Managing memory and reducing I/O cost for correlation matrix calculation in bioinformatics

The generation of a correlation matrix from a large set of long gene sequences is a common requirement in many bioinformatics problems such as phylogenetic analysis. The generation is not only computationally intensive but also requires significant memory resources as, typically, few gene sequences can be simultaneously stored in primary memory. The standard practice in such computation is to use frequent input/output (I/O) operations. Therefore, minimizing the number of these operations will yield much faster run-times. This paper develops an approach for the faster and scalable computing of large-size correlation matrices through the full use of available memory and a reduced number of I/O operations. The approach is scalable in the sense that the same algorithms can be executed on different computing platforms with different amounts of memory and can be applied to different problems with different correlation matrix sizes. The significant performance improvement of the approach over the existing approaches is demonstrated through benchmark examples.

Computer simulation of underground blast response of pile in saturated soil

This paper treats the blast response of a pile foundation in saturated sand using explicit nonlinear finite element analysis, considering complex material behavior of soil and soil–pile interaction. Blast wave propagation in the soil is studied and the horizontal deformation of pile and effective stresses in the pile are presented. Results indicate that the upper part of the pile to be vulnerable and the pile response decays with distance from the explosive. The findings of this research provide valuable information on the effects of underground explosions on pile foundation and will guide future development, validation and application of computer models.

Engaging students in authoring and playing computer games

Computer games have become a commonplace but engaging activity among students. They enjoy playing computer games as they can perform larger-than-life activities virtually such as jumping from great heights, flying planes, and racing cars; actions that are otherwise not possible in real life. Computer games also offer user interactivity which gives them a certain appeal. Considering this appeal, educators should consider integrating computer games into student learning and to encourage students to author computer games of their own. It is thought that students can be engaged in learning by authoring and using computer games and can also gain essential skills such as collaboration, teamwork, problem solving and deductive reasoning. The research in this study revolves around building student engagement through the task of authoring computer games. The study aims to demonstrate how the creation and sharing of student-authored educational games might facilitate student engagement and how ICT (information and communication technology) plays a supportive role in student learning. Results from this study may lead to the broader integration of computer games into student learning and contribute to similar studies. In this qualitative case study, based in a state school in a low socio-economic area west of Brisbane, Australia, students were selected in both junior and senior secondary classes who have authored computer games as a part of their ICT learning. Senior secondary students (Year 12 ICT) were given the task of programming the games, which were to be based on Mathematics learning topics while the junior secondary students (Year 8 ICT) were given the task of creating multimedia elements for the games. A Mathematics teacher volunteered to assist in the project and provided guidance on the inclusion of suitable Mathematics curricular content into these computer games. The student-authored computer games were then used to support another group of Year 8 Mathematics students to learn the topics of Area, Volume and Time. Data was collected through interviews, classroom observations and artefacts. The teacher researcher, acting in the role of ICT teacher, coordinated with the students and the Mathematics teacher to conduct this study. Instrumental case study was applied as research methodology and Third Generation Activity Theory served as theoretical framework for this study. Data was analysed adopting qualitative coding procedures. Findings of this study indicate that having students author and play computer games promoted student engagement and that ICT played a supportive role in learning and allowed students to gain certain essential skills. Although this study will suggest integrating computer games to support classroom learning, it cannot be presumed that computer games are an immediate solution for promoting student engagement.

CADDS: an automated die design system for sheet-metal blanking

This article reports on the design and implementation of a Computer-Aided Die Design System (CADDS) for sheet-metal blanks. The system is designed by considering several factors, such as the complexity of blank geometry, reduction in scrap material, production requirements, availability of press equipment and standard parts, punch profile complexity, and tool elements manufacturing method. The interaction among these parameters and how they affect designers' decision patterns is described. The system is implemented by interfacing AutoCAD with the higher level languages FORTRAN 77 and AutoLISP. A database of standard die elements is created by parametric programming, which is an enhanced feature of AutoCAD. The greatest advantage achieved by the system is the rapid generation of the most efficient strip and die layouts, including information about the tool configuration.

