• A Framework for Web-Based Immersive Analytics

      John, Nigel; Ritsos, Panagiotis; Butcher, Peter W. S. (University of Chester, 2020-08-17)
      The emergence of affordable Virtual Reality (VR) interfaces has reignited the interest of researchers and developers in exploring new, immersive ways to visualise data. In particular, the use of open-standards Web-based technologies for implementing VR experiences in a browser aims to enable their ubiquitous and platform-independent adoption. In addition, such technologies work in synergy with established visualization libraries, through the HTML Document Object Model (DOM). However, creating Immersive Analytics (IA) experiences remains a challenging process, as the systems that are currently available require knowledge of game engines, such as Unity, and are often intrinsically restricted by their development ecosystem. This thesis presents a novel approach to the design, creation and deployment of Immersive Analytics experiences through the use of open-standards Web technologies. It presents <VRIA>, a Web-based framework for creating Immersive Analytics experiences in VR that was developed during this PhD project. <VRIA> is built upon WebXR, A-Frame, React and D3.js, and offers a visualization creation workflow which enables users of different levels of expertise to rapidly develop Immersive Analytics experiences for the Web. The aforementioned reliance on open standards and the synergies with popular visualization libraries make <VRIA> ubiquitous and platform-independent in nature. Moreover, by using WebXR’s progressive enhancement, the experiences <VRIA> is able to create are accessible on a plethora of devices. This thesis presents an elaboration on the motivation for focusing on open-standards Web technologies, presents the <VRIA> visualization creation workflow and details the underlying mechanics of our framework. It reports on optimisation techniques, integrated into <VRIA>, that are necessary for implementing Immersive Analytics experiences with the necessary performance profile on the Web. It discusses scalability implications of the framework and presents a series of use case applications that demonstrate the various features of <VRIA>. Finally, it describes the lessons learned from the development of the framework, discusses current limitations, and outlines further extensions.
    • 2^n Bordered Constructions of Self-Dual codes from Group Rings

      Dougherty, Steven; Gildea, Joe; Kaya, Abidin; University of Scranton; University of Chester; Sampoerna Academy (Elsevier, 2020-08-04)
      Self-dual codes, which are codes that are equal to their orthogonal, are a widely studied family of codes. Various techniques involving circulant matrices and matrices from group rings have been used to construct such codes. Moreover, families of rings have been used, together with a Gray map, to construct binary self-dual codes. In this paper, we introduce a new bordered construction over group rings for self-dual codes by combining many of the previously used techniques. The purpose of this is to construct self-dual codes that were missed using classical construction techniques by constructing self-dual codes with different automorphism groups. We apply the technique to codes over finite commutative Frobenius rings of characteristic 2 and several group rings and use these to construct interesting binary self-dual codes. In particular, we construct some extremal self-dual codes length 64 and 68, constructing 30 new extremal self-dual codes of length 68.
    • Optimization of anti-wear and anti-bacterial properties of beta TiNb alloy via controlling duty cycle in open-air laser nitriding

      Chang, Xianwen; Smith, Graham; Quinn, James; Carson, Louise; Chan, Chi-Wai; Lee, Seunghwan; Technical University of Denmark (Chang, Lee), University of Chester (Smith), Queens University Belfast (Quinn, Chan) (Elsevier, 2020-07-09)
      A multifunctional beta TiNb surface, featuring wear-resistant and antibacterial properties, was successfully created by means of open-air fibre laser nitriding. Beta TiNb alloy was selected in this study as it has low Young’s modulus, is highly biocompatible, and thus can be a promising prosthetic joint material. It is, however, necessary to overcome intrinsically weak mechanical properties and poor wear resistance of beta TiNb in order to cover the range of applications to loadbearing and/or shearing parts. To this end, open-air laser nitriding technique was employed. A control of single processing parameter, namely duty cycle (between 5% and 100%), led to substantially different structural and functional properties of the processed beta TiNb surfaces as analyzed by an array of analytical tools. The TiNb samples nitrided at the DC condition of 60% showed a most enhanced performance in terms of improving surface hardness, anti-friction, antiwear and anti-bacterial properties in comparison with other conditions. These findings are expected to be highly important and useful when TiNb alloys are considered as materials for hip/knee articular joint implants
    • An analysis of the L1 scheme for stochastic subdiffusion problem driven by integrated space-time white noise

