• Comment on “Observations of ammonia, nitric acid, and fine particles in a rural gas production region” by Yi Li, Florian M. Schwandnera, H. James Sewell, Angela Zivkovich, Mark Tigges, Suresh Raja, Stephen Holcomb, John V. Molenar, Lincoln Sherman, Cassie Archuleta, Taehyoung Lee and Jeffrey L. Collett Jr. Atmospheric Environment (in press)

      Phillips, Gavin J.; University of Chester (Elsevier, 2014-03)
      Peer reviewed commentary on a research paper. An artefact of the detection of nitric acid (HNO3) by denuder methods is discussed. This artefact arises from the likely reaction of dinitrogen pentoxide (N2O5) on the denuder train resulting in the report of some fraction of N2O5 as HNO3.
    • Comparative Performance Modelling of Heat Pump based Heating Systems using Dynamic Carbon Intensity

      Counsell, John M.; Khalid, Yousaf; Stewart, Matt; University of Chester (IET, 2018-11-31)
      Modern buildings and homes utilise multiple systems for energy generation, supply and storage in order to maintain occupant comfort, reduce operating costs and CO2 emissions. In recent times electricity generation and supply network (UK National Grid) have had to manage variable supply from renewable sources such as wind turbines and photovoltaics. This resulting supply mixture has a dynamic profile at intermittent times. To manage excess supply, the options are either to reduce the generation by power stations/renewables or reinforce the power infrastructure with storage capability. This has given rise to calls for electrification of services in streamlining the supply profile through intelligent demand response such as electric heating and vehicles. Furthermore, due to zero carbon energy sources with dynamic supply profile, the carbon intensity is no longer constant. This impacts the seasonal CO2 emissions calculations and also the design and performance of electrical powered heat pump based heating systems. The RISE (Renewable Integrated Sustainable Electric) heating system was developed (funded by the UK Research and Innovation), where an electrical powered Heat pump is combined with electric thermal storage allowing low cost and low carbon electricity to be utilised. For such a system more realistic performance analysis requires dynamic carbon intensity calculations to assess impact on its ability to maintain comfort, low operating costs and low carbon emissions. The paper builds upon previously published research on the RISE system comparing with domestic Gas Condensing Boiler (GCB) using static carbon calculations. This paper presents a comparison between the RISE system and standard domestic electrical powered Air Source Heat Pump (ASHP) when using static and dynamic carbon intensity profiles. The Inverse Dynamics based Energy Assessment and Simulation (IDEAS) framework is utilised for modelling and dynamic simulation of building and heating system, operating cost and estimation of annual emissions based on half hourly (HH) dynamic CO2 intensity figures rather than annual average. The results show that with dynamic carbon intensity calculations, both electric heat pump based heating systems, RISE and ASHP show a significant increase (>15%) in carbon emissions for space heating. The results also show that whilst the RISE system’s thermal storage helps to reduce running costs using a time of use tariff (TOU), it only provides a small benefit in carbon emissions.
    • Comparative Potential of Natural Gas, Coal and Biomass Fired Power Plant with Post - combustion CO2 Capture and Compression

      Ali, Usman; Font Palma, Carolina; Akram, Muhammad; Agbonghae, Elvis O.; Ingham, Derek B.; Pourkashanian, Mohamed; University of Sheffield, University of Chester, Nigerian National Petroleum Corporation (Elsevier, 2017-06-07)
      The application of carbon capture and storage (CCS) and carbon neutral techniques should be adopted to reduce the CO2 emissions from power generation systems. These environmental concerns have renewed interest towards the use of biomass as an alternative to fossil fuels. This study investigates the comparative potential of different power generation systems, including NGCC with and without exhaust gas recirculation (EGR), pulverised supercritical coal and biomass fired power plants for constant heat input and constant fuel flowrate cases. The modelling of all the power plant cases is realized in Aspen Plus at the gross power output of 800 MWe and integrated with a MEA-based CO2 capture plant and a CO2 compression unit. Full-scale detailed modelling of integrated power plant with a CO2 capture and compression system for biomass fuel for two different cases is reported and compared with the conventional ones. The process performance, in terms of efficiency, emissions and potential losses for all the cases, is analysed. In conclusion, NGCC and NGCC with EGR integrated with CO2 capture and compression results in higher net efficiency and least efficiency penalty reduction. Further, coal and biomass fired power plants integrated with CO2 capture and compression results in higher specific CO2 capture and the least specific losses per unit of the CO2 captured. Furthermore, biomass with CO2 capture and compression results in negative emissions.
    • Comparing and combining time series trajectories using Dynamic Time Warping

