Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems

We describe the application of a special purpose board for molecular dynamics simulations, named MDGRAPE-3, to the problem of simulating periodic bio-molecular systems. MDGRAPE-3 is the latest board in a series of hardware accelerators designed to calculate the nonbonding long-range interactions much more rapidly than normal processors. So far, MDGRAPEs were mainly applied to isolated systems, where very many nonbonded interactions were calculated without any distance cutoff. However, in order to regulate the density and pressure during simulations of membrane embedded protein systems, one has to evaluate interactions under periodic boundary conditions. For this purpose, we implemented the Particle-Mesh Ewald (PME) method, and its approximation with distance cutoffs and charge neutrality as proposed by Wolf et al., using MDGRAPE-3. When the two methods were applied to simulations of two periodic biomolecular systems, a single MDGRAPE-3 achieved 30-40 times faster computation times than a single conventional processor did in the both cases. Both methods are shown to have the same molecular structures and dynamics of the systems.     

On an integrable two-component Camassa-Holm shallow water system

The interest in the Camassa-Holm equation inspired the search for various generalizations of this equation with interesting properties and applications. In this Letter we deal with such a two-component integrable system of coupled equations. First we derive the system in the context of shallow water theory. Then we show that while small initial data develop into global solutions, for some initial data wave breaking occurs. We also discuss the solitary wave solutions. Finally, we present an explicit construction for the peakon solutions in the short wave limit of system.     

Annulation of ketones with vinamidinium hexafluorophosphate salts: an efficient preparation of trisubstituted pyridines

alpha-Aryl ketones react with vinamidinium hexafluorophosphate salts to give access to the corresponding 3-arylpyridines. The annulation reactions proceed in good to excellent yields with vinamidinium salts containing electron-withdrawing groups at the beta-position (R(2)). The reaction was applied to the preparation of the COX-2 specific inhibitor 5-chloro-3-(4-methylsulfonyl)phenyl-2-(2-methyl-5-pyridinyl)pyridine (1), as well as a series of analogues.     

A practical synthesis of a COX-2-specific inhibitor

A number of synthetic strategies to the Cox-2 specific inhibitor 1 have been described. These studies have led to the identification of a novel pyridine construction using annulation of ketone 2 using a vinamidinium species 29 and ammonia in 97% assay yield. Three approaches to the synthesis of ketone 2 are described that allow for its preparation in large quantities in >65% overall yield from methyl 6-methylnicotinate.     

A practical synthesis of 5-(chloromethyl)furo[2,3-b]pyridine,a key intermediate for the HIV protease inhibitor,L-754,394

A practical synthesis of 5-(chloromethyl)furo[2,3-b]pyridine ( 10 ), the side chain used to incorporate a key pharmacophore of the HIV protease inhibitor, L-754,394, is described. The synthesis was accomplished in ten steps and in 15% overall yield from commercially available methyl 2-furoate.     

Study of the 8Be first T = 2 state with 4He + α and 7Li + p initiated excitation functions

In a high resolution study of the ⁴He + α initiated excitation functions in the region of the ⁸Be first T = 2 state, weak resonance excursions have been observed in some reaction channels yielding the total width Γ = 14.7 ± 4.0 keV. No resonance excursion has been observed in the ⁴He + α elastic scattering yielding the branching ratio Γ_α/Γ ≦ 0.003 for the decay of the ⁸Be first T = 2 state into two α-particles. For the decay to the low-lying states of ⁶Li and ⁷Li lower limits of the branching ratio are given. The reinvestigation of the ⁷Li+p initiated excitation functions revealed no resonance anomaly in the region of the ⁸Be first T = 2 state. The upper limit Γ_p/Γ ≦ 0.023 has been derived for the proton decay to the ⁷Li_g.s.. The results are compared with previous measurements and with shell-model calculations.     

One-nucleon transfer reactions in the12C+12C system at 344.5 MeV

Angular distributions of cross sections have been measured for single nucleon transfer reactions induced by 344.5 MeV¹²C ions on a¹²C target. DWBA analyses have been performed for transitions to discrete final states. Spectroscopic information has been derived and is compared with results of other studies.     

Synthesis,DFT calculations and characterisation of new mixed Pt(II) complexes with 3-thiolanespiro-5<Emphasis Type="Italic">′</Emphasis>-hydantoin and 4-thio-1<Emphasis Type="Italic">H</Emphasis>-tetrahydropyranspiro-5<Emphasis Type="Italic">′</Emphasis>-hydantoin

Cisplatin is an anticancer drug widely used in the treatment of a wide range of solid tumours (head and neck, lung, bladder etc.), testicular and ovarian cancers. Because of its severe toxicity profile and spontaneous development of drug resistance in tumours, a number of Pt(II) complexes have been synthesised and tested for anti-tumour activity. Some of the investigations have focused on using ligands bearing donor atoms other than N (e.g., S, P, O). Two new mixed Pt(II) complexes of the general formula cis-[Pt(NH₃)LCl₂] where L is 3-thiolanespiro-5′-hydantoin and 4-thio-1H-tetrahydropyranspiro-5′-hydantom were synthesised. The complexes were studied by elemental analysis, melting points, IR and ¹H NMR spectra. The hybrid DFT calculations were used for optimisation of the structure geometries of the ligands III, IV and their Pt(II) complexes V and VI. The structural parameters so calculated, such as bond lengths and angles, are in good agreement with the experimental data for similar hydantoins and their platinum complexes. The results showed that the geometries of complexes V and VI are plane square and the bounding of ligands III and IV with platinum ions is effected by the sulphur atom from the cyclic ring. The complexes thus obtained were chemically examined in comparison with previously synthesised and published complexes of the general formula cis-[PtL₂Cl₂] (VII and VIII) with the same ligands. The new compounds V and VI, as well as the previously investigated complexes (VII and VIII), were analysed for cytotoxicity in vitro on SKW-3 and HL-60 human tumour cell lines. The results showed that all the complexes exerted concentration-dependent anti-proliferative activity.     

Plasma immersion ion implantation for silicon processing

Plasma Immersion Ion Implantation (PIII) is a technology which is currently widely investigated as an alternative to conventional beam line implantation for ultrashallow doping beyond the 0.15 μm technology. However, there are several other application areas in modern semiconductor processing. In this paper a detailed discussion of the PIII process for semiconductors and of actual as well as future applications is given. Besides the well known advantages of PIII — fast process, implantation of the whole surface, low cost of ownership — several peculiarities — like spread of the implantation energy due to finite rise time or collisions, no mass separation, high secondary electron emission — must be mentioned. However, they can be overcome by adjusting the system and the process parameters. Considering the applications, ultrashallow junction formation by PIII is an established industrial process, whereas SIMOX and Smart‐Cut by oxygen and hydrogen implantation are current topics between research and introduction into industry. Further applications of PIII, of which some already are research topics and some are only investigated by conventional ion implantation, include seeding for metal deposition, gettering of metal impurities, etch stop layers and helium implantation for localized lifetime control.