      Yan, Yubin; Yan, Yuyuan; Wu, Xiaolei; University of Chester, Lvliang University, Jimei University (Elsevier, 2020-06-02)
      We consider the strong convergence of the numerical methods for solving stochastic subdiffusion problem driven by an integrated space-time white noise. The time fractional derivative is approximated by using the L1 scheme and the time fractional integral is approximated with the Lubich's first order convolution quadrature formula. We use the Euler method to approximate the noise in time and use the truncated series to approximate the noise in space. The spatial variable is discretized by using the linear finite element method. Applying the idea in Gunzburger \et (Math. Comp. 88(2019), pp. 1715-1741), we express the approximate solutions of the fully discrete scheme by the convolution of the piecewise constant function and the inverse Laplace transform of the resolvent related function. Based on such convolution expressions of the approximate solutions, we obtain the optimal convergence orders of the fully discrete scheme in spatial multi-dimensional cases by using the Laplace transform method and the corresponding resolvent estimates.
    • New binary self-dual codes via a generalization of the four circulant construction

      Gildea, Joe; Kaya, Abidin; Yildiz, Bahattin; University of Chester ; Sampoerna University ; Northern Arizona University (Croatian Mathematical Society, 2020-05-31)
      In this work, we generalize the four circulant construction for self-dual codes. By applying the constructions over the alphabets $\mathbb{F}_2$, $\mathbb{F}_2+u\mathbb{F}_2$, $\mathbb{F}_4+u\mathbb{F}_4$, we were able to obtain extremal binary self-dual codes of lengths 40, 64 including new extremal binary self-dual codes of length 68. More precisely, 43 new extremal binary self-dual codes of length 68, with rare new parameters have been constructed.
    • Higher Order Time Stepping Methods for Subdiffusion Problems Based on Weighted and Shifted Grünwald–Letnikov Formulae with Nonsmooth Data

      Yan, yubin; Wang, Yanyong; Yan, Yuyuan; Pani, Amiya K.; University of Chester, Lvliang University, Jimei University, Indian Institute of Technology Bombay (Springer Link, 2020-05-19)
      Two higher order time stepping methods for solving subdiffusion problems are studied in this paper. The Caputo time fractional derivatives are approximated by using the weighted and shifted Gr\"unwald-Letnikov formulae introduced in Tian et al. [Math. Comp. 84 (2015), pp. 2703-2727]. After correcting a few starting steps, the proposed time stepping methods have the optimal convergence orders $O(k^2)$ and $ O(k^3)$, respectively for any fixed time $t$ for both smooth and nonsmooth data. The error estimates are proved by directly bounding the approximation errors of the kernel functions. Moreover, we also present briefly the applicabilities of our time stepping schemes to various other fractional evolution equations. Finally, some numerical examples are given to show that the numerical results are consistent with the proven theoretical results.
    • A Modified Bordered Construction for Self-Dual Codes from Group Rings

      Kaya, Abidin; Tylyshchak, Alexander; Yildiz, Bahattin; Gildea, Joe; University of Chester; Sampoerna University; Uzhgorod State University; Northern Arizona University (Jacodesmath Institute, 2020-05-07)
      We describe a bordered construction for self-dual codes coming from group rings. We apply the constructions coming from the cyclic and dihedral groups over several alphabets to obtain extremal binary self-dual codes of various lengths. In particular we find a new extremal binary self-dual code of length 78.
    • Interactive Three-Dimensional Simulation and Visualisation of Real Time Blood Flow in Vascular Networks