      Vaughan, Neil; Gabrys, Bogdan; Bournemouth University (Elsevier, 2016-09-04)
      This research proposes the application of dynamic time warping (DTW) algorithm to analyse multivariate data from virtual reality training simulators, to assess the skill level of trainees. We present results of DTW algorithm applied to trajectory data from a virtual reality haptic training simulator for epidural needle insertion. The proposed application of DTW algorithm serves two purposes, to enable (i) two trajectories to be compared as a similarity measure and also enables (ii) two or more trajectories to be combined together to produce a typical or representative average trajectory using a novel hierarchical DTW process. Our experiments included 100 expert and 100 novice simulator recordings. The data consists of multivariate time series data-streams including multi-dimensional trajectories combined with force and pressure measurements. Our results show that our proposed application of DTW provides a useful time-independent method for (i) comparing two trajectories by providing a similarity measure and (ii) combining two or more trajectories into one, showing higher performance compared to conventional methods such as linear mean. These results demonstrate that DTW can be useful within virtual reality training simulators to provide a component in an automated scoring and assessment feedback system.
    • Comparing Terahertz transmission response on pH-dependent apomyoglobin proteins dynamics with circular dichroism

      Qiu, Junyi; Yang, Bin; Sushko, Oleksandr; Pikersgill, Richard W.; Donnan, Robert S.; University of Chester (IEEE, 2014-12-08)
      Terahertz time domain spectroscopy (THz-TDS) was used to study the transmission responses of pH-dependent apomyoglobin (ApoMb) dissolved solutions in 0.2-2.2 THz frequency domain, the THz-TDS technique was also benchmarked against circular dichroism (CD) by studying pH-related folding states changes of ApoMb protein. Results revealed that differences of pH-dependent ApoMb/water dynamics can be detected directly by the THz refractive index spectrum, and these differences are further proved to be caused mainly the effect of protonation of water and possibly water response leaded by protein conformation change.
    • Comparison of numerical methods for fractional differential equations

      Ford, Neville J.; Connolly, Joseph A. (American Institute of Mathematical Sciences/Shanghai Jiao Tong University, 2006-06)
      This article discusses and evaluates the merits of five numerical methods for the solution of single term fractional differential equations.
    • A Compensation Method for Active Phased Array Antennas : Using a Strain-Electromagnetic Coupling Model

      Shi, Yu; Wang, Congsi; Wang, Yan; Yuan, Shuai; Duan, Baoyan; Lian, Peiyuan; Xue, Song; Du, Biao; Gao, Wei; Wang, Zhihai; et al.
      Physical deformation due to service loads seriously degrades the electromagnetic performance of active phased array antennas. However, traditional displacement-based compensation methods are moderately difficult to use because displacement measurements generally require stable references, which are hard to realize for antennas in service. For deformed antennas, strain information is directly related to their displacement, and strain sensors can overcome carrier platform constraints to measure real-time strain without affecting the antenna radiation-field distribution. We thus present a compensation method based on strain information for in-service antennas. First, the minimum number of strain sensors is determined as the main modal-order-based modal effective mass fraction. According to the modal method and analysis of spatial phase-distribution errors related to strain, a coupled strain-electromagnetic model is established to evaluate antenna performance from the measured strain. The corresponding excitation phase from the measured strain is adjusted to compensate antenna performance. Finally, the method is experimentally validated using an X-band active phased array antenna under the influence of typical deformation conditions for both boresightand scanned beams. The results demonstrate that the presented method can effectively compensate for the performance of service antennas directly from the measured strain information.
    • Composite Constructions of Self-Dual Codes from Group Rings and New Extremal Self-Dual Binary Codes of Length 68

      Dougherty, Steven; Gildea, Joe; Kaya, Abidin; Korban, Adrian; University of Scranton; University of Chester; Sampoerna University ; University of Chester (American Institute of Mathematical Sciences, 2019-11-30)
      We describe eight composite constructions from group rings where the orders of the groups are 4 and 8, which are then applied to find self-dual codes of length 16 over F4. These codes have binary images with parameters [32, 16, 8] or [32, 16, 6]. These are lifted to codes over F4 + uF4, to obtain codes with Gray images extremal self-dual binary codes of length 64. Finally, we use a building-up method over F2 + uF2 to obtain new extremal binary self-dual codes of length 68. We construct 11 new codes via the building-up method and 2 new codes by considering possible neighbors.
    • Composite Matrices from Group Rings, Composite G-Codes and Constructions of Self-Dual Codes

