Database of atomistic reaction mechanisms with application to kinetic Monte Carlo

Kinetic Monte Carlo is a method used to model the state-to-state kinetics of atomic systems when all reaction mechanisms and rates are known a priori. Adaptive versions of this algorithm use saddle searches from each visited state so that unexpected and complex reaction mechanisms can also be included. Here, we describe how calculated reaction mechanisms can be stored concisely in a kinetic database and subsequently reused to reduce the computational cost of such simulations. As all accessible reaction mechanisms available in a system are contained in the database, the cost of the adaptive algorithm is reduced towards that of standard kinetic Monte Carlo.     

SYNTHESIS AND CHARACTERIZATION OF SOME THERMOTROPIC LIQUID CRYSTALLINE POLYAMIDES

A series of novel mesogenic polyamides containing a flexible pendent side group wassynthesized by solution condensation polymerization. The new monomers, diacids and di-amines containing flexible elements of diferent lengths, were also synthesized and character-ized by ~1HNMR, mass spectroscopy and elemental analysis. The polymers were character-ized by viscosity measurements, differential scanning calorimetry (DSC), X-ray diffiactionand polarizing optical microscopy These studies revealed that polyamides containingflexible elements of a sufficient length exhibited thermotropic liquid crystalline(LC) pro-perties. The melting temperatures of this series of polymers were particularly sensitive tothe length of the flexible segment on the main chain and that of the flexible pendent esterside chain. Lyotropic LC behaviours were also observed in solution.     

Practical adaptive synchronization of a class of uncertain chaotic systems

This paper studies the practical adaptive synchronization of a class of uncertain chaotic systems in the drive-response framework. An adaptive response system is designed to practically synchronize a given drive chaotic system with uncertainties. An improved adaptation law on the upper bound of uncertainties is proposed to guarantee the boundedness of both the synchronization error and the estimated feedback coupling gains. The efficiency and effectiveness of the proposed approach is illustrated by computer simulation.     

A computational study of a gradient-based log-barrier algorithm for a class of large-scale SDPs

 The authors of this paper recently introduced a transformation [4] that converts a class of semidefinite programs (SDPs) into nonlinear optimization problems free of matrix-valued constraints and variables. This transformation enables the application of nonlinear optimization techniques to the solution of certain SDPs that are too large for conventional interior-point methods to handle efficiently. Based on the transformation, we proposed a globally convergent, first-order (i.e., gradient-based) log-barrier algorithm for solving a class of linear SDPs. In this paper, we discuss an efficient implementation of the proposed algorithm and report computational results on semidefinite relaxations of three types of combinatorial optimization problems. Our results demonstrate that the proposed algorithm is indeed capable of solving large-scale SDPs and is particularly effective for problems with a large number of constraints. Received: June 22, 2001 / Accepted: January 20, 2002 Published online: December 9, 2002 RID="†" ID="†"Computational results reported in this paper were obtained on an SGI Origin2000 computer at Rice University acquired in part with support from NSF Grant DMS-9872009. RID="⋆" ID="⋆"This author was supported in part by NSF Grants CCR-9902010, INT-9910084 and CCR-0203426 RID="⋆⋆" ID="⋆⋆"This author was supported in part by NSF Grants CCR-9902010, INT-9910084 and CCR-0203113 RID="⋆⋆⋆" ID="⋆⋆⋆"This author was supported in part by DOE Grant DE-FG03-97ER25331, DOE/LANL Contract 03891-99-23 and NSF Grant DMS-9973339. Key Words. semidefinite program – semidefinite relaxation – nonlinear programming – interior-point methods – limited memory quasi-Newton methods. Mathematics Subject Classification (1991): 90C06, 90C27, 90C30.     

Mannose derived hexacoordinated phosphate--a generally efficient chiral anion for asymmetric applications

Mannose derived hexacoordinated phosphate--prepared in two steps from methyl-alpha-D-mannopyranoside--is a chiral anionic auxiliary with broad asymmetric efficiency.     

Environment-independent 14-helix formation in short beta-peptides: striking a balance between shape control and functional diversity

We report a significant and unanticipated advance in the study of beta-amino acid-based foldamers: a small proportion of highly preorganized residues can impart high stability to a specific helical secondary structure in water. Most of the residues in these beta-peptides (2 and 3) are intrinsically flexible. Flexible beta-amino acids can be readily and enantiospecifically prepared in functionally diverse forms, but preorganized residues with side chains are rare and challenging to synthesize. Our findings demonstrate that interspersing a few copies of an unfunctionalized but rigid residue among a larger number of flexible residues with diverse side chains is a viable strategy for creating beta-peptides that adopt the 14-helix conformation and therefore display side chains in a predictable spatial arrangement. These results are significant because they enhance the prospects of developing beta-peptides with useful activities.     

Secondary structural preferences of 2,2-disubstituted pyrrolidine-4-carboxylic acid oligomers: beta-peptide foldamers that cannot form internal hydrogen bonds

We examine a new class of beta-peptides, 2,2-disubstituted pyrrolidine-4-carboxylic acid oligomers, and show that they manifest discrete conformational preferences despite the impossibility of internal hydrogen bonding. Numerous beta-peptide families have been described that display specific secondary structural preferences, but all of the conformations characterized in detail so far have contained internal hydrogen bonds. Internal hydrogen bonding is observed within the most common secondary structures of conventional peptides as well. Identifying foldamers in which shape control is independent of hydrogen bonding is significant in two ways. At a fundamental level, foldamers in this small but growing class are interesting because their shapes are controlled by distinctive networks of noncovalent forces. At a practical level, non-hydrogen bonded foldamers may be useful in biomedical applications because the low intrinsic polarity of their backbones may promote bioavailability.