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.

Computer simulation of radio-frequency methane/hydrogen plasmas and their interaction with GaAs Surfaces

The following thesis describes the computer modelling of radio frequency capacitively coupled methane/hydrogen plasmas and the consequences for the reactive ion etching of (100) GaAs surfaces. In addition a range of etching experiments was undertaken over a matrix of pressure, power and methane concentration. The resulting surfaces were investigated using X-ray photoelectron spectroscopy and the results were discussed in terms of physical and chemical models of particle/surface interactions in addition to the predictions for energies, angles and relative fluxes to the substrate of the various plasma species. The model consisted of a Monte Carlo code which followed electrons and ions through the plasma and sheath potentials whilst taking account of collisions with background neutral gas molecules. The ionisation profile output from the electron module was used as input for the ionic module. Momentum scattering interactions of ions with gas molecules were investigated via different models and compared against results given by quantum mechanical code. The interactions were treated as central potential scattering events and the resulting neutral cascades were followed. The resulting predictions for ion energies at the cathode compared well to experimental ion energy distributions and this verified the particular form of the electrical potentials used and their applicability in the particular geometry plasma cell used in the etching experiments. The final code was used to investigate the effect of external plasma parameters on the mass distribution, energy and angles of all species impingent on the electrodes. Comparisons of electron energies in the plasma also agreed favourably with measurements made using a Langmuir electric probe. The surface analysis showed the surfaces all to be depleted in arsenic due to its preferential removal and the resultant Ga:As ratio in the surface was found to be directly linked to the etch rate. The etch rate was determined by the methane flux which was predicted by the code.

Technical and economic simulation of biomass pyrolysis processes for fuels and electricity

There is considerable concern over the increased effect of fossil fuel usage on the environment and this concern has resulted in an effort to find alternative, environmentally friendly energy sources. Biomass is an available alternative resource which may be converted by flash pyrolysis to produce a crude liquid product that can be used directly to substitute for conventional fossil fuels or upgraded to a higher quality fuel. Both the crude and upgraded products may be utilised for power generation. A computer program, BLUNT, has been developed to model the flash pyrolysis of biomass with subsequent upgrading, refining or power production. The program assesses and compares the economic and technical opportunities for biomass thermochemical conversion on the same basis. BLUNT works by building up a selected processing route from a number of process steps through which the material passes sequentially. Each process step has a step model that calculates the mass and energy balances, the utilities usage and the capital cost for that step of the process. The results of the step models are combined to determine the performance of the whole conversion route. Sample results from the modelling are presented in this thesis. Due to the large number of possible combinations of feeds, conversion processes, products and sensitivity analyses a complete set of results is impractical to present in a single publication. Variation of the production costs for the available products have been illustrated based on the cost of a wood feedstock. The effect of selected macroeconomic factors on the production costs of bio-diesel and gasoline are also given.

Computer simulation of moist agglomerate collisions

This thesis considers the computer simulation of moist agglomerate collisions using the discrete element method (DEM). The study is confined to pendular state moist agglomerates, at which liquid is presented as either absorbed immobile films or pendular liquid bridges and the interparticle force is modelled as the adhesive contact force and interstitial liquid bridge force. Algorithms used to model the contact force due to surface adhesion, tangential friction and particle deformation have been derived by other researchers and are briefly described in the thesis. A theoretical study of the pendular liquid bridge force between spherical particles has been made and the algorithms for the modelling of the pendular liquid bridge force between spherical particles have been developed and incorporated into the Aston version of the DEM program TRUBAL. It has been found that, for static liquid bridges, the more explicit criterion for specifying the stable solution and critical separation is provided by the total free energy. The critical separation is given by the cube root of liquid bridge volume to a good approximation and the 'gorge method' of evaluation based on the toroidal approximation leads to errors in the calculated force of less than 10%. Three dimensional computer simulations of an agglomerate impacting orthogonally with a wall are reported. The results demonstrate the effectiveness of adding viscous binder to prevent attrition, a common practice in process engineering. Results of simulated agglomerate-agglomerate collisions show that, for colinear agglomerate impacts, there is an optimum velocity which results in a near spherical shape of the coalesced agglomerate and, hence, minimises attrition due to subsequent collisions. The relationship between the optimum impact velocity and the liquid viscosity and surface tension is illustrated. The effect of varying the angle of impact on the coalescence/attrition behaviour is also reported. (DX 187, 340).