      Dougherty, Steven; Gildea, Joe; Korban, Adrian; Kaya, Abidin; University of Scranton; University of Chester; Harmony School of Technology (Springer, 2021-05-19)
      In this work, we define composite matrices which are derived from group rings. We extend the idea of G-codes to composite G-codes. We show that these codes are ideals in a group ring, where the ring is a finite commutative Frobenius ring and G is an arbitrary finite group. We prove that the dual of a composite G-code is also a composite G-code. We also define quasi-composite G-codes. Additionally, we study generator matrices, which consist of the identity matrices and the composite matrices. Together with the generator matrices, the well known extension method, the neighbour method and its generalization, we find extremal binary self-dual codes of length 68 with new weight enumerators for the rare parameters $\gamma$ = 7; 8 and 9: In particular, we find 49 new such codes. Moreover, we show that the codes we find are inaccessible from other constructions.
    • Computational and mathematical modelling of plant species interactions in a harsh climate

      Lumb, Patricia M.; Potter, Jacqueline; Ford, Neville J.; Ekaka-A, Enu-Obari N. (University of Liverpool (University of Chester), 2009-07)
      This thesis will consider the following assumptions which are based on a few insights about the artic climate: (1)the artic climate can be characterised by a growing season called summer and a dormat season called winter (2)in the summer season growing conditions are reasonably favourable and species are more likely to compete for plentiful resources (3)in the winter season there would be no further growth and the plant populations would instead by subjected to fierce weather events such as storms which is more likely to lead to the destruction of some or all of the biomass. Under these assumptions, is it possible to find those change in the environment that might cause mutualism (see section 1.9.2) from competition (see section 1.9.1) to change? The primary aim of this thesis to to provide a prototype simulation of growth of two plant species in the artic that: (1)take account of different models for summer and winter seasons (2)permits the effects of changing climate to be seen on each type of plant species interaction.
    • Computational approaches to parameter estimation and model selection in immunology

      Baker, Christopher T. H.; Bocharov, Gennady; Ford, Judith M.; Lumb, Patricia M.; Norton, Stewart J.; Paul, C. A. H.; Junt, Tobias; Krebs, Philippe; Ludewig, Burkhard (Elsevier, 2005-12-01)
      This article seeks to illustrate the computational implementation of an information-theoretic approach (associated with a maximum likelihood treatment) to modelling in immunology.
    • Computational aspects of time-lag models of Marchuk type that arise in immunology

      Baker, Christopher T. H.; Bocharov, Gennady; University of Chester ; Institute of Numerical Mathematics, Russian Academy of Sciences (de Gryuter, 2005)
      In his book published in English translation in 1983, Marchuk proposed a set of evolutionary equations incorporating delay-differential equations, and the corresponding initial conditions as a model ('Marchuk's model') for infectious diseases. The parameters in this model (and its subsequent extensions) represent scientifically meaningful characteristics. For a given infection, the parameters can be estimated using observational data on the course of the infection. Sensitivity analysis is an important tool for understanding a particular model; this can be viewed as an issue of stability with respect to structural perturbations in the model. Examining the sensitivity of the models based on delay differential equations leads to systems of neutral delay differential equations. Below we formulate a general set of equations for the sensitivity coefficients for models comprising neutral delay differential equations. We discuss computational approaches to the sensitivity of solutions — (i) sensitivity to the choice of model, in particular, to the lag parameter τ > 0 and (ii) sensitivity to the initial function — of dynamical systems with time lag and illustrate them by considering the sensitivity of solutions of time-lag models of Marchuk type.
    • Computational benchmarking for ultrafast electron dynamics: wavefunction methods vs density functional theory

      Oliveira, Micael J. T.; Mignolet, Benoit; Kus, Tomasz; Papadopoulos, Theodoros A.; Remacle, Francoise; Verstraete, Matthieu J.; University of Chester (American Chemical Society, 2015-05-12)
      Attosecond electron dynamics in small- and medium-sized molecules, induced by an ultrashort strong optical pulse, is studied computationally for a frozen nuclear geometry. The importance of exchange and correlation effects on the nonequilibrium electron dynamics induced by the interaction of the molecule with the strong optical pulse is analyzed by comparing the solution of the time-dependent Schrodinger equation based on the correlated field-free stationary electronic states computed with the equation-of-motion coupled cluster singles and doubles and the complete active space multi-configurational self-consistent field methodologies on one hand, and various functionals in real-time time-dependent density functional theory (TD-DFT) on the other. We aim to evaluate the performance of the latter approach, which is very widely used for nonlinear absorption processes and whose computational cost has a more favorable scaling with the system size. We focus on LiH as a toy model for a nontrivial molecule and show that our conclusions carry over to larger molecules, exemplified by ABCU (C10H19N). The molecules are probed with IR and UV pulses whose intensities are not strong enough to significantly ionize the system. By comparing the evolution of the time-dependent field-free electronic dipole moment, as well as its Fourier power spectrum, we show that TD-DFT performs qualitatively well in most cases. Contrary to previous studies, we find almost no changes in the TD-DFT excitation energies when excited states are populated. Transitions between states of different symmetries are induced using pulses polarized in different directions. We observe that the performance of TD-DFT does not depend on the symmetry of the states involved in the transition.
    • Computational methods for a mathematical model of propagation of nerve impulses in myelinated axons

