Development of hardware accelerator for molecular dynamics simulations: a computation board that calculates nonbonded interactions in cooperation with fast multipole method

Evaluation of long-range Coulombic interactions still represents a bottleneck in the molecular dynamics (MD) simulations of biological macromolecules. Despite the advent of sophisticated fast algorithms, such as the fast multipole method (FMM), accurate simulations still demand a great amount of computation time due to the accuracy/speed trade-off inherently involved in these algorithms. Unless higher order multipole expansions, which are extremely expensive to evaluate, are employed, a large amount of the execution time is still spent in directly calculating particle-particle interactions within the nearby region of each particle. To reduce this execution time for pair interactions, we developed a computation unit (board), called MD-Engine II, that calculates nonbonded pairwise interactions using a specially designed hardware. Four custom arithmetic-processors and a processor for memory manipulation ("particle processor") are mounted on the computation board. The arithmetic processors are responsible for calculation of the pair interactions. The particle processor plays a central role in realizing efficient cooperation with the FMM. The results of a series of 50-ps MD simulations of a protein-water system (50,764 atoms) indicated that a more stringent setting of accuracy in FMM computation, compared with those previously reported, was required for accurate simulations over long time periods. Such a level of accuracy was efficiently achieved using the cooperative calculations of the FMM and MD-Engine II. On an Alpha 21264 PC, the FMM computation at a moderate but tolerable level of accuracy was accelerated by a factor of 16.0 using three boards. At a high level of accuracy, the cooperative calculation achieved a 22.7-fold acceleration over the corresponding conventional FMM calculation. In the cooperative calculations of the FMM and MD-Engine II, it was possible to achieve more accurate computation at a comparable execution time by incorporating larger nearby regions.     

A novel carbon skeletal trichothecane, tenuipesine A, isolated from an entomopathogenic fungus, Paecilomyces tenuipes

Tenuipesine A (1), a novel trichothecane with an unprecedented carbon-migrated skeleton that embodies of a cyclopropane ring, was isolated from cultivated fruiting bodies of Paecilomyces tenuipes (Isaria japonica), a popular entomopathogenic fungi employed in folk medicine and health foods in China, Korea, and Japan. The structure was determined on the basis of two-dimensional NMR data. Its stereochemistry was elucidated by spectroscopic data and the chemical transformation of the coexisting trichothecene, 4beta-acetoxy-12,13-epoxytrichothec-9-ene-3alpha,15-diol (2). [structure: see text]     

Influence of melatonin on reproductive behavior in male rats.

The influence of melatonin on reproductive behavior was examined by administering it to pinealectomized male rats for 30 consecutive days. After the 30-d administration of melatonin or vehicle, each male rat was introduced into a female rat's cage on the day of proestrus and allowed to mate overnight. All rats administered the vehicle and the pinealectomized rats copulated; five of the twelve melatonin (8.0 mg/kg)-treated rats did not copulate. These findings suggest that melatonin inhibits the reproductive behavior of male rats.     

Radioactive nuclides in the marine environment--distribution and behaviour of 95Zr, 95Nb originated from fallout

To investigate behaviour of 95Zr, 95Nb in the marine environment, various samples have been collected and measured by means of Ge(Li) gamma-ray spectrometry and/or radiochemical analysis during a period from 1974 to 1982 at coastal area of Tokai-mura, Ibaraki prefecture. Concentration of the nuclides in seaweeds increased remarkably after atmospheric nuclear detonation by P.R. of China, and the activity ratio between the nuclides changed by time was not fit well by the transient decay equation. Concentration variation in sea water was smaller than that in sea weeds, and the minimum change in sea sediment. Increase of concentration in these environmental samples was observed in chronological order of sea water, sea weeds then sediment after detonations, suggesting that the uptake of the nuclides by these sea weeds from sea water is faster than that via root. Observed concentration factors on the nuclides by sea weeds were calculated from the observed concentrations in sea water and sea weeds. Maximum values on 95Zr and 95Nb were 2110, 2150, respectively for Ecklonia cava and Eisenia bicyclis.     