      John, Nigel; Pop, Serban; Holland, Mark, I (University of ChesterUnviersity of Chester, 2020-05)
      One of the challenges in cardiovascular disease management is the clinical decision-making process. When a clinician is dealing with complex and uncertain situations, the decision on whether or how to intervene is made based upon distinct information from diverse sources. There are several variables that can affect how the vascular system responds to treatment. These include: the extent of the damage and scarring, the efficiency of blood flow remodelling, and any associated pathology. Moreover, the effect of an intervention may lead to further unforeseen complications (e.g. another stenosis may be “hidden” further along the vessel). Currently, there is no tool for predicting or exploring such scenarios. This thesis explores the development of a highly adaptive real-time simulation of blood flow that considers patient specific data and clinician interaction. The simulation should model blood realistically, accurately, and through complex vascular networks in real-time. Developing robust flow scenarios that can be incorporated into the decision and planning medical tool set. The focus will be on specific regions of the anatomy, where accuracy is of the utmost importance and the flow can develop into specific patterns, with the aim of better understanding their condition and predicting factors of their future evolution. Results from the validation of the simulation showed promising comparisons with the literature and demonstrated a viability for clinical use.
    • The past, present and future of indoor air chemistry

      Bekö, Gabriel; Carslaw, Nicola; Fauser, Patrick; Kauneliene, Violeta; Nehr, Sascha; Phillips, Gavin; Saraga, Dikaia; Schoemaecker, Coralie; Wierzbicka, Aneta; Querol, Xavier; et al. (Wiley, 2020-04-25)
      This is an editorial contribution to the Journal Indoor Air on the future direction of indoor air chemistry research.
    • Graphene Oxide Bulk Modified Screen-Printed Electrodes Provide Beneficial Electroanalytical Sensing Capabilities

      Rowley-Neale, Samuel; Brownson, Dale; Smith, Graham; Banks, Craig; Manchester Metropolitan University; University of Chester (MDPI, 2020-03-19)
      We demonstrate a facile methodology for the mass production of graphene oxide (GO) bulk modified screen-printed electrodes (GO-SPEs) that are economical, highly reproducible and provide analytically useful outputs. Through fabricating GO-SPEs with varying percentage mass incorporations (2.5, 5, 7.5 and 10%) of GO, an electrocatalytic effect towards the chosen electroanalytical probes is observed, that increases with greater GO incorporated compared to bare/ graphite SPEs. The optimum mass ratio of 10% GO to 90% carbon ink displays an electroanalytical signal towards dopamine (DA) and uric acid (UA), which is ca. ×10 greater in magnitude than that achievable at a bare/unmodified graphite SPE. Furthermore, 10% GO-SPEs exhibit a competitively low limit of detection (3σ) towards DA at ca. 81 nM, which is superior to that of a bare/unmodified graphite SPE at ca. 780 nM. The improved analytical response is attributed to the large number of oxygenated species inhabiting the edge and defect sites of the GO nanosheets, which are available to exhibit electrocatalytic responses towards inner-sphere electrochemical analytes. Our reported methodology is simple, scalable, and cost effective for the fabrication of GO-SPEs, that display highly competitive LODs, and is of significant interest for use in commercial and medicinal applications
    • Mathematical Modelling of DNA Methylation

      Roberts, Jason; Zagkos, Loukas (University of Chester, 2020-03-09)
      DNA methylation is a key epigenetic process which has been intimately associated with gene regulation. In recent years growing evidence has associated DNA methylation status with a variety of diseases including cancer, Alzheimer’s disease and cardiovascular disease. Moreover, changes to DNA methylation have also recently been implicated in the ageing process. The factors which underpin DNA methylation are complex, and remain to be fully elucidated. Over the years mathematical modelling has helped to shed light on the dynamics of this important molecular system. Although the existing models have contributed significantly to our overall understanding of DNA methylation, they fall short of fully capturing the dynamics of this process. In this work DNA methylation models are developed and improved and their suitability is demonstrated through mathematical analysis and computational simulation. In particular, a linear and nonlinear deterministic model are developed which capture more fully the dynamics of the key intracellular events which characterise DNA methylation. Furthermore, uncertainty is introduced into the model to describe the presence of intrinsic and extrinsic cell noise. This way a stochastic model is constructed and presented which accounts for the stochastic nature in cell dynamics. One of the key predictions of the model is that DNA methylation dynamics do not alter when the quantity of DNA methylation enzymes change. In addition, the nonlinear model predicts DNA methylation promoter bistability, which is commonly observed experimentally. Moreover, a new way of modelling DNA methylation uncertainty is introduced.
    • G-codes over Formal Power Series Rings and Finite Chain Rings