      Lima, Pedro M.; Ford, Neville J.; Lumb, Patricia M.; CEMAT, IST, Lisbon ; University of Chester ; University of Chester (Elsevier, 2014-06-26)
      This paper is concerned with the approximate solution of a nonlinear mixed type functional differential equation (MTFDE) arising from nerve conduction theory. The equation considered describes conduction in a myelinated nerve axon. We search for a monotone solution of the equation defined in the whole real axis, which tends to given values at ±∞. We introduce new numerical methods for the solution of the equation, analyse their performance, and present and discuss the results of the numerical simulations.
    • Computational Modelling Folate Metabolism and DNA Methylation: Implications for Understanding Health and Ageing

      Mc Auley, Mark T.; Mooney, Kathleen M.; Salcedo-Sora, J. Enrique; University of Chester; Edge Hill University; Liverpool Hope University (Oxford University Press, 2016-12-21)
      Dietary folates have a key role to play in health as deficiencies in the intake of these B vitamins have been implicated in a wide variety of clinical conditions. The reason for this is folates function as single carbon donors in the synthesis of methionine and nucleotides. Moreover, folates have a vital role to play in the epigenetics of mammalian cells by supplying methyl groups for DNA methylation reactions. Intriguingly, a growing body of experimental evidence suggests DNA methylation status could be a central modulator of the ageing process. This has important health implications because the methylation status of the human genome could be used to infer age-related disease risk. Thus, it is imperative we further our understanding of the processes which underpin DNA methylation and how these intersect with folate metabolism and ageing. The biochemical and molecular mechanisms which underpin these processes are complex. However, computational modelling offers an ideal framework for handling this complexity. A number of computational models have been assembled over the years, but to date no model has represented the full scope of the interaction between the folate cycle and the reactions which govern the DNA methylation cycle. In this review we will discuss several of the models which have been developed to represent these systems. In addition we will present a rationale for developing a combined model of folate metabolism and the DNA methylation cycle.
    • Computational modelling with functional differential equations: Identification, selection, and sensitivity

      Baker, Christopher T. H.; Bocharov, Gennady; Paul, C. A. H.; Rihan, F. A. R.; University College Chester ; Institute of Numerical Mathematics, Russian Academy of Sciences ; University of Salford (Elsevier, 2005-05)
      Mathematical models based upon certain types of differential equations, functional differential equations, or systems of such equations, are often employed to represent the dynamics of natural, in particular biological, phenomena. We present some of the principles underlying the choice of a methodology (based on observational data) for the computational identification of, and discrimination between, quantitatively consistent models, using scientifically meaningful parameters. We propose that a computational approach is essential for obtaining meaningful models. For example, it permits the choice of realistic models incorporating a time-lag which is entirely natural from the scientific perspective. The time-lag is a feature that can permit a close reconciliation between models incorporating computed parameter values and observations. Exploiting the link between information theory, maximum likelihood, and weighted least squares, and with distributional assumptions on the data errors, we may construct an appropriate objective function to be minimized computationally. The minimizer is sought over a set of parameters (which may include the time-lag) that define the model. Each evaluation of the objective function requires the computational solution of the parametrized equations defining the model. To select a parametrized model, from amongst a family or hierarchy of possible best-fit models, we are able to employ certain indicators based on information-theoretic criteria. We can evaluate confidence intervals for the parameters, and a sensitivity analysis provides an expression for an information matrix, and feedback on the covariances of the parameters in relation to the best fit. This gives a firm basis for any simplification of the model (e.g., by omitting a parameter).
    • Computational simulation of the damage response for machining long fibre reinforced plastic (LFRP) composite parts: A review

