Development of a parallel molecular dynamics code on SIMD computers: Algorithm for use of pair list criterion

In recent years several implementations of molecular dynamics (MD) codes have been reported on multiple instruction multiple data (MIMD) machines. However, very few implementations of MD codes on single instruction multiple data (SIMD) machines have been reported. The difficulty in using pair lists of nonbonded interactions is the major problem with MD codes for SIMD machines, such that, generally, the full connectivity computation has been used. We present an algorithm, the global cut-off algorithm (GCA), which permits the use of pair lists on SIMD machines. GCA is based on a probabilistic approach and requires the cut-off condition to be simultaneously verified on all nodes of the machine. The MD code used was taken from the GROMOS package; only the routines involved in the pair lists and in the computation of nonbonded interactions were rewritten for a parallel architecture. The remaining calculations were performed on the host computer. The algorithm has been tested on Quadrics computers for configurations of 32, 128, and 512 processors and for systems of 4000, 8000, 15,000, and 30,000 particles. Quadrics was developed by Istituto Nazionale di Fisica Nucleare (INFN) and marketed by Alenia Spazio. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 685–694, 1998     

Synthesis and characterization of poly(3-alkylthiophenes) with NLO chromophoric groups in side chains

Polythiophene copolymers containing alkyl side chains of different length and partially functionalized with chromophoric groups have been synthesized by FeCl₃ oxidative coupling of 3-alkylthiophenes and functionalized 3-alkylthiophenes. Composition, molecular weigth and configuration of the soluble fraction of the copolymers have been investigated and some structure-property correlations have been evidenced.     

Engineered Green Fluorescence Proteins for Proteomics and Biomolecular Electronic Applications

The discovery of the photochromic characteristics of engineered green fluorescent proteins (GFPs) allows new proteomics and biomolecular electronic applications. In particular, photoreversibility among two distinct optical states can lead to the realization of a bio-optical high density storage memory. Here we review our recent work on an optically bistable GFP and we report the recent developments of self-assembly methods for spatial immobilization of proteins into well-definite 2D patterns.     

An investigation of the condensation kinetics in poly(ester-amide) and poly(ester-sulphide) preparation

Synthetic processes leading to hydrophilic biodegradable polymers for bio-inspired applications were investigated from a kinetic point of view. In accordance with the reported mechanism of ester aminolysis, polycondensation reactions of α-amino-ω-esters, diesters, and diamines resulted markedly dependent on the basicity of the alkoxide leaving-group, being relatively fast for penthachlorophenate monomers. Furthermore, experimental data concerning the homopolycondensation of penthachlorophenyl α-amino-ω-oligo(ethyleneglycol) succinates of different degree of oligomerization clearly showed the existence of concurrent first and second-order processes, which were attributed to the intramolecular cyclization and intermolecular polycondensation reaction, respectively. In contrast to theoretical predictions based on the collision theory, however, minor incidence of the cyclization reaction was shown by the shortest monomers, thus suggesting a significant kinetic effect due to steric hindrance and solvent-reagent interactions. Analysis of the base-catalyzed Michael-type addition of α,ω-oligo(oxyethylene)dithiols to methyl (meth)acrylate allowed for the optimization of the relevant polymerization process involving hydrophilic diacrylates. Interestingly, very low reaction rates were determined for methacrylic components, supposedly because of steric and electronic factors connected to the presence of the α-methyl group. Minor effects on the reaction rate were also induced by solvent polarity and catalyst nature.