The synthesis and properties of ferroceno[1′,2′;1″,2″]bis(1,3-dithiol-2-thione and -2-one) derivatives

The t-butyl and bis(t-butyl) derivatives of hexathia[3.3]ferrocenophane were prepared from the corresponding trithia[3]ferrocenophanes. The former was a mixture of chair-chair and chair-boat isomers, and the latter existed only chair-boat isomer. The hexathia[3.3]ferrocenophanes were led to the tetrathiols with LiAlH₄, which allowed to react with 1,1′-thiocarbonyldiimidazol to give the corresponding ferroceno[1′,2′;1″,2″]bis(1,3-dithiol-2-thione) derivatives. Mono t-butyl and unsubstituted analogs were prepared in a similar manner. The X-ray structural determination showed that these derivatives adopted the conformation in which the 1,3-dithiol-2-thione rings were heaped on top of each other. In the crystal of ferroceno[1′,2′;1″,2″]bis(1,3-dithiol-2-thione), the molecules packed so as to put the axis of molecule in order and to overlap one another above and below. The desulfurizative coupling of the ferroceno[1′,2′;1″,2″]bis(1,3-dithiol-2-thione) derivatives was unsuccessful.     

Synthesis,including asymmetric synthesis,of 3-oxabicyclo[3.1.0]hexanes and bicyclo[3.1.0]hexanes by the 1,5-CH insertion of cyclopropylmagnesium carbenoids as the key reaction

The addition reactions of α,β-unsaturated carbonyl compounds with dichloromethyl p-tolyl sulfoxide in the presence of NaHMDS or LDA resulted in the formation of adducts, 1-chlorocyclopropyl p-tolyl sulfoxides bearing a carbonyl group at the 2-position, in almost quantitative yields. The carbonyl group of the adducts was transformed to various ether groups to give 1-chlorocyclopropyl p-tolyl sulfoxides bearing an ether functional group at the 2-position in short steps. Treatment of these products with i-PrMgCl at low temperature afforded cyclopropylmagnesium carbenoids via the sulfoxide-magnesium exchange reaction. 1,5-Carbon–hydrogen insertion (1,5-CH insertion) reaction of the generated magnesium carbenoid intermediates took place to give 3-oxabicyclo[3.1.0]hexanes or bicyclo[3.1.0]hexanes bearing an ether group at the 4-position in moderate to good yields. When this procedure was carried out starting with enantiopure dichloromethyl p-tolyl sulfoxide, enantiopure 3-oxabicyclo[3.1.0]hexanes were obtained in good overall yields. These procedures provide a good way for the synthesis, including asymmetric synthesis, of multisubstituted 3-oxabicyclo[3.1.0]hexanes and bicyclo[3.1.0]hexanes from α,β-unsaturated carbonyl compounds and dichloromethyl p-tolyl sulfoxide in short steps.     

Mimicking an antimicrobial peptide polymyxin B by use of cyclodextrin

Cyclodextrin derivatives prepared to mimic a membrane active antibacterial peptide polymyxin B strongly permeabilized bacterial membrane and inhibited bacterial proliferation.     

Experimental determination of fracture toughness of CFRP by Raman Coating Method

Summary  Strain distribution near the crack tip of Raman-inactive Carbon Fiber Reinforced Plastics (CFRP) was measured by Raman spectroscopy. A PbO thin film was deposited on the measured surface of the specimen by physical vapor deposition (PVD). The results agree well with those obtained by conventional experimental methods and FEM analysis. The proposed method allows to investigate fracture toughness of Raman-inactive materials. Received 8 December 1999; accepted for publication 28 March 2000     

Optical anisotropy in solution-cast film of cellulose triacetate

The out-of-plane birefringence and its wavelength dispersion are studied employing solution-cast films of cellulose triacetate (CTA). In solution-cast process, CTA molecules are induced to align in the film plane. Although refractive index is the lowest in the oriented direction for the CTA films stretched more than 110 %, refractive index is found to be the lowest in the normal direction for the unstretched cast film. Attenuated total reflection measurements reveal that in-plane alignment of the acetyl group which provides strong polarizability anisotropy is responsible for the phenomenon. Furthermore, the out-of-plane birefringence is found to increase with increasing wavelength, i.e. extraordinary wavelength dispersion, whereas a stretched CTA film shows ordinary wavelength dispersion. The level of the out-of-plane birefringence in cast films depends on the preparation conditions, which is predictable considering the evaporation rate. Moreover, it is demonstrated for the first time that the out-of-plane birefringence and its wavelength dispersion can be modified by addition of a certain plasticizer such as tricresyl phosphate (TCP). During the evaporation, TCP molecules orient in the film plane accompanying the orientation of CTA chains by intermolecular orientation correlation, called nematic interaction. This technique will widen the scope of material design of retardation films because there are numerous liquid compounds having strong polarizability anisotropy.