Networks for systems biology: conceptual connection of data and function

The purpose of this study is to survey the use of networks and network-based methods in systems biology. This study starts with an introduction to graph theory and basic measures allowing to quantify structural properties of networks. Then, the authors present important network classes and gene networks as well as methods for their analysis. In the last part of this study, the authors review approaches that aim at analysing the functional organisation of gene networks and the use of networks in medicine. In addition to this, the authors advocate networks as a systematic approach to general problems in systems biology, because networks are capable of assuming multiple roles that are very beneficial connecting experimental data with a functional interpretation in biological terms.

Evaluating Train Protection Systems

This paper arose from the work carried out for the Cullen/Uff Joint Inquiry into Train Protection Systems. It is concerned with the problem of evaluating the benefits of safety enhancements in order to avoid rare, but catastrophic accidents, and the role of Operations Research in the process. The problems include both input values and representation of outcomes. A key input is the value of life. This paper briefly discusses why the value of life might vary from incident to incident and reviews alternative estimates before producing a 'best estimate' for rail. When the occurrence of an event is uncertain, the normal method is to apply a single 'expected' value. This paper argues that a more effective method of representing such situations is through Monte-Carlo simulation and demonstrates the use of the methodology on a case study of the decision as to whether or not advanced train protection (ATP) should have been installed on a route to the west of London. This paper suggests that the output is more informative than traditional cost-benefit appraisals or engineering event tree approaches. It also shows that, unlike the results from utilizing the traditional approach, the value of ATP on this route would be positive over 50% of the time.

Rapid Implementation and Optimisation of DSP Systems on SoPC Heterogeneous Platforms

The emergence of programmable logic devices as processing platforms for digital signal processing applications poses challenges concerning rapid implementation and high level optimization of algorithms on these platforms. This paper describes Abhainn, a rapid implementation methodology and toolsuite for translating an algorithmic expression of the system to a working implementation on a heterogeneous multiprocessor/field programmable gate array platform, or a standalone system on programmable chip solution. Two particular focuses for Abhainn are the automated but configurable realisation of inter-processor communuication fabrics, and the establishment of novel dedicated hardware component design methodologies allowing algorithm level transformation for system optimization. This paper outlines the approaches employed in both these particular instances.

Development and Validation of a Forklift Truck Powertrain Simulation

Fuel economy has become an important consideration in forklift truck design, particularly in Europe. A simulation of the fuel consumption and performance of a forklift truck has been developed, validated and subsequently used to determine the energy consumed by individual powertrain components during drive cycles.
The truck used in this study has a rated lifting capacity of 2500kg, and is powered by a 2.6 litre naturally aspirated diesel engine with a fuel pump containing a mechanical variable-speed governor. The drivetrain consisted of a torque convertor, hydraulic clutch and single speed transmission.
AVL Cruise was used to simulate the vehicle powertrain, with coupled Mathworks Simulink models used to simulate the hydraulic and control systems and governor. The vehicle has been simulated on several performance and fuel consumption drive cycles with the main focus being the VDI 2198 fuel consumption drive cycle.
To validate the model, a truck was instrumented and measurements taken to compare the performance and instantaneous fuel consumption to simulated values. The fuel injector pump was modified and calibrated to enable instantaneous fuel flow to be measured.
The model has been validated to within acceptable limits and has been used to investigate the effect four different torque converters have on the fuel consumption and performance of the forklift truck. The study demonstrates how the model can be used to compare the fuel consumption and performance trade-offs when selecting drivetrain components.

WIQ:Work-intensive query scheduling for in-memory database systems

We propose a novel admission control policy for database queries. Our methodology uses system measurements of CPU utilization and query backlogs to determine interference between queries in execution on the same database server. Query interference may arise due to the concurrent access of hardware and software resources and can affect performance in positive and negative ways. Specifically our admission control considers the mix of jobs in service and prioritizes the query classes consuming CPU resources more efficiently. The policy ignores I/O subsystems and is therefore highly appropriate for in-memory databases. We validate our approach in trace-driven simulation and show performance increases of query slowdowns and throughputs compared to first-come first-served and shortest expected processing time first scheduling. Simulation experiments are parameterized from system traces of a SAP HANA in-memory database installation with TPC-H type workloads. © 2012 IEEE.

Mechanical characterization of the varian Exact-arm and R-arm support systems for eight aS500 electronic portal imaging devices

The aim of this study is to compare the positioning accuracy at different gantry angles of two electronic portal imaging devices (EPIDs) support arm systems by using EPID difference images as a measure for displacement. This work presents a comparison of the mechanical performance of eight Varian aS500 (Varian Medical Systems, Palo Alto, CA) EPIDs, mounted using either the Varian Exact-arm or R-arm.