      Wang, Xiaonan; Wang, Fuji; Gu, Tianyu; Jia, Zhenyuan; Shi, Yu; Dalian University of Technology; University of Chester
      Long fibre reinforced plastics (LFRPs) possess excellent mechanical properties and are widely used in the aerospace, transportation and energy sectors. However, their anisotropic and inhomogeneous characteristics as well as their low thermal conductivity and specific heat capacity make them prone to subsurface damage, delamination and thermal damage during the machining process, which seriously reduces the bearing capacity and shortens the service life of the components. To improve the processing quality of composites, finite element (FE) models were developed to investigate the material removal mechanism and to analyse the influence of the processing parameters on the damage. A review of current studies on composite processing modelling could significantly help researchers to understand failure initiation and development during machining and thus inspire scholars to develop new models with high prediction accuracy and computational efficiency as well as a wide range of applications. To this aim, this review paper summarises the development of LFRP machining simulations reported in the literature and the factors that can be considered in model improvement. Specifically, the existing numerical models that simulate the mechanical and thermal behaviours of LFRPs and LFRP-metal stacks in orthogonal cutting, drilling and milling are analysed. The material models used to characterise the constituent phases of the LFRP parts are reviewed. The mechanism of material removal and the damage responses during the machining of LFRP laminates under different tool geometries and processing parameters are discussed. In addition, novel and objective evaluations that concern the current simulation studies are conducted to summarise their advantages. Aspects that could be improved are further detailed, to provide suggestions for future research relating to the simulation of LFRP machining.
    • Computational systems biology for aging research

      Mc Auley, Mark T.; Mooney, Kathleen M.; University of Chester ; Edge Hill University (Karger, 2015)
      Computational modelling is a key component of systems biology and integrates with the other techniques discussed thus far in this book by utilizing a myriad of data that are being generated to quantitatively represent and simulate biological systems. This chapter will describe what computational modelling involves; the rationale for using it, and the appropriateness of modelling for investigating the aging process. How a model is assembled and the different theoretical frameworks that can be used to build a model are also discussed. In addition, the chapter will describe several models which demonstrate the effectiveness of each computational approach for investigating the constituents of a healthy aging trajectory. Specifically, a number of models will be showcased which focus on the complex age-related disorders associated with unhealthy aging. To conclude, we discuss the future applications of computational systems modelling to aging research.
    • Computationally modeling lipid metabolism and aging: A mini-review

      Mc Auley, Mark T.; Mooney, Kathleen M.; University of Chester; Edge Hill University (Elsevier, 2014-11-15)
      One of the greatest challenges in biology is to improve the understanding of the mechanisms which underpin aging and how these affect health. The need to better understand aging is amplified by demographic changes, which have caused a gradual increase in the global population of older people. Aging western populations have resulted in a rise in the prevalence of age-related pathologies. Of these diseases, cardiovascular disease is the most common underlying condition in older people. The dysregulation of lipid metabolism due to aging impinges significantly on cardiovascular health. However, the multifaceted nature of lipid metabolism and the complexities of its interaction with aging make it challenging to understand by conventional means. To address this challenge computational modeling, a key component of the systems biology paradigm is being used to study the dynamics of lipid metabolism. This mini-review briefly outlines the key regulators of lipid metabolism, their dysregulation, and how computational modeling is being used to gain an increased insight into this system.
    • Computer Modelling for Nutritionists

      Mc Auley, Mark Tomás; University of Chester
      This book is about computational modelling of nutrient focused biological systems. The book is aimed at students, researchers, and those with an interest in learning how to build a computational model. The book is the product of many years of teaching computational modelling to undergraduates, postgraduates, and researchers with limited, or no background in computational modelling. What I learned from these experiences is those new to modelling are invariably apprehensive about it, and approach it with a degree of trepidation, or even scepticism. However, from tentative initial steps, they quickly realize that modelling is not as challenging, or as academically intimidating as they initially perceive it; and after gaining familiarity with the essential components of model building they rapidly become cognisant, that it offers an alternative lens to view a biological system, and learn new insights about its underlying dynamic behaviour. In this book I provide a practical introduction to modelling, for those who are interested in exploring the dynamics of nutrient based systems. My rationale for undertaking this project is based on my experience of interacting with nutritionists in recent years. As a result of many fruitful discussions I identified a growing need for a book of this nature, which is specifically tailored to nutritionists. My aims are to provide the reader with a solid grounding in computational modelling, and how it dovetails within the burgeoning field of systems biology. For the reader this will involve learning how a model is assembled, what software tools are available for model building, what the different paradigms are for simulating a model, and how to analyse and interpret the output from in silico simulations. The only expectation I make of you, as a reader, is that you are enthusiastic about learning how to use new software tools. In exchange for your engagement I will provide you with ample practical exercises, which will help to consolidate your learning, and will make your computational modelling journey a rewarding and enjoyable experience.