Desalination of brackish water by a batch reverse osmosis desalink system for use with solar thermal energy

For remote, semi-arid areas, brackish groundwater (BW) desalination powered by solar energy may serve as the most technically and economically viable means to alleviate the water stresses. For such systems, high recovery ratio is desired because of the technical and economical difficulties of concentrate management. It has been demonstrated that the current, conventional solar reverse osmosis (RO) desalination can be improved by 40–200 times by eliminating unnecessary energy losses. In this work, a batch-RO system that can be powered by a thermal Rankine cycle has been developed. By directly recycling high pressure concentrates and by using a linkage connection to provide increasing feed pressures, the batch-RO has been shown to achieve a 70% saving in energy consumption compared to a continuous single-stage RO system. Theoretical investigations on the mass transfer phenomena, including dispersion and concentration polarization, have been carried out to complement and to guide experimental efforts. The performance evaluation of the batch-RO system, named DesaLink, has been based on extensive experimental tests performed upon it. Operating DesaLink using compressed air as power supply under laboratory conditions, a freshwater production of approximately 300 litres per day was recorded with a concentration of around 350 ppm, whilst the feed water had a concentration range of 2500–4500 ppm; the corresponding linkage efficiency was around 40%. In the computational aspect, simulation models have been developed and validated for each of the subsystems of DesaLink, upon which an integrated model has been realised for the whole system. The models, both the subsystem ones and the integrated one, have been demonstrated to predict accurately the system performance under specific operational conditions. A simulation case study has been performed using the developed model. Simulation results indicate that the system can be expected to achieve a water production of 200 m3 per year by using a widely available evacuated tube solar collector having an area of only 2 m2. This freshwater production would satisfy the drinking water needs of 163 habitants in the Rajasthan region, the area for which the case study was performed.

Molecular dynamics simulation of brittle fracture in silicon

The fracture process involves converting potential energy from a strained body into surface energy, thermal energy, and the energy needed to create lattice defects. In dynamic fracture, energy is also initially converted into kinetic energy. This paper uses molecular dynamics (MD) to simulate brittle frcture in silicon and determine how energy is converted from potential energy (strain energy) into other forms.

Energy hole mitigation through cooperative transmission in wireless sensor networks

The energy balancing capability of cooperative communication is utilized to solve the energy hole problem in wireless sensor networks. We first propose a cooperative transmission strategy, where intermediate nodes participate in two cooperative multi-input single-output (MISO) transmissions with the node at the previous hop and a selected node at the next hop, respectively. Then, we study the optimization problems for power allocation of the cooperative transmission strategy by examining two different approaches: network lifetime maximization (NLM) and energy consumption minimization (ECM). For NLM, the numerical optimal solution is derived and a searching algorithm for suboptimal solution is provided when the optimal solution does not exist. For ECM, a closed-form solution is obtained. Numerical and simulation results show that both the approaches have much longer network lifetime than SISO transmission strategies and other cooperative communication schemes. Moreover, NLM which features energy balancing outperforms ECM which focuses on energy efficiency, in the network lifetime sense.

Sizing energy storage on the 11kV distribution network

The cost and limited flexibility of traditional approaches to 11kV network reinforcement threatens to constrain the uptake of low carbon technologies. Ofgem has released £500m of funding for DNOs to trial innovative techniques and share the learning with the rest of the industry. One of the techniques under study is the addition of Energy Storage at key substations to the network to help with peak load lopping. This paper looks in detail at the sizing algorithm for use in the assessment of alternatives to traditional reinforcement and investigates a method of sizing a battery for use on a Network taking into account load growth, capacity fade and battery lifecycle issues. A further complication to the analysis is the method of operation of the battery system and how this affects the Depth of Discharge (DoD). The proposed method is being trialled on an area of 11kV network in Milton Keynes Central area and the simulation results are presented in this paper.

A multi-modular second life hybrid battery energy storage system for utility grid applications