An Energy Conserving Finite Difference Scheme for Simulation of Collisions

Nonlinear phenomena play an essential role in the sound production process of many musical instruments. A common source of these effects is object collision, the numerical simulation of which is known to give rise to stability
issues. This paper presents a method to construct numerical schemes that conserve the total energy in simulations of one-mass systems involving collisions, with no conditions imposed on any of the physical or numerical parameters.
This facilitates the adaptation of numerical models to experimental data, and allows a more free parameter adjustment in sound synthesis explorations. The energy preservedness of the proposed method is tested and demonstrated though several examples, including a bouncing ball and a non-linear oscillator, and implications regarding the wider applicability are discussed.

Evaluation of a substructured soft Real-time Hybrid Test for performing Seismic analysis of complex structural systems

The hybrid test method is a relatively recently developed dynamic testing technique that uses numerical modelling combined with simultaneous physical testing. The concept of substructuring allows the critical or highly nonlinear part of the structure that is difficult to numerically model with accuracy to be physically tested whilst the remainder of the structure, that has a more predictable response, is numerically modelled. In this paper, a substructured soft-real time hybrid test is evaluated as an accurate means of performing seismic tests of complex structures. The structure analysed is a three-storey, two-by-one bay concentrically braced frame (CBF) steel structure subjected to seismic excitation. A ground storey braced frame substructure whose response is critical to the overall response of the structure is tested, whilst the remainder of the structure is numerically modelled. OpenSees is used for numerical modelling and OpenFresco is used for the communication between the test equipment and numerical model. A novel approach using OpenFresco to define the complex numerical substructure of an X-braced frame within a hybrid test is also presented. The results of the hybrid tests are compared to purely numerical models using OpenSees and a simulated test using a combination of OpenSees and OpenFresco. The comparative results indicate that the test method provides an accurate and cost effective procedure for performing
full scale seismic tests of complex structural systems.

Linear Optics Simulation of Quantum Non-Markovian Dynamics

The simulation of open quantum dynamics has recently allowed the direct investigation of the features of system-environment interaction and of their consequences on the evolution of a quantum system. Such interaction threatens the quantum properties of the system, spoiling them and causing the phenomenon of decoherence. Sometimes however a coherent exchange of information takes place between system and environment, memory effects arise and the dynamics of the system becomes non-Markovian. Here we report the experimental realisation of a non-Markovian process where system and environment are coupled through a simulated transverse Ising model. By engineering the evolution in a photonic quantum simulator, we demonstrate the role played by system-environment correlations in the emergence of memory effects.

TLM2.0 based timing accurate modeling method for complex NoC systems

Scalability and efficiency of on-chip communication of emerging Multiprocessor System-on-Chip (MPSoC) are critical design considerations. Conventional bus based interconnection schemes no longer fit for MPSoC with a large number of cores. Networks-on-Chip (NoC) is widely accepted as the next generation interconnection scheme for large scale MPSoC. The increase of MPSoC complexity requires fast and accurate system-level modeling techniques for rapid modeling and veri-fication of emerging MPSoCs. However, the existing modeling methods are limited in delivering the essentials of timing accuracy and simulation speed. This paper proposes a novel system-level Networks-on-Chip (NoC) modeling method, which is based on SystemC and TLM2.0 and capable of delivering timing accuracy close to cycle accurate modeling techniques at a significantly lower simulation cost. Experimental results are presented to demonstrate the proposed method. ©2010 IEEE.

Pre-charging and DC Fault Ride-Through of Hybri MMC Based HVDC Systems

Compared to half-bridge based MMCs, full-bridge based systems have the advantage of blocking dc fault, but at the expense of increased power semiconductors and power losses. In view of the relationships among ac/dc voltages and currents in full-bridge based MMC with the negative voltage state, this paper provides a detailed analysis on the link between capacitor voltage variation and the maximum modulation index. A hybrid MMC, consisting of mixed half-bridge and full-bridge circuits to combine their respective advantages is investigated in terms of its pre-charging process and transient dc fault ride-through capability. Simulation and experiment results demonstrate the feasibility and validity of the proposed strategy for a full-bridge based MMC and the hybrid MMC.

Three-port DC-DC Converter for Stand-Alone Photovoltaic Systems

System efficiency and cost effectiveness are of critical importance for photovoltaic (PV) systems. This paper addresses the two issues by developing a novel three-port DC-DC converter for stand-alone PV systems, based on an improved Flyback-Forward topology. It provides a compact single-unit solution with a combined feature of optimized maximum power point tracking (MPPT), high step-up ratio, galvanic isolation and multiple operating modes for domestic and aerospace applications. A theoretical analysis is conducted to analyze the operating modes followed by simulation and experimental work. The paper is focused on a comprehensive modulation strategy utilizing both PWM and phase-shifted control that satisfies the requirement of PV power systems to achieve MPPT and output voltage regulation. A 250 W converter was designed and prototyped to provide experimental verification in term of system integration and high conversion efficiency.