Coordinated probabilistic optimal decision-making model for multi-area ATC with risk control

In the decision-making of multi-area ATC (Available Transfer Capacity) in electricity market environment, the existing resources of transmission network should be optimally dispatched and coordinately employed on the premise that the secure system operation is maintained and risk associated is controllable. The non-sequential Monte Carlo simulation is used to determine the ATC probability density distribution of specified areas under the influence of several uncertainty factors, based on which, a coordinated probabilistic optimal decision-making model with the maximal risk benefit as its objective is developed for multi-area ATC. The NSGA-II is applied to calculate the ATC of each area, which considers the risk cost caused by relevant uncertainty factors and the synchronous coordination among areas. The essential characteristics of the developed model and the employed algorithm are illustrated by the example of IEEE 118-bus test system. Simulative result shows that, the risk of multi-area ATC decision-making is influenced by the uncertainties in power system operation and the relative importance degrees of different areas.

A Systematic review of a statistical vacuum circuit breaker model for condition monitoring

Vacuum circuit breaker (VCB) overvoltage failure and its catastrophic failures during shunt reactor switching have been analyzed through computer simulations for multiple reignitions with a statistical VCB model found in the literature. However, a systematic review (SR) that is related to the multiple reignitions with a statistical VCB model does not yet exist. Therefore, this paper aims to analyze and explore the multiple reignitions with a statistical VCB model. It examines the salient points, research gaps and limitations of the multiple reignition phenomenon to assist with future investigations following the SR search. Based on the SR results, seven issues and two approaches to enhance the current statistical VCB model are identified. These results will be useful as an input to improve the computer modeling accuracy as well as the development of a reignition switch model with point-on-wave controlled switching for condition monitoring

Slotted cooperative communication in half duplex relay networks

In cooperative communication systems, several wireless communication terminals collaborate to form a virtual-multiple antenna array system and exploit the spatial diversity to achieve a better performance. This thesis proposes a practical slotted protocol for cooperative communication systems with half-duplex single antennas. The performance of the proposed slotted cooperative communication protocol is evaluated in terms of the pairwise error probability and the bit error rate. The proposed protocol achieves the multiple-input single-output performance bound with a novel relay ordering and scheduling strategy.

Sample size considerations and augmentation of computer experiments

Computer Experiments, consisting of a number of runs of a computer model with different inputs, are now common-place in scientific research. Using a simple fire model for illustration some guidelines are given for the size of a computer experiment. A graph is provided relating the error of prediction to the sample size which should be of use when designing computer experiments. Methods for augmenting computer experiments with extra runs are also described and illustrated. The simplest method involves adding one point at a time choosing that point with the maximum prediction variance. Another method that appears to work well is to choose points from a candidate set with maximum determinant of the variance covariance matrix of predictions.

Assessment of precision timing and real-time data networks for digital substation automation

This project researched the performance of emerging digital technology for high voltage electricity substations that significantly improves safety for staff and reduces the potential impact on the environment of equipment failure. The experimental evaluation used a scale model of a substation control system that incorporated real substation control and networking equipment with real-time simulation of the power system. The outcomes confirm that it is possible to implement Ethernet networks in high voltage substations that meet the needs of utilities; however component-level testing of devices is necessary to achieve this. The assessment results have been used to further develop international standards for substation communication and precision timing.

Monte Carlo verification of intensity modulated radiotherapy treatments using EPIDS

