An improved Monte Carlo scheme for simulation of synthesis of nanoparticles in reverse micelles

An improved Monte Carlo technique is presented in this work to simulate nanoparticle formation through a micellar route. The technique builds on the simulation technique proposed by Bandyopadhyaya et al. (Langmuir 2000, 16, 7139) which is general and rigorous but at the same time very computation intensive, so much so that nanoparticle formation in low occupancy systems cannot be simulated in reasonable time. In view of this, several strategies, rationalized by simple mathematical analyses, are proposed to accelerate Monte Carlo simulations. These are elimination of infructuous events, removal of excess reactant postreaction, and use of smaller micelle population a large number of times. Infructuous events include collision of an empty micelle with another empty one or with another one containing only one molecule or only a solid particle. These strategies are incorporated in a new simulation technique which divides the entire micelle population in four classes and shifts micelles from one class to other as the simulation proceeds. The simulation results, throughly tested using chi-square and other tests, show that the predictions of the improved technique remain unchanged, but with more than an order of magnitude decrease in computational effort for some of the simulations reported in the literature. A post priori validation scheme for the correctness of the simulation results has been utilized to propose a new simulation strategy to arrive at converged simulation results with near minimum computational effort.

PROTEIN DISULFIDE ANALYSIS AND DESIGN

The significant contribution of naturally occurring disulfide bonds to protein stability has encouraged development of methods to engineer non-native disulfides in proteins. These have yielded mixed results. We summarize applications of the program MODIP for disulfide engineering. The program predicts sites in proteins where disulfides can be stably introduced. The program has also been used as an aid in conformational analysis of naturally occurring disulfides in a-helices, antiparallel and parallel beta-strands. Disulfides in a-helices occur only at N-termini, where the first cysteine residue is the N-cap residue of the helix. The disulfide occurs as a CXXC motif and can possess redox activity. In antiparallel beta-strands, disulfides occur exclusively at non-hydrogen bonded (NHB) registered pairs of antiparallel beta-sheets with only 1 known natural example occurring at a hydrogen bonded (HB) registered pair. Conformational analysis suggests that disulfides between HB residue pairs are under torsional strain. A similar analysis to characterize disulfides in parallel beta-strands was carried out. We observed that only 9 instances of cross-strand disulfides exist in a non-redundant dataset. Stereochemical analysis shows that while tbe chi(square) angles are similar to those of other disulfides, the chi(1) and chi(2) angles show more variation and that one of tbe strands is generally an edge strand.