Volume 110, Issue 6, 08 February 1999
Index of content:
- POLYMERS, BIOPOLYMERS, AND COMPLEX SYSTEMS
110(1999); http://dx.doi.org/10.1063/1.477844View Description Hide Description
We present a new Monte Carlo scheme for the efficient simulation of multi-polymer systems. The method permits chains to be inserted into the system using a biased growth technique. The growth proceeds via the use of a retractable feeler, which probes possible pathways ahead of the growing chain. By recoiling from traps and excessively dense regions, the growth process yields high success rates for both chain construction and acceptance. Extensive tests of the method using self-avoiding walks on a cubic lattice show that for long chains and at high densities it is considerably more efficient than configurational bias Monte Carlo, of which it may be considered a generalization.
110(1999); http://dx.doi.org/10.1063/1.477845View Description Hide Description
Spectraldiffusion waiting time experiments at 100 mK combined with aging time experiments are used to shed light on the features of the energy landscape of a cytochrome c-type protein and the respective conformational dynamics. The energy landscape shows features of a hierarchical organization. The time law which governs the dynamics in conformational phase space is a power law. The respective processes seem to be related to generalized diffusive-like motions.
Integral equation theory of single-chain polymers: Comparison with simulation data for hard-sphere and square-well chains110(1999); http://dx.doi.org/10.1063/1.477846View Description Hide Description
A systematic comparison of computer simulation data for linear hard-sphere and square-well chains with the results of single-chain integral equation is reported. The single-chain integral equation is derived from the polymer Kirkwood hierarchy for site–site or pair distribution functions. Quantities compared include radius of gyration, end-to-end distance, and internal energy. We examine chain lengths up to 1000 sites for hard-sphere chains. The radius of gyration and end-to-end distance from the theory are found to agree quantitatively with Monte Carlo simulation data. Results for square-well chains with the range are compared with Monte Carlo and constant temperature molecular dynamics simulation data for chains having up to 64 sites. The radius of gyration and internal energy generally deviate from simulation data by about 10% for reduced temperatures greater than 1. The values of the radius of gyration at reduced temperatures below 1 are larger than those from simulations.
110(1999); http://dx.doi.org/10.1063/1.477847View Description Hide Description
The vibrational frequencies of a number of all trans polyenes ranging from to have been calculated within the density functional approach using a generalized gradient corrected exchange-correlation functional and a gaussian basis set. A remarkably good agreement with available experimental data is obtained. A correlation of the normal frequencies along the polyene series is presented describing the motions according to a nodal analysis. The results obtained are also correlated with the vibrations of an infinite polyenic chain.