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.     

A digital photography framework enabling affective awareness in home communication

By transforming the personal computer into a communication appliance, the Internet has initiated the true home computing revolution. As a result, Computer Mediated Communication (CMC) technologies are increasingly used in domestic settings, and are changing the way people keep in touch with their relatives and friends. This article first looks at how CMC tools are currently used in the home, and points at some of their benefits and limitations. Most of these tools supportexplicit interpersonal communication, by providing a new medium for sustaining conversations. The need for tools supportingimplicit interaction between users, in more natural and effottless ways, is then argued for. The idea of affective awareness is introduced as a general sense of being in touch with one's family and friends. Finally, the KAN-G framework, which enables affective awareness through the exchange of digital photographs, is described. Various components, which make the capture, distribution, observation and annotation of snapshots easy and effortless, are discussed.     

Fabrication of particle-free thin films by laser ablation combined with an electron beam

Particle-free silicon and nickel thin films were successfully fabricated by laser-ablating a melted section of their target surface, which gives a high evaporation pressure at the melting point. The influence of direct evaporation from a melted target was reduced negligibly by melting the target only locally with a focused electron beam (e-beam) and increasing the laser frequency. The silicon films fabricated by the present method, pulse laser deposition of a partially molten target, were able to firmly adhere to the substrates and withstood steel needle scratching, unlike e-beam-evaporated films.     

High Temperature Schottky Barrier on n-Type SrTiO3 and Its Sensitivity to Ambient Gases

Metal or oxide electrodes (Pt, Au, Ag, (La, Sr)CoO₃) were deposited on single crystals of 0.02 mol% Nb doped SrTiO₃ by pulsed laser deposition. Current-voltage and capacitance-voltage responses were measured using three-terminal electrode configuration. Under high oxygen partial pressures, clear rectification behaviors were observed. Diffusion model well explained the current vs. voltage relationship with ideality factors close to unity. The barrier height varied reversibly with oxygen partial pressure, and was almost independent of the electrode materials, which suggested that the Fermi level at the interface was pinned by the surface states. The origin of the surface states was discussed in terms of oxygen adsorption or oxidative formation of metal vacancies around the surface. Chemical interaction between the surface and oxygen and resulting cation rearrangement was concluded to play an important role from the long stabilization time on oxygen partial pressure change. The water vapor pressure dependence of the barrier height was also explained by competitive adsorption of oxygen and water.     

Catalytic effect of bis (cyclopentadienyl) nickel II on the improvement of the hydrogenation-dehydrogenation of Mg-MgH2 system

Bis(cyclopentadienyl) nickel II is one of the best precursors of nickel catalyst which remarkably improved the hydrogen absorption-desorption of Mg–MgH₂ system. The X-ray photoelectron spectroscopy (XPS) and Furrier Transformed Infrared Spectroscopy (FTIR) analyses revealed that bis (cyclopentadienyl) nickel II decomposed into metallic nickel during ball milling with MgH₂. The nickel thus formed has homogeneously doped over the Mg - MgH₂ surface. The Ni-doped Mg-MgH₂ have shown the excellent catalytic effect on hydrogen absorption-desorption. The catalyzed MgH₂ could desorb hydrogen below 225 °C (T_onset) under Ar flow, and absorb hydrogen at 50 °C under 1.5 MPa H₂ pressure. The hydrogen absorption-desorption temperatures are remarkably decreased as compared to the uncatalyzed Mg-MgH₂ system under the identical experimental conditions.     