      Dougherty, Steven; Gildea, Joe; Korban, Adrian; University of Scranton; University of Chester (2020-02-29)
      In this work, we define $G$-codes over the infinite ring $R_\infty$ as ideals in the group ring $R_\infty G$. We show that the dual of a $G$-code is again a $G$-code in this setting. We study the projections and lifts of $G$-codes over the finite chain rings and over the formal power series rings respectively. We extend known results of constructing $\gamma$-adic codes over $R_\infty$ to $\gamma$-adic $G$-codes over the same ring. We also study $G$-codes over principal ideal rings.
    • New Extremal Self-Dual Binary Codes of Length 68 via Composite Construction, F2 + uF2 Lifts, Extensions and Neighbors

      Dougherty, Steven; Gildea, Joe; Korban, Adrian; Kaya, Abidin; University of Scranton; University of Chester; University of Chester; Sampoerna Academy; (Inderscience, 2020-02-29)
      We describe a composite construction from group rings where the groups have orders 16 and 8. This construction is then applied to find the extremal binary self-dual codes with parameters [32, 16, 8] or [32, 16, 6]. We also extend this composite construction by expanding the search field which enables us to find more extremal binary self-dual codes with the above parameters and with different orders of automorphism groups. These codes are then lifted to F2 + uF2, to obtain extremal binary images of codes of length 64. Finally, we use the extension method and neighbor construction to obtain new extremal binary self-dual codes of length 68. As a result, we obtain 28 new codes of length 68 which were not known in the literature before.
    • Terahertz Probing Irreversible Phase Transitions Related to Polar Clusters in Bi0.5Na0.5TiO3-based Ferroelectric

      Yang, Bin; University of Chester (Wiley-VCH, 2020-02-16)
      Electric-field-induced phase transitions in Bi0.5Na0.5TiO3 (BNT)-based relaxor ferroelectrics are essential to the controlling of their electrical properties and consequently in revolutionizing their dielectric and piezoelectric applications. However, the fundamental understanding of these transitions is a long-standing challenge due to their complex crystal structures. Given the structural inhomogeneity at the nanoscale or sub-nanoscale in these materials, dielectric response characterization based on terahertz (THz) electromagnetic-probe beam-fields, is intrinsically coordinated to lattice dynamics during DC-biased poling cycles. The complex permittivity reveals the field-induced phase transitions to be irreversible. This profoundly counters the claim of reversibility, the conventional support for which, is based upon the peak that is manifest in each of four quadrants of the current-field curves. The mechanism of this irreversibility is solely attributed to polar clusters in the transformed lattices. These represent an extrinsic factor which is quiescent in the THz spectral domain.
    • Modified Quadratic Residue Constructions and New Exermal Binary Self-Dual Codes of Lengths 64, 66 and 68

      Gildea, Joe; Hamilton, Holly; Kaya, Abidin; Yildiz, Bahattin; University of Chester; University of Chester; Sampoerna University; Northern Arizona University (Elsevier, 2020-02-10)
      In this work we consider modified versions of quadratic double circulant and quadratic bordered double circulant constructions over the binary field and the rings F2 +uF2 and F4 +uF4 for different prime values of p. Using these constructions with extensions and neighbors we are able to construct a number of extremal binary self-dual codes of different lengths with new parameters in their weight enumerators. In particular we construct 2 new codes of length 64, 4 new codes of length 66 and 14 new codes of length 68. The binary generator matrices of the new codes are available online at [8].
    • High‐order ADI orthogonal spline collocation method for a new 2D fractional integro‐differential problem