The modern grid system or the smart grid is likely to be populated with multiple distributed energy sources, e.g. wind power, PV power, Plug-in Electric Vehicle (PEV). It will also include a variety of linear and nonlinear loads. The intermittent nature of renewable energies like PV, wind turbine and increased penetration of Electric Vehicle (EV) makes the stable operation of utility grid system challenging. In order to ensure a stable operation of the utility grid system and to support smart grid functionalities such as, fault ride-through, frequency response, reactive power support, and mitigation of power quality issues, an energy storage system (ESS) could play an important role. A fast acting bidirectional energy storage system which can rapidly provide and absorb power and/or VARs for a sufficient time is a potentially valuable tool to support this functionality. Battery energy storage systems (BESS) are one of a range suitable energy storage system because it can provide and absorb power for sufficient time as well as able to respond reasonably fast. Conventional BESS already exist on the grid system are made up primarily of new batteries. The cost of these batteries can be high which makes most BESS an expensive solution. In order to assist moving towards a low carbon economy and to reduce battery cost this work aims to research the opportunities for the re-use of batteries after their primary use in low and ultra-low carbon vehicles (EV/HEV) on the electricity grid system. This research aims to develop a new generation of second life battery energy storage systems (SLBESS) which could interface to the low/medium voltage network to provide necessary grid support in a reliable and in cost-effective manner. The reliability/performance of these batteries is not clear, but is almost certainly worse than a new battery. Manufacturers indicate that a mixture of gradual degradation and sudden failure are both possible and failure mechanisms are likely to be related to how hard the batteries were driven inside the vehicle. There are several figures from a number of sources including the DECC (Department of Energy and Climate Control) and Arup and Cenex reports indicate anything from 70,000 to 2.6 million electric and hybrid vehicles on the road by 2020. Once the vehicle battery has degraded to around 70-80% of its capacity it is considered to be at the end of its first life application. This leaves capacity available for a second life at a much cheaper cost than a new BESS Assuming a battery capability of around 5-18kWhr (MHEV 5kWh - BEV 18kWh battery) and approximate 10 year life span, this equates to a projection of battery storage capability available for second life of >1GWhrs by 2025. Moreover, each vehicle manufacturer has different specifications for battery chemistry, number and arrangement of battery cells, capacity, voltage, size etc. To enable research and investment in this area and to maximize the remaining life of these batteries, one of the design challenges is to combine these hybrid batteries into a grid-tie converter where their different performance characteristics, and parameter variation can be catered for and a hot swapping mechanism is available so that as a battery ends it second life, it can be replaced without affecting the overall system operation. This integration of either single types of batteries with vastly different performance capability or a hybrid battery system to a grid-tie 3 energy storage system is different to currently existing work on battery energy storage systems (BESS) which deals with a single type of battery with common characteristics. This thesis addresses and solves the power electronic design challenges in integrating second life hybrid batteries into a grid-tie energy storage unit for the first time. This study details a suitable multi-modular power electronic converter and its various switching strategies which can integrate widely different batteries to a grid-tie inverter irrespective of their characteristics, voltage levels and reliability. The proposed converter provides a high efficiency, enhanced control flexibility and has the capability to operate in different operational modes from the input to output. Designing an appropriate control system for this kind of hybrid battery storage system is also important because of the variation of battery types, differences in characteristics and different levels of degradations. This thesis proposes a generalised distributed power sharing strategy based on weighting function aims to optimally use a set of hybrid batteries according to their relative characteristics while providing the necessary grid support by distributing the power between the batteries. The strategy is adaptive in nature and varies as the individual battery characteristics change in real time as a result of degradation for example. A suitable bidirectional distributed control strategy or a module independent control technique has been developed corresponding to each mode of operation of the proposed modular converter. Stability is an important consideration in control of all power converters and as such this thesis investigates the control stability of the multi-modular converter in detailed. Many controllers use PI/PID based techniques with fixed control parameters. However, this is not found to be suitable from a stability point-of-view. Issues of control stability using this controller type under one of the operating modes has led to the development of an alternative adaptive and nonlinear Lyapunov based control for the modular power converter. Finally, a detailed simulation and experimental validation of the proposed power converter operation, power sharing strategy, proposed control structures and control stability issue have been undertaken using a grid connected laboratory based multi-modular hybrid battery energy storage system prototype. The experimental validation has demonstrated the feasibility of this new energy storage system operation for use in future grid applications.

A review of the effects of distributed energy resources and power-electronic controlled loading on distribution network stability

This paper looks at potential distribution network stability problems under the Smart Grid scenario. This is to consider distributed energy resources (DERs) e.g. renewable power generations and intelligent loads with power-electronic controlled converters. The background of this topic is introduced and potential problems are defined from conventional power system stability and power electronic system stability theories. Challenges are identified with possible solutions from steady-state limits, small-signal, and large-signal stability indexes and criteria. Parallel computation techniques might be included for simulation or simplification approaches are required for a largescale distribution network analysis.

Energy-efficient multihop cooperative MISO transmission with optimal hop distance in wireless ad hoc networks

In this paper, we investigate the hop distance optimization problem in ad hoc networks where cooperative multiinput- single-output (MISO) is adopted to improve the energy efficiency of the network. We first establish the energy model of multihop cooperative MISO transmission. Based on the model, the energy consumption per bit of the network with high node density is minimized numerically by finding an optimal hop distance, and, to get the global minimum energy consumption, both hop distance and the number of cooperating nodes around each relay node for multihop transmission are jointly optimized. We also compare the performance between multihop cooperative MISO transmission and single-input-single-output (SISO) transmission, under the same network condition (high node density). We show that cooperative MISO transmission could be energyinefficient compared with SISO transmission when the path-loss exponent becomes high. We then extend our investigation to the networks with varied node densities and show the effectiveness of the joint optimization method in this scenario using simulation results. It is shown that the optimal results depend on network conditions such as node density and path-loss exponent, and the simulation results are closely matched to those obtained using the numerical models for high node density cases.

