of the central advantages of the Herman Kluk Semiclassical Initial Value Representation (SCIVR) of the quantum propagator is that through its prefactor it approximately conserves unitarity for relatively long times. Its main disadvantage is that the prefactor appearing in the SCIVR propagator is expensive to compute as the dimensionality of the problem increases. When using the SCIVR series method for computation of the numerically exact quantum dynamics, the expense becomes even larger, since each term in the series involves a product of propagators, each with its own prefactor.

A prefactor free semiclassical initial value series representation of the propagator.

A new class of prefactor free semiclassical initial value representations (SCIVR) of the quantum propagator is presented. The derivation is based on the physically motivated demand, that on the average in phase space and in time, the propagator obey the exact quantum equation of motion. The resulting SCIVR series representation of the exact quantum propagator is also free of prefactors.

Low temperature extension of the generalized Zusman phase space equations for electron transfer.

In a previous paper [J. Chem. Phys.

Monte Carlo method for evaluating the quantum real time propagator.

A new exact representation of the quantum propagator is derived in terms of semiclassical initial value representations. The resulting expression may be expanded in a series, of which the leading order term is the semiclassical one. Motion of a Gaussian wave packet on a symmetric double well potential is used to demonstrate numerical convergence of the series and the ability to compute each element in the series using Monte Carlo methods.