Purpose: Electronic Portal Imaging Devices (EPIDs) are available with most linear accelerators (Amonuk, 2002), the current technology being amorphous silicon flat panel imagers. EPIDs are currently used routinely in patient positioning before radiotherapy treatments. There has been an increasing interest in using EPID technology tor dosimetric verification of radiotherapy treatments (van Elmpt, 2008). A straightforward technique involves the EPID panel being used to measure the fluence exiting the patient during a treatment which is then compared to a prediction of the fluence based on the treatment plan. However, there are a number of significant limitations which exist in this Method: Resulting in a limited proliferation ot this technique in a clinical environment. In this paper, we aim to present a technique of simulating IMRT fields using Monte Carlo to predict the dose in an EPID which can then be compared to the measured dose in the EPID. Materials: Measurements were made using an iView GT flat panel a-SI EPfD mounted on an Elekta Synergy linear accelerator. The images from the EPID were acquired using the XIS software (Heimann Imaging Systems). Monte Carlo simulations were performed using the BEAMnrc and DOSXVZnrc user codes. The IMRT fieids to be delivered were taken from the treatment planning system in DICOMRT format and converted into BEAMnrc and DOSXYZnrc input files using an in-house application (Crowe, 2009). Additionally. all image processing and analysis was performed using another in-house application written using the Interactive Data Language (IDL) (In Visual Information Systems). Comparison between the measured and Monte Carlo EPID images was performed using a gamma analysis (Low, 1998) incorporating dose and distance to agreement criteria. Results: The fluence maps recorded by the EPID were found to provide good agreement between measured and simulated data. Figure 1 shows an example of measured and simulated IMRT dose images and profiles in the x and y directions. "A technique for the quantitative evaluation of dose distributions", Med Phys, 25(5) May 1998 S. Crowe, 1. Kairn, A. Fielding, "The Development of a Monte Carlo system to verify Radiotherapy treatment dose calculations", Radiotherapy & Oncology, Volume 92, Supplement 1, August 2009, Pages S71-S71.

Computer modeling of diffusion in biological tissues

Molecular-level computer simulations of restricted water diffusion can be used to develop models for relating diffusion tensor imaging measurements of anisotropic tissue to microstructural tissue characteristics. The diffusion tensors resulting from these simulations can then be analyzed in terms of their relationship to the structural anisotropy of the model used. As the translational motion of water molecules is essentially random, their dynamics can be effectively simulated using computers. In addition to modeling water dynamics and water-tissue interactions, the simulation software of the present study was developed to automatically generate collagen fiber networks from user-defined parameters. This flexibility provides the opportunity for further investigations of the relationship between the diffusion tensor of water and morphologically different models representing different anisotropic tissues.

Monitoring user activity on smart mobile devices

The invention relates to a method for monitoring user activity on a mobile device, comprising an input and an output unit, comprising the following steps preferably in the following order: detecting and / or logging user activity on said input unit, identifying a foreground running application, hashing of a user-interface-element management list of the foreground running application, and creating a screenshot comprising items displayed on said input unit. The invention also relates to a method for analyzing user activity at a server, comprising the following step: obtaining at least one of an information about detected and / or logged user activity, an information about a foreground running application, a hashed user-interface-element management list and a screenshot from a mobile device. Further, a computer program product is provided, comprising one or more computer readable media having computer executable instructions for performing the steps of at least one of the aforementioned methods.

Quantum one-time programs

A one-time program is a hypothetical device by which a user may evaluate a circuit on exactly one input of his choice, before the device self-destructs. One-time programs cannot be achieved by software alone, as any software can be copied and re-run. However, it is known that every circuit can be compiled into a one-time program using a very basic hypothetical hardware device called a one-time memory. At first glance it may seem that quantum information, which cannot be copied, might also allow for one-time programs. But it is not hard to see that this intuition is false: one-time programs for classical or quantum circuits based solely on quantum information do not exist, even with computational assumptions. This observation raises the question, "what assumptions are required to achieve one-time programs for quantum circuits?" Our main result is that any quantum circuit can be compiled into a one-time program assuming only the same basic one-time memory devices used for classical circuits. Moreover, these quantum one-time programs achieve statistical universal composability (UC-security) against any malicious user. Our construction employs methods for computation on authenticated quantum data, and we present a new quantum authentication scheme called the trap scheme for this purpose. As a corollary, we establish UC-security of a recent protocol for delegated quantum computation.

Building the computer mediated distance learning community: Issues and observations drawn from teaching and learning

This paper discusses computer mediated distance learning on a Master's level course in the UK and student perceptions of this as a quality learning environment.