      Yan, Yubin; Qiao, Leijie; Xu, Da; University of Chester, UK; Guangdong University of Technology, PR. China; Hunan Normal University, P. R. China (John Wiley & Sons Ltd, 2020-02-05)
      We use the generalized L1 approximation for the Caputo fractional deriva-tive, the second-order fractional quadrature rule approximation for the inte-gral term, and a classical Crank-Nicolson alternating direction implicit (ADI)scheme for the time discretization of a new two-dimensional (2D) fractionalintegro-differential equation, in combination with a space discretization by anarbitrary-order orthogonal spline collocation (OSC) method. The stability of aCrank-Nicolson ADI OSC scheme is rigourously established, and error estimateis also derived. Finally, some numerical tests are given
    • Additively Manufactured Graphitic Electrochemical Sensing Platforms

      Foster, Christopher W; El Bardisy, Hadil M; Down, Michael P; Keefe, Edmund M; Smith, Graham C; Banks, Craig E; Manchester Metropolitan University (Foster, El Bardisy, Down, Keefe, Banks), University of Chester (Smith) (Elsevier, 2020-02-01)
      Additive manufacturing (AM)/3D printing technology provides a novel platform for the rapid prototyping of low cost 3D platforms. Herein, we report for the first time, the fabrication, characterisation (physicochemical and electrochemical) and application (electrochemical sensing) of bespoke nanographite (NG)-loaded (25 wt. %) AM printable (via fused deposition modelling) NG/PLA filaments. We have optimised and tailored a variety of NG-loaded filaments and their AM counterparts in order to achieve optimal printability and electrochemical behaviour. Two AM platforms, namely AM macroelectrodes (AMEs) and AM 3D honeycomb (macroporous) structures are benchmarked against a range of redox probes and the simultaneous detection of lead (II) and cadmium (II). This proof-of-concept demonstrates the impact that AM can have within the area of electroanalytical sensors.
    • Effects of obesity on cholesterol metabolism and its implications for healthy ageing.

      Mc Auley, Mark Tomás; University of Chester (Cambridge University Press, 2020-01-27)
      The last few decades have witnessed a global rise in the number of older people. Despite this demographic shift, morbidity within this population group is high. Many factors influence healthspan; however an obesity pandemic is emerging as a significant determinant of older peoples’ health. It is well established obesity adversely effects several metabolic systems. However, due to its close association with overall cardiometabolic health, the impact obesity has on cholesterol metabolism needs to be recognised. The aim of this review is to critically discuss the effects obesity has on cholesterol metabolism and to reveal its significance for healthy ageing.
    • Constructing Self-Dual Codes from Group Rings and Reverse Circulant Matrices

      Gildea, Joe; Kaya, Abidin; Korban, Adrian; Yildiz, Bahattin; University of Chester; Sampoerna Academy; Northern Arizona University (American Institute of Mathematical Sciences, 2020-01-20)
      In this work, we describe a construction for self-dual codes in which we employ group rings and reverse circulant matrices. By applying the construction directly over different alphabets, and by employing the well known extension and neighbor methods we were able to obtain extremal binary self-dual codes of different lengths of which some have parameters that were not known in the literature before. In particular, we constructed three new codes of length 64, twenty-two new codes of length 68, twelve new codes of length 80 and four new codes of length 92.
    • Columnar self-assembly, electrochemical and luminescence properties of basket-shaped liquid crystalline derivatives of Schiff-base-moulded p-tert-butyl-calix[4]arene

      Sharma, Vinay S.; orcid: 0000-0003-4970-0676; Sharma, Anuj S.; Worthington, Sheena J. B.; Shah, Priyanka A.; orcid: 0000-0002-1386-6984; Shrivastav, Pranav S.; orcid: 0000-0002-1284-1558 (Royal Society of Chemistry (RSC), 2020)
      A new family of blue-light emitting supramolecular basket-shaped liquid crystalline compounds based on p-tert-butyl-calix[4]arene core to form self-assembly and columnar hexagonal phase.