Prediction of protein B-factor profiles

The polypeptide backbones and side chains of proteins are constantly moving due to thermal motion and the kinetic energy of the atoms. The B-factors of protein crystal structures reflect the fluctuation of atoms about their average positions and provide important information about protein dynamics. Computational approaches to predict thermal motion are useful for analyzing the dynamic properties of proteins with unknown structures. In this article, we utilize a novel support vector regression (SVR) approach to predict the B-factor distribution (B-factor profile) of a protein from its sequence. We explore schemes for encoding sequences and various settings for the parameters used in SVR. Based on a large dataset of high-resolution proteins, our method predicts the B-factor distribution with a Pearson correlation coefficient (CC) of 0.53. In addition, our method predicts the B-factor profile with a CC of at least 0.56 for more than half of the proteins. Our method also performs well for classifying residues (rigid vs. flexible). For almost all predicted B-factor thresholds, prediction accuracies (percent of correctly predicted residues) are greater than 70%. These results exceed the best results of other sequence-based prediction methods. (C) 2005 Wiley-Liss, Inc.

Evidence for energy relaxation via a radiative cascade in surface-passivated PbS quantum dots

Multiple emission peaks have been observed from surface passivated PbS nanocrystals displaying strong quantum confinement. The emission spectra are shown to be strongly dependent on the excited-state parity. We also find that intraband energy relaxation from initial states excited far above the band-edge is nearly three orders of magnitude slower than that found in other nanocrystal quantum dots, providing evidence of inefficient energy relaxation via phonon emission. The initial-state parity dependence of the photoluminescent emission properties suggests that energy relaxation from the higher excited states occurs via a radiative cascade, analogous to energy relaxation in atomic systems. Such radiative cascade emission is possible from ideal zero-dimensional semiconductors, where electronic transitions can be decoupled from phonon modes.

Entropy generation for microscale forced convection: effects of different thermal boundary conditions, velocity slip, temperature jump, viscous dissipation, and duct geometry

This work presents closed form solutions for fully developed temperature distribution and entropy generation due to forced convection in microelectromechanical systems (MEMS) in the Slip-flow regime, for which the Knudsen number lies within the range 0.001