• Characterising small solutions in delay differential equations through numerical approximations

      Ford, Neville J.; Lunel, Sjoerd M. V. (Manchester Centre for Computational Mathematics, 2003-05-23)
      This paper discusses how the existence of small solutions for delay differential equations can be predicted from the behaviour of the spectrum of the finite dimensional approximations.
    • Characterising small solutions in delay differential equations through numerical approximations

      Ford, Neville J.; Lunel, Sjoerd M. V. (Elsevier Science, 2002-09-25)
      This article discusses how the existence of small solutions for delay differential equations can be predicted from the behaviour of the spectrum of the finite dimensional approximations.
    • Characteristic functions of differential equations with deviating arguments

      Baker, Christopher T. H.; Ford, Neville J.; University of Manchester; University of Chester (Elsevier, 2019-04-24)
      The material here is motivated by the discussion of solutions of linear homogeneous and autonomous differential equations with deviating arguments. If $a, b, c$ and $\{\check{\tau}_\ell\}$ are real and ${\gamma}_\natural$ is real-valued and continuous, an example with these parameters is \begin{equation} u'(t) = \big\{a u(t) + b u(t+\check{\tau}_1) + c u(t+\check{\tau}_2) \big\} { \red +} \int_{\check{\tau}_3}^{\check{\tau}_4} {{\gamma}_\natural}(s) u(t+s) ds \tag{\hbox{$\rd{\star}$}} . \end{equation} A wide class of equations ($\rd{\star}$), or of similar type, can be written in the {\lq\lq}canonical{\rq\rq} form \begin{equation} u'(t) =\DSS \int_{\tau_{\rd \min}}^{\tau_{\rd \max}} u(t+s) d\sigma(s) \quad (t \in \Rset), \hbox{ for a suitable choice of } {\tau_{\rd \min}}, {\tau_{\rd \max}} \tag{\hbox{${\rd \star\star}$}} \end{equation} where $\sigma$ is of bounded variation and the integral is a Riemann-Stieltjes integral. For equations written in the form (${\rd{\star\star}}$), there is a corresponding characteristic function \begin{equation} \chi(\zeta) ):= \zeta - \DSS \int_{\tau_{\rd \min}}^{\tau_{\rd \max}} \exp(\zeta s) d\sigma(s) \quad (\zeta \in \Cset), \tag{\hbox{${\rd{\star\star\star}}$}} \end{equation} %%($ \chi(\zeta) \equiv \chi_\sigma (\zeta)$) whose zeros (if one considers appropriate subsets of equations (${\rd \star\star}$) -- the literature provides additional information on the subsets to which we refer) play a r\^ole in the study of oscillatory or non-oscillatory solutions, or of bounded or unbounded solutions. We show that the related discussion of the zeros of $\chi$ is facilitated by observing and exploiting some simple and fundamental properties of characteristic functions.
    • Combining Kronecker product approximation with discrete wavelet transforms to solve dense, function-related linear systems

      Ford, Judith M.; Tyrtyshnikov, Eugene E.; Chester College of Higher Education ; Russian Academy of Sciences (Society for Industrial and Applied Mathematics, 2003-11)
    • 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.
    • 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 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 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 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).
    • Concerning periodic solutions to non-linear discrete Volterra equations with finite memory

      Baker, Christopher T. H.; Song, Yihong; University of Chester (University of Chester, 2007)
      In this paper we discuss the existence of periodic solutions of discrete (and discretized) non-linear Volterra equations with finite memory. The literature contains a number of results on periodic solutions of non linear Volterra integral equations with finite memory, of a type that arises in biomathematics. The “summation” equations studied here can arise as discrete models in their own right but are (as we demonstrate) of a type that arise from the discretization of such integral equations. Our main results are in two parts: (i) results for discrete equations and (ii) consequences for quadrature methods applied to integral equations. The first set of results are obtained using a variety of fixed point theorems. The second set of results address the preservation of properties of integral equations on discretizing them. An expository style is adopted and examples are given to illustrate the discussion.
    • 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.
    • Constructions for Self-Dual Codes Induced from Group Rings

      Gildea, Joe; Kaya, Abidin; Taylor, Rhian; Yildiz, Bahattin; University of Chester; Sampoerna Academy, University of Chester; Northern Arizona University (Elsevier, 2018-02-03)
      In this work, we establish a strong connection between group rings and self-dual codes. We prove that a group ring element corresponds to a self-dual code if and only if it is a unitary unit. We also show that the double-circulant and four-circulant constructions come from cyclic and dihedral groups, respectively. Using groups of order 8 and 16 we find many new construction methods, in addition to the well-known methods, for self-dual codes. We establish the relevance of these new constructions by finding many extremal binary self-dual codes using them, which we list in several tables. In particular, we construct 10 new extremal binary self-dual codes of length 68.
    • Crank-Nicolson finite element discretizations for a two-dimenional linear Schroedinger-type equation posed in noncylindrical domain

      Antonopoulou, Dimitra; Karali, Georgia D.; Plexousakis, Michael; Zouraris, Georgios; University of Chester (AMS, 2014-11-05)
      Motivated by the paraxial narrow–angle approximation of the Helmholtz equation in domains of variable topography, we consider an initialand boundary-value problem for a general Schr¨odinger-type equation posed on a two space-dimensional noncylindrical domain with mixed boundary conditions. The problem is transformed into an equivalent one posed on a rectangular domain, and we approximate its solution by a Crank–Nicolson finite element method. For the proposed numerical method, we derive an optimal order error estimate in the L2 norm, and to support the error analysis we prove a global elliptic regularity theorem for complex elliptic boundary value problems with mixed boundary conditions. Results from numerical experiments are presented which verify the optimal order of convergence of the method.
    • Data aggregation in wireless sensor networks with minimum delay and minimum use of energy: A comparative study

      Qayyum, Bushra; Saeed, Mohammed; Roberts, Jason A.; University of Chester ; Al Khawarizmi University College ; University of Chester (British Computer Society, 2015)
      The prime objective of deploying large- scale wireless sensor networks is to collect information from to control systems associated with these networks. Wireless sensor networks are widely used in application domains such as security and inspection, environmental monitoring, warfare, and other situations especially where immediate responses are required such as disasters and medical emergency. Whenever there is a growth there are challenges and to cope with these challenges strategies and solutions must be developed. This paper discusses the recently addressed issues of data aggregation through presenting a comparative study of different research work done on minimizing delay in different structures of wireless sensor networks. Finally we introduce our proposed method to minimize both delay and power consumption using a tree based clustering scheme with partial data aggregation.
    • Data-driven selection and parameter estimation for DNA methylation mