Design of a grid service-based platform for in silico protein-ligand screenings

Grid computing offers the powerful alternative of sharing resources on a worldwide scale, across different institutions to run computationally intensive, scientific applications without the need for a centralized supercomputer. Much effort has been put into development of software that deploys legacy applications on a grid-based infrastructure and efficiently uses available resources. One field that can benefit greatly from the use of grid resources is that of drug discovery since molecular docking simulations are an integral part of the discovery process. In this paper, we present a scalable, reusable platform to choreograph large virtual screening experiments over a computational grid using the molecular docking simulation software DOCK. Software components are applied on multiple levels to create automated workflows consisting of input data delivery, job scheduling, status query, and collection of output to be displayed in a manageable fashion for further analysis. This was achieved using Opal OP to wrap the DOCK application as a grid service and PERL for data manipulation purposes, alleviating the requirement for extensive knowledge of grid infrastructure. With the platform in place, a screening of the ZINC 2,066,906 compound "drug-like" subset database against an enzyme's catalytic site was successfully performed using the MPI version of DOCK 5.4 on the PRAGMA grid testbed. The screening required 11.56 days laboratory time and utilized 200 processors over 7 clusters.     

Two-stage nuclear demagnetization refrigerator

Two-stage nuclear demagnetization has been performed using PrCu₆ and Cu as coolants. The Cu nuclear stage reached temperatures as low as 10 K with a rate of temperature rise of less than a few K/h. The corresponding conduction electron temperature is estimated to be less than 50 K. A nuclear orientation thermometer of Al ⁵⁴Mn has been successfully used to measure temperatures down to 10 K.Supported by the Japan Society for the Promotion of Science.     

Magnetic resonance studies of some antiferromagnetic Gd-monopnictides and Gd-monochalcogenides

We report the results of electron paramagnetic resonance studies of GdX (X=As, Sb, Bi, S, Se). The temperature dependence of the linewidth H and effective g-factorg _eff are discussed. Values for the Néel temperatureT _N are inferred from coincident anomalies in H andg _eff. In the cases of X=S and Se, our estimates ofT _N are significantly lower than theT _N inferred from static susceptibility measurements. A possible source of the discrepancy is discussed.Supported by the National Science Foundation Grant No. DMR-74-08033.Work performed under the auspices of the U.S. ERDA.Supported by the National Science Foundation.     

Interdiffusivities matrix of CaO-Al2O3-SiO2 melt at 1723 K to 1823 K

Ternary oxide mixtures of lime, alumina, and silica were premelted and quenched to produce glassy cylinders. A diffusion couple was selected from the mixtures of six different compositions in such a way that the average composition could be 40 wt pct CaO-20 wt pct A1₂O₃ = 40 wt pct SiO₂. Penetration curves of the components were measured with a X-ray microprobe analyzer. The interdiffusivities matrix defined with the Matano interface has been obtained from 52 successful diffusion runs at 1723 K to 1823 K as follows; 1 $$\begin{gathered} \tilde D_{10 - 10}^{30} = 8.9 \times 10^{ - 11} \exp ( - \frac{{253,700}}{{RT}})(m^2 /s) \hfill \\ \tilde D_{10 - 20}^{30} = - 2.5 \times 10^{ - 11} \exp ( - \frac{{194,300}}{{RT}})(m^2 /s) \hfill \\ \end{gathered} $$ 2 $$\begin{gathered} \tilde D_{20 - 10}^{30} = - 4.0 \times 10^{ - 11} \exp ( - \frac{{177,600}}{{RT}})(m^2 /s) \hfill \\ \tilde D_{20 - 20}^{30} = 6.12 \times 10^{ - 11} \exp ( - \frac{{318,400}}{{RT}})(m^2 /s) \hfill \\ \end{gathered} $$ where symbols, 10, 20, and 30 mean CaO, A1₂O₃, and SiO₂, respectively, and the activation energies are in Joules per mole. The diffusion composition paths obtained are discussed in relation to Cooper’s parallelogram. The composition dependency of the above interdiffusivities is estimated from the quasibinary interdiffusivities in all composition ranges of the present oxide system in liquid state.     

Resolving permutation ambiguity in correlation-based blind image separation

We address the problem of permutation ambiguity in blind separation of multiple mixtures of multiple images (resulting, for instance, from multiple reflections through a thick grass plate or through two overlapping glass plates) with unknown mixing coefficients. In this paper, first we devise a generalized multiple correlation measure between one gray image and a set of multiple gray images and derive a decorrelation-based blind image separation algorithm. However, many blind image separation methods, including this algorithm, suffer from a permutation ambiguity problem that the success of the separation depends upon the selection of permutations corresponding to the orders of the update operations. To solve the problem, we improve the first algorithm above by decorrelating the mixtures while searching for the appropriate update permutation using a pruning technique. We show its effectiveness through experiments with artificially mixed images and real images.     

Analysis of PD-generated SF/sub 6/ decomposition gases adsorbed on carbon nanotubes

Chemical byproducts analysis has been recognized as a powerful diagnosis method for SF₆ gas-insulated switchgear (GIS). The authors have previously demonstrated that a carbon nanotube (CNT) gas sensor could detect partial discharge (PD) generated in SF₆ gas. However, PD-generated decomposition gas species, which were responsible for the CNT gas sensor response, have not been identified yet. In this paper, two kinds of experiments were conducted in order to identify the responsible decomposition gas species. At first, the decomposition gas molecules adsorbed on CNTs were analyzed by Fourier transformation infrared (FTIR) spectroscopy. FTIR absorbance was observed around 735 cm^-1 after CNTs were exposed to PD generated in SF₆. In the second experiment, the CNT gas sensor responses to typical SF₆ decomposition products (HF and SF₄) were examined. The CNT gas sensor responded to these gases in the same way as to PD generated in SF₆. SF₄ response was larger than HF response. Based on these results, SF ₄ and SOF₂ emerged as candidates for the responsible decomposition gases. Electrochemical interactions between adsorbed gas molecules and CNT were discussed based on theoretical predictions of molecular orbital calculations. The calculation results suggested that both of SOF₂ and SF₄ could increase the CNT gas sensor conductance     

Magnetization Reversal by Electrical Spin Injection in Ferromagnetic (Ga,Mn)As-Based Magnetic Tunnel Junctions

We report current-induced magnetization reversal in a ferromagnetic semiconductor-based magnetic tunnel junction (Ga,Mn)As/AlAs/(Ga,Mn)As prepared by molecular beam epitaxy on a p-GaAs(001) substrate. A change in magneto-resistance that is asymmetric with respect to the current direction is found with the excitation current of 10⁶ A/cm². Contributions of both unpolarized and spin-polarized components are examined, and we conclude that the partial magnetization reversal occurs in the (Ga,Mn)As layer having smaller magnetization with the spin-polarized tunneling current of 10⁵ A/cm².     

A flexible videoconference system based on multiagent framework

We present a design and implementation of a flexible videoconference system (VCS) using multiagent computing technology. The proposed system, we named FVCS, aims to reduce the burden of the users under the operational environment with insufficient computational resources, such as the Internet environment with small-scale computers at homes and offices, by embedding flexibility to the conventional videoconference system. In this paper, we design and implement FVCS with knowledge-based multiagent framework to realize adaptability of FVCS. We also evaluate the adaptability of the prototype systems of FVCS based on an operational situation observed in its experiments. From the result of the experiments, we conclude that the multiagent-based design and implementation is reasonable for construction of FVCS.