Thermal Stability,Optical Transmittance,and Refractive Index Dispersion of La2O3–Nb2O5–Al2O3 Glasses

La₂O₃–Nb₂O₅–Al₂O₃ high‐refractive‐index glasses were fabricated by containerless processing, and the glass‐forming region was determined. The thermal stability, density, optical transmittance, and the refractive index dispersion of these glasses were investigated. All the glasses were colorless and transparent in the visible to near infrared (NIR) region and had high refractive index with low wavelength dispersion. Some of these glasses were found to have significantly high glass‐forming ability. These results indicate that the ternary glasses are suitable for optical applications in the visible to NIR region. The effects of the substitution of Al₂O₃ for Nb₂O₅ on optical properties were discussed on the basis of the Drude–Voigt equation. It was suggested that the substitution of Al₂O₃ for Nb₂O₅ increased the molecular density and suppressed a decrease in the refractive index, even when both the average oscillator strength and inherent absorption wavelength decreased in La₂O₃–Nb₂O₅–Al₂O₃ glasses. These results are helpful for designing new optical glasses controlled to have a higher refractive index and lower wavelength dispersion.     

H∞ control and filtering with initial uncertainty for infinite dimensional systems

The H_∞-control problem with a non-zero initial condition for infinite dimensional systems is considered The initial conditions are assumed to be in some subspace. First the H_∞ problem with full information is considered and necessary and sufficient conditions for the norm of an input-output operator to be less than a given number are obtained, The characterization of all admissible controllers is also given. This result is then used to solve the general H^∞ control problem and the filtering problem with initial uncertainty. The filtering problem on finite horizon involves the estimate of the state at final time. The set of all suboptimal filters is given both on finite and infinite horizons.     

Dual-Mode Space-Temporal Simultaneous Processing Equalizer

A tapped delayed line adaptive array antenna (TDL-AAA) and a space-temporal simultaneous processing equalizer (ST-SPE) are proposed as simple space-temporal equalizers based on minimum mean square error (MMSE) criterion. The ST-SPE has a compact hardware with a small number of taps compared to that of the TDL-AAA. The ST-SPE can reduce the computational complexity of the space-temporal joint equalization and it works effectively under the minimum phase condition such as appeared at line-of-sight (LOS) propagation environments at a high antenna height base station. However the ST-SPE cannot work under a non-minimum phase condition caused under N-LOS (non-line-of-sight). On the other hand, the TDL-AAA whose reference signal is synchronized at the center tap (TDL-AAA_C) can work even in the non-minimum phase condition. In this paper, we propose a dual-mode space-temporal simultaneous processing equalizer (Dual-mode ST-SPE) which has a simple configuration and also works in non-minimum phase condition. The Dual-mode ST-SPE can reduce the computational complexity compared to the TDL-AAA_C. Yoshihiro Ichikawa received the B.E. degree in department of communication engineering, in National Defense Academy in 1995, and M.E. and D.E. degree from Ibaraki University in 2001 and 2004, respectively. He joined the Japan Air Self Defense Force in 1995. His research interests are an adaptive algorithm, an antenna design, and an adaptive array antenna. Shigeki Obote received his B.E., M.E. and D.E. degrees in electrical and electronic engineering from Tottori University, Tottori, Japan, in 1996, 1998 and 2000, respectively. Since 2000, he has been with department of media and telecommunications engineering, faculty of engineering, Ibaraki University, Ibaraki, Japan, where he is currently a associate professor. His research interests are in adaptive array antenna and wireless communications systems. Kenichi Kagoshima received the B.E., M.E. and D.E. degrees in electronics engineering from the Tokyo Institute of Technology, Tokyo, Japan, in 1969, 1971, and 1974, respectively. He joined the Nippon Telegraph and Telephone Corporation (NTT) Laboratory in 1974 and researched and developed many kinds of radio communication antennas. Since 1997, he has been a professor at Ibaraki University, Ibaraki, Japan. Dr. Kagoshima was a Secretary and Treasure, Vice Chairman, and Chairman of the IEEE AP-S Tokyo Chapter in 1992, 1993, and 1994, respectively. He was a chair of antennas and propagation professional group of IEICE in 1999 and 2000. In 1973, he received the Yonezawa Prize for Young Engineers and 1998, best paper award from IEICE, respectively.