Solar PV-powered SRM drive for EVs with flexible energy control functions

Electric vehicles (EVs) provide a feasible solution to reducing greenhouse gas emissions and thus become a hot topic for research and development. Switched reluctance motors (SRMs) are one of promised motors for EV applications. In order to extend the EVs’ driving miles, the use of photovoltaic (PV) panels on the vehicle helps decrease the reliance on vehicle batteries. Based on phase winding characteristics of SRMs, a tri-port converter is proposed in this paper to control the energy flow between the PV panel, battery and SRM. Six operating modes are presented, four of which are developed for driving and two for standstill on-board charging. In the driving modes, the energy decoupling control for maximum power point tracking (MPPT) of the PV panel and speed control of the SRM are realized. In the standstill charging modes, a grid-connected charging topology is developed without a need for external hardware. When the PV panel directly charges the battery, a multi-section charging control strategy is used to optimize energy utilization. Simulation results based on Matlab/Simulink and experiments prove the effectiveness of the proposed tri-port converter, which has potential economic implications to improve the market acceptance of EVs.

New modular structure DC-DC converter without electrolytic capacitors for renewable energy applications

Electrolytic capacitors are extensively used in power converters but they are bulky, unreliable, and have short lifetimes. This paper proposes a new capacitor-free high step-up dc-dc converter design for renewable energy applications such as photovoltaics (PVs) and fuel cells. The primary side of the converter includes three interleaved inductors, three main switches, and an active clamp circuit. As a result, the input current ripple is greatly reduced, eliminating the necessity for an input capacitor. In addition, zero voltage switching (ZVS) is achieved during switching transitions for all active switches, so that switching losses can be greatly reduced. Furthermore, a three-phase modular structure and six pulse rectifiers are employed to reduce the output voltage ripple. Since magnetic energy stored in the leakage inductance is recovered, the reverse-recovery issue of the diodes is effectively solved. The proposed converter is justified by simulation and experimental tests on a 1-kW prototype.

New integrated multilevel converter for switched reluctance motor drives in plug-in hybrid electric vehicles with flexible energy conversion

This paper presents an integrated multilevel converter of switched reluctance motors (SRMs) fed by a modular front-end circuit for plug-in hybrid electric vehicle (PHEV) applications. Several operating modes can be achieved by changing the on-off states of the switches in the front-end circuit. In generator driving mode, the battery bank is employed to elevate the phase voltage for fast excitation and demagnetization. In battery driving mode, the converter is reconfigured as a four-level converter, and the capacitor is used as an additional charge capacitor to produce multilevel voltage outputs, which enhances the torque capability. The operating modes of the proposed drive are explained and the phase current and voltage are analyzed in details. The battery charging is naturally achieved by the demagnetization current in motoring mode and by the regenerative current in braking mode. Moreover, the battery can be charged by the external AC source or generator through the proposed converter when the vehicle is in standstill condition. The SRM-based PHEV can operate at different speeds by coordinating the power flow between the generator and battery. Simulation in MATLAB/Simulink and experiments on a three-phase 12/8 SRM confirm the effectiveness of the proposed converter topology.

On the role of surface roughness in the aerodynamic performance and energy conversion of horizontal wind turbine blades:a review

Summary: Renewable energy is one of the main pillars of sustainable development, especially in developing economies. Increasing energy demand and the limitation of fossil fuel reserves make the use of renewable energy essential for sustainable development. Wind energy is considered to be one of the most important resources of renewable energy. In North African countries, such as Egypt, wind energy has an enormous potential; however, it faces quite a number of technical challenges related to the performance of wind turbines in the Saharan environment. Seasonal sand storms affect the performance of wind turbines in many ways, one of which is increasing the wind turbine aerodynamic resistance through the increase of blade surface roughness. The power loss because of blade surface deterioration is significant in wind turbines. The surface roughness of wind turbine blades deteriorates because of several environmental conditions such as ice or sand. This paper is the first review on the topic of surface roughness effects on the performance of horizontal-axis wind turbines. The review covers the numerical simulation and experimental studies as well as discussing the present research trends to develop a roadmap for better understanding and improvement of wind turbine performance in deleterious environments.