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.     

An Interactive Design System of Free‐Formed Bamboo‐Copters

We present an interactive design system for designing free‐formed bamboo‐copters, where novices can easily design free‐formed, even asymmetric bamboo‐copters that successfully fly. The designed bamboo‐copters can be fabricated using digital fabrication equipment, such as a laser cutter. Our system provides two useful functions for facilitating this design activity. First, it visualizes a simulated flight trajectory of the current bamboo‐copter design, which is updated in real time during the user's editing. Second, it provides an optimization function that automatically tweaks the current bamboo‐copter design such that the spin quality—how stably it spins—and the flight quality—how high and long it flies—are enhanced. To enable these functions, we present non‐trivial extensions over existing techniques for designing free‐formed model airplanes [ UKSI14 ], including a wing discretization method tailored to free‐formed bamboo‐copters and an optimization scheme for achieving stable bamboo‐copters considering both spin and flight qualities.     

Estimation of a nonvisible field-of-view mobile target incorporating optical and acoustic sensors

This paper presents a nonvisible field-of-view (NFOV) target estimation approach that incorporates optical and acoustic sensors. An optical sensor can accurately localize a target in its field-of-view whereas the acoustic sensor could estimate the target location over a much larger space, but only with limited accuracy. A recursive Bayesian estimation framework where observations of the optical and acoustic sensors are probabilistically treated and fused is proposed in this paper. A technique to construct the observation likelihood when two microphones are used as the acoustic sensor is also described. The proposed technique derives and stores the interaural level difference of observations from the two microphones for different target positions in advance and constructs the likelihood through correlation. A parametric study of the proposed acoustic sensing technique in a controlled test environment, and experiments with an NFOV target in an actual indoor environment are presented to demonstrate the capability of the proposed technique.     

Compressive multi-spectral imaging using self-correlations of images based on hierarchical joint sparsity models

We propose a novel multi-spectral imaging method based on compressive sensing (CS). In CS theory, the enhancement of signal sparsity is important for accurate signal reconstruction. The main novelty of the proposed method is the employment of a self-correlation of an image, that is a local intensity similarity and multi-spectral correlation, to enhance the sparsity of the multi-spectral image to be recovered. Local intensity similarity, which is based on the concept that spatial changes in intensity are likely to be similar within local regions, contributes to sparsity enhancement. Furthermore, we exploit multi-spectral correlation to improve the sparsity of the multi-spectral components to be recovered. In order to simultaneously exploit different types of characteristics (i.e., local intensity similarity and multi-spectral correlation) for representing a signal as sufficiently sparse, we introduce a hierarchical joint sparsity model in the CS image recovery process. Our experiments show that the use of a self-correlation significantly improves the performance of multi-spectral image reconstruction.     

Performance of SOR methods on modern vector and scalar processors

The building-cube method (BCM) is a new generation algorithm for CFD simulations. The basic idea of BCM is to simplify the algorithm in all stages of flow computation to achieve large-scale simulations. Calculation of a pressure field using the Successive Over Relaxation (SOR) method consumes most of the total execution time required for BCM. In this paper, effective implementations on modern vector and scalar processors are investigated. NEC SX-9 and Intel Nehalem-EX are the latest vector and scalar processors. Those processors have much higher peak performances than their previous-generation processors. However, their memory bandwidth improvement cannot catch up with the performance improvement of processors. This is the so-called memory wall problem. In our paper, we discuss optimization techniques for implementation of the SOR method based on architectural characteristics of these modern processors, and evaluate their effects on the sustained performances of these processors for BCM.     

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.     

A pilot survey of 39 Victorian WWTP effluents using a high speed luminescent umu test in conjunction with a novel GC-MS-database technique for automatic identification of micropollutants

In 2007, samples of treated effluent were collected at point of discharge to the environment from 39 wastewater treatment plants (WWTPs) located across Victoria, Australia grouped by treatment type. Sample genotoxicity was assessed with a high-throughput luminescent umu test method using Salmonella typhimurium TL210 strain, with and without addition of a commercially available metabolic activation system. Samples were also screened using a gas chromatographic-mass spectrometric mass-structure database recognition method. A genotoxic response was observed in half of the samples tested without metabolic activation system (相似文献   

High rate nitrogen removal by the CANON process at ambient temperature

Completely autotrophic nitrogen removal over nitrite (CANON) is a cost-effective nitrogen removal process. Implementation of the CANON process relies on the cooperation of ammonium-oxidizing and Anammox bacteria, as well as the inhibition of nitrite-oxidizing bacteria. Strict limitations on dissolved oxygen (DO) concentration in the reactor, and the addition of sufficient inorganic carbon in the influent, were adopted as the main operational strategies. The reactor was fed with synthetic inorganic wastewater composed mainly of NH(4)(+)-N, and operated for 106 days. Stable nitrogen removal rates (NRR) of around 1.4 kg N m(-3) d(-1) were obtained at ambient temperature. Morphological characteristics and analysis of bacterial community confirmed the formation of functional outer aerobic and inner anaerobic granular sludge, providing evidence of stable nitrogen removal.     

Construction of a brain–machine hybrid system to evaluate adaptability of an insect

Insects perform adaptive behavior according to changing environmental conditions using comparatively small brains. Because adaptability is generated through the relationship among brain, body and environment, it is necessary to examine how a brain works under these conditions. In this study, to understand neural processing involved in adaptive behavior, we constructed a brain–machine hybrid system using motor signals related to the steering behavior of the male silkworm moth for controlling a two-wheeled mobile robot. We developed this hybrid system according to the following steps. (1) We selected steering signals corresponding to walking direction that were activated during neck swinging induced by optic flow and pheromone stimuli. (2) To control a robot by neural activity, we implemented a spike-behavior conversion rule such that frequency of the left and right neck motor neurons’ spikes was linearly converted into rotation of the wheels. (3) For electrophysiological multi-unit recordings on a robot, we developed small amplifiers. Using this hybrid system, we could observe the programmed behavioral pattern and orientation toward a pheromone source. Moreover, we compared the orientation behavior of moths and that of the hybrid system at different pheromone stimulus frequencies. From these experiments, we concluded that we could reconstruct silkworm moth behavior on the hybrid system.     

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.