Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

Survery and simulation of energy use in the European building stock

the work towards increased energy efficiency. In order to plan and perform effective energy renovation of the buildings, it is necessary to have adequate information on the current status of the buildings in terms of architectural features and energy needs. Unfortunately, the official statistics do not include all of the needed information for the whole building stock.   This paper aims to fill the gaps in the statistics by gathering data from studies, projects and national energy agencies, and by calibrating TRNSYS models against the existing data to complete missing energy demand data, for countries with similar climate, through simulation. The survey was limited to residential and office buildings in the EU member states (before July 2013). This work was carried out as part of the EU FP7 project iNSPiRe.   The building stock survey revealed over 70% of the residential and office floor area is concentrated in the six most populated countries. The total energy consumption in the residential sector is 14 times that of the office sector. In the residential sector, single family houses represent 60% of the heated floor area, albeit with different share in the different countries, indicating that retrofit solutions cannot be focused only on multi-family houses.   The simulation results indicate that residential buildings in central and southern European countries are not always heated to 20 °C, but are kept at a lower temperature during at least part of the day. Improving the energy performance of these houses through renovation could allow the occupants to increase the room temperature and improve their thermal comfort, even though the potential for energy savings would then be reduced.

Energy performance comparison of three innovative HVAC systems for renovation through dynamic simulation

In this paper, dynamic simulation was used to compare the energy performance of three innovativeHVAC systems: (A) mechanical ventilation with heat recovery (MVHR) and micro heat pump, (B) exhaustventilation with exhaust air-to-water heat pump and ventilation radiators, and (C) exhaust ventilationwith air-to-water heat pump and ventilation radiators, to a reference system: (D) exhaust ventilation withair-to-water heat pump and panel radiators. System A was modelled in MATLAB Simulink and systems Band C in TRNSYS 17. The reference system was modelled in both tools, for comparison between the two.All systems were tested with a model of a renovated single family house for varying U-values, climates,infiltration and ventilation rates.It was found that A was the best system for lower heating demand, while for higher heating demandsystem B would be preferable. System C was better than the reference system, but not as good as A or B.The difference in energy consumption of the reference system was less than 2 kWh/(m2a) betweenSimulink and TRNSYS. This could be explained by the different ways of handling solar gains, but also bythe fact that the TRNSYS systems supplied slightly more than the ideal heating demand.

Offshore Wind Energy System with DC Transmission Discrete Mass: Modeling and Simulation

This paper presents an integrated model for an offshore wind energy system taking into consideration a contribution for the marine wave and wind speed with perturbations influences on the power quality of current injected into the electric grid. The paper deals with the simulation of one floating offshore wind turbine equipped with a PMSG and a two-level converter connected to an onshore electric grid. The use of discrete mass modeling is accessed in order to reveal by computing the THD on how the perturbations of the captured energy are attenuated at the electric grid injection point. Two torque actions are considered for the three-mass modeling, the aerodynamic on the flexible part and on the rigid part of the blades. Also, a torque due to the influence of marine waves in deep water is considered. PI fractional-order control supports the control strategy. A comparison between the drive train models is presented.

Blade pitch control malfunction simulation in a wind energy conversion system with MPC five-level converter

This paper is on a wind energy conversion system simulation of a transient analysis due to a blade pitch control malfunction. The aim of the transient analysis is the study of the behavior of a back-to-back multiple point clamped five-level full-power converter implemented in a wind energy conversion system equipped with a permanent magnet synchronous generator. An alternate current link connects the system to the grid. The drive train is modeled by a three-mass model in order to simulate the dynamic effect of the wind on the tower. The control strategy is based on fractional-order control. Unbalance voltages in the DC-link capacitors are lessen due to the control strategy, balancing the capacitor banks voltages by a selection of the output voltage vectors. Simulation studies are carried out to evaluate not only the system behavior, but also the quality of the energy injected into the electric grid.

Offshore Wind Energy Conversion System Connected to the Electric Grid: Modeling and Simulation

This paper is on modeling and simulation for an offshore wind system equipped with a semi-submersible floating platform, a wind turbine, a permanent magnet synchronous generator, a multiple point clamped four level or five level full-power converter, a submarine cable and a second order filter. The drive train is modeled by three mass model considering the resistant stiffness torque, structure and tower in deep water due to the moving surface elevation. The system control uses PWM by space vector modulation associated with sliding mode and proportional integral controllers. The electric energy is injected into the electric grid either by an alternated current link or by a direct current link. The model is intend to be a useful tool for unveil the behavior and performance of the offshore wind system, especially for the multiple point clamped full-power converter, under normal operation or under malfunctions.

Effects of collimator backscatter in an Elekta linac by Monte Carlo simulation

The effects of radiation backscattered from the secondary collimators into the monitor chamber in an Elekta linac (producing 6 and 10 MV photon beams) are investigated using BEAMnrc Monte Carlo simulations. The degree and effects of this backscattered radiation are assessed by evaluating the changes to the calculated dose in the monitor chamber, and by determining a correction factor for those changes. Additionally, the fluency and energy characteristics of particles entering the monitor chamber from the downstream direction are evaluated by examining BEAMnrc phase-space data. It is shown that the proportion of particles backscattered into the monitor chamber is small (<0.35 %), for all field sizes studied. However, when the backscatter plate is removed from the model linac, these backscattered particles generate a noticeable increase in dose to the monitor chamber (up to approximate to 2.4 % for the 6 MV beam and up to 4.4 % for the 10 MV beam). With its backscatter plate in place, the Elekta linac (operating at 6 and 10 MV) is subject to negligible variation of monitor chamber dose with field size. At these energies, output variations in photon beams produced by the clinical Elekta linear accelerator can be attributed to head scatter alone. Corrections for field-size-dependence of monitor chamber dose are not necessary when running Monte Carlo simulations of the Elekta linac operating at 6 and 10 MV.

