DYNGA: a general purpose QM-MM-MD program. I. Application to water

We present a general purpose QM-MM-MD engine (DYNGA) designed to test alternative hybrid Hamiltonians geared towards the treatment of problems of interest in structural biology including the use of experimental data constraints. In this first presentation we use DYNGA to explore the behaviour of a traditional QM-MM approach in the treatment of the water—water interaction. We find the potential energy hypersurface for the water dimer computed with the HF 4–31G*/TIP3P hybrid Hamiltonian tends to be too flat. We also explore the effect of using traditional QM-MM techniques on proton wires and conclude there is a need for improvement, possibly addressed by using polarizable force fields.     

Optimization of the synthesis of poly(octadecyl acrylate) by atom transfer radical polymerization and the preparation of all comblike amphiphilic diblock copolymers

The atom transfer radical polymerization of octadecyl acrylate (ODA) has been investigated and optimized to produce polymers with predetermined molecular weights and narrow polydispersities (<1.2). The poor solubility of the catalytic system formed with conventional ligands such as the N‐(n‐propyl)‐2‐pyridylmethanimine and 2,2′‐bipyridine with Cu(I)Br in nonpolar reaction conditions gave poor control over molecular weight characteristics in ODA polymerizations. The use of N‐(n‐octyl)‐2‐pyridylmethanimine in combination with Cu(I)Br yielded a more soluble catalyst that improved control over the polymerization. The products from the polymerizations were further improved when an initiator, octadecyl 2‐bromo‐2‐methyl‐propanoate, similar in structure to the monomer, was used. Together, these modifications produced polymerizations that showed true controlled character as well as products with predetermined molecular weights and narrow polydispersities. Diblock copolymers of PODA were prepared with methyl methacrylate (MMA) and olig(oethylene glycol) methyl ether methacrylate (OEGMA). The PODA‐block‐POEGMA copolymers are the first examples of all comblike amphiphilic block copolymers. One of PODA‐block‐POEGMA copolymer samples has been shown to self‐assemble as micelles in a dilute aqueous solution. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 1129–1143, 2005     

The upper critical field of superconducting polysulfur nitride, (SN)x

A measurement of the temperature and angular dependence of the upper critical magnetic field H_c² in crystals of polymeric (SN)_x is reported. A large anisotropy is observed at all temperatures with H_c²6 = 8.1 ± 0.4 kOe parallel to, and H_c²⊥ = 870 ± 80 Oe perpendicular to, the polymer axis at 0°K. The results are explained in terms of the polymeric crystal structure and fibrous morphology of (SN)_x.     

Hydrogen diffusion and electronic metastability in amorphous silicon

Hydrogen diffusion and its role in the many electronic metastability phenomena in hydrogenated amorphous silicon (a-Si:H) is reviewed. A-Si:H contains about 10 at% hydrogen, most of which is bonded to silicon. The hydrogen diffuses at relatively low temperatures by releasing hydrogen from the Si-H bonds into interstitial sites. The reactions of hydrogen with the silicon dangling bonds and the weak bonds provide a hydrogen-mediated mechanism for electron-structural interactions, which are manifested as electronic metastability. The annealing of light-induced defects, the equilibration of defects and dopants, the stretched exponential relaxation kinetics, and the atomic structure formed during growth, are all attributed to hydrogen diffusion.     

On the sensitivity of transient photodecay measurements as a probe of localised state distributions in amorphous semiconductors

An investigation is reported of the extent to which structure in the density of localised states in amorphous semiconductor films may be detected from photodecay measurements. Transient photocurrents are computed by a Monte Carlo technique, for the case of an exponential tail of states upon which a sharp rectangular feature has been superimposed. It is shown that a ‘rectangular’ component of energy width kT must protrude from the background exponential tail by at least a factor of 5 in density, in order to exert a readily-detectable influence upon the transient photodecay. It is further demonstrated that the presence of deep-lying features in the distribution of localised states may easily modify the transient decay over a wide range of time; underlining the difficulty of interpreting such data.     

Three-dimensional unsteady flow simulations: Alternative strategies for a volume-averaged calculation

This work builds on a SIMPLE-type code to produce two numerical codes of greatly improved speed and accuracy for solution of the Navier–Stokes equations. Both implicit and explicit codes employ an improved QUICK (quadratic upstream interpolation for convective kinematics) scheme to finite difference convective terms for non-uniform grids. The PRIME (update pressure implicit, momentum explicit) algorithm is used as the computational procedure for the implicit code. Use of both the ICCG (incomplete Cholesky decomposition, conjugate gradient) method and the MG (multigrid) technique to enhance solution execution speed is illustrated. While the implicit code is first-order in time, the explicit is second-order accurate. Two- and three-dimensional forced convection and sidewall-heated natural convection flows in a cavity are chosen as test cases. Predictions with the new schemes show substantial computational savings and very good agreement when compared to previous simulations and experimental data.