Efficient domain partitioning algorithms for global optimization of rational and Lipschitz continuous functions

A domain partitioning algorithm for minimizing or maximizing a Lipschitz continuous function is enhanced to yield two new, more efficient algorithms. The use of interval arithmetic in the case of rational functions and the estimates of Lipschitz constants valid in subsets of the domain in the case of others and the addition of local optimization have resulted in an algorithm which, in tests on standard functions, performs well.     

Nondifferential optimization via adaptive smoothing

The problem of minimizing a nondifferential functionx f(x) (subject, possibly, to nondifferential constraints) is considered. Conventional algorithms are employed for minimizing a differential approximationf off (subject to differentiable approximations ofg). The parameter is adaptively reduced in such a way as to ensure convergence to points satisfying necessary conditions of optimality for the original problem.This research was supported by the UK Science and Engineering Research Council, the National Science Foundation under Grant No. ECS-8121149, and the Joint Services Electronics Program, Contract No. F49620-79-C-0178.     

Rapid parameterization of small molecules using the force field toolkit

The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide‐scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error‐prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM‐compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure‐solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). © 2013 Wiley Periodicals, Inc.     

Visualization of enantiomers in cholesteric solvents through deuterium NMR

Abstract

Proton decoupled deuterium NMR of mixtures of enantiomers in homogeneously oriented cholesteric solvents produces simple spectra with linewidths of 10 to 50 Hz in cases where the proton spectra would give second order patterns so complicated as to defy analysis. The chiral solvent orders each of a pair of enantiomers differently which results in a difference in the residual quadrupolar coupling constant yielding well resolved spectra for each enantiomer. That the technique constitutes a new tool for measurement of enantiomeric ratios is illustrated using several chiral benzylic alcohols.     

Adlayer morphologies and free energy landscapes of clusters of bis-fullerenes on model gold surfaces

There have been a few experimental reports of self-assembled adlayers of bis-fullerene molecules on solid substrates. Most of these studies suggest the adsorbate molecules are lying down on the surface, with the fullerene moieties almost close packed. However, very little theoretical work has been carried out on such systems, and little is known about the roles played by different parts of the potential energy in driving the self-assembly. We carry out a Temperature Replica Exchange Monte Carlo study here of two representative bis-fullerene molecules on a metal substrate. We use a coarse-grained model potential energy function, in which certain parameters can be varied within the range of their experimental uncertainty. The molecules investigated consist of two fullerene moieties bonded by a rigid bridging group. In particular, the effect of the strength of the fullerene interaction E(FG) with the substrate (nominally Au(111)) has been investigated in detail. To ensure efficient sampling of the rugged potential energy surfaces encountered in the simulations, we utilize replica exchange techniques. These enable us to construct free energy landscapes for the system. We find that for relatively low values of E(FG) the molecules form standing-up adlayers. By contrast, for higher values of E(FG), lying-down adlayers dominate. For one molecule, two different crystalline adlayer morphologies have been identified. The detailed structure of the lying-down layer is a function of the temperature and of the group used to bridge the fullerene moieties.     

An efficient algorithm for solving inequalities

An efficient algorithm for solving a finite system of inequalities in a finite number of iterations is described and analyzed.This work was supported by the UK Science and Engineering Research Council     

Energy Planning and Policy

Journal of the Operational Research Society -