Impact and energy absorption of empty and foam-filled conical tubes

Foam-filled conical tubes have recently emerged as efficient energy absorbing devices to mitigate the adverse effects of impacts. The primary aim of this thesis was to generate research and design information on the impact and energy absorption response of empty and foam-filled conical tubes, and to facilitate their application in energy absorbing systems under axial and oblique loading conditions representative of those typically encountered in crashworthiness and impact applications. Finite element techniques supported by experiments and existing results were used in the investigation. Major findings show that the energy absorption response can be effectively controlled by varying geometry and material parameters. A useful empirical formula was developed for providing engineering designers with an initial estimate of the load ratio and hence energy absorption performances of these devices. It was evident that foam-filled conical tubes enhance the energy absorption capacity and stabilise the crush response for both axial and oblique impact loading without a significant increase in the initial peak load. This is practically beneficial when higher kinetic energy needs to be absorbed, thus reducing the impact force transmitted to the protected structure and occupants. Such tubes also increase and maintain the energy absorption capacity under global bending as well as minimise the reduction of energy absorption capacity with increasing load angle. Furthermore, the results also highlight the feasibility of adding a foam-filled conical tube as a supplementary device in energy absorbing systems, since the overall energy absorption performance of such systems can be favourably enhanced by only including a relatively small energy absorbing device. Above all, the results demonstrate the superior performance of foam-filled conical tube for mitigating impact energy in impact and crashworthiness applications.

Dynamic energy absorption characteristics of foam-filled conical tubes under oblique impact loading

This paper treats the crush behaviour and energy absorption response of foam-filled conical tubes subjected to oblique impact loading. Dynamic computer simulation techniques validated by experimental testing are used to carry out a parametric study of such devices. The study aims at quantifying the energy absorption of empty and foam-filled conical tubes under oblique impact loading, for variations in the load angle and geometry parameters of the tube. It is evident that foam-filled conical tubes are preferable as impact energy absorbers due to their ability to withstand oblique impact loads as effectively as axial impact loads. Furthermore, it is found that the energy absorption capacity of filled tubes is better maintained compared to that of empty tubes as the load orientation increases. The primary outcome of this study is design information for the use of foam-filled conical tubes as energy absorbers where oblique impact loading is expected.

Simulation and measurement of an electrostatic discharge

Electrostatic discharge is the sudden and brief electric current that flashes between two objects at different voltages. This is a serious issue ranging in application from solid-state electronics to spectacular and dangerous lightning strikes (arc flashes). The research herein presents work on the experimental simulation and measurement of the energy in an electrostatic discharge. The energy released in these discharges has been linked to ignitions and burning in a number of documented disasters and can be enormously hazardous in many other industrial scenarios. Simulations of electrostatic discharges were designed to specifications by IEC standards. This is typically based on the residual voltage/charge on the discharge capacitor, whereas this research examines the voltage and current in the actual spark in order to obtain a more precise comparative measurement of the energy dissipated.

Parallel linear system solution and its application to railway power network simulation

The Streaming SIMD extension (SSE) is a special feature embedded in the Intel Pentium III and IV classes of microprocessors. It enables the execution of SIMD type operations to exploit data parallelism. This article presents improving computation performance of a railway network simulator by means of SSE. Voltage and current at various points of the supply system to an electrified railway line are crucial for design, daily operation and planning. With computer simulation, their time-variations can be attained by solving a matrix equation, whose size mainly depends upon the number of trains present in the system. A large coefficient matrix, as a result of congested railway line, inevitably leads to heavier computational demand and hence jeopardizes the simulation speed. With the special architectural features of the latest processors on PC platforms, significant speed-up in computations can be achieved.

A review of simulation models for railway systems

With the advances in computer hardware and software development techniques in the past 25 years, digital computer simulation of train movement and traction systems has been widely adopted as a standard computer-aided engineering tool [1] during the design and development stages of existing and new railway systems. Simulators of different approaches and scales are used extensively to investigate various kinds of system studies. Simulation is now proven to be the cheapest means to carry out performance predication and system behaviour characterisation. When computers were first used to study railway systems, they were mainly employed to perform repetitive but time-consuming computational tasks, such as matrix manipulations for power network solution and exhaustive searches for optimal braking trajectories. With only simple high-level programming languages available at the time, full advantage of the computing hardware could not be taken. Hence, structured simulations of the whole railway system were not very common. Most applications focused on isolated parts of the railway system. It is more appropriate to regard those applications as primarily mechanised calculations rather than simulations. However, a railway system consists of a number of subsystems, such as train movement, power supply and traction drives, which inevitably contains many complexities and diversities. These subsystems interact frequently with each other while the trains are moving; and they have their special features in different railway systems. To further complicate the simulation requirements, constraints like track geometry, speed restrictions and friction have to be considered, not to mention possible non-linearities and uncertainties in the system. In order to provide a comprehensive and accurate account of system behaviour through simulation, a large amount of data has to be organised systematically to ensure easy access and efficient representation; the interactions and relationships among the subsystems should be defined explicitly. These requirements call for sophisticated and effective simulation models for each component of the system. The software development techniques available nowadays allow the evolution of such simulation models. Not only can the applicability of the simulators be largely enhanced by advanced software design, maintainability and modularity for easy understanding and further development, and portability for various hardware platforms are also encouraged. The objective of this paper is to review the development of a number of approaches to simulation models. Attention is, in particular, given to models for train movement, power supply systems and traction drives. These models have been successfully used to enable various ‘what-if’ issues to be resolved effectively in a wide range of applications, such as speed profiles, energy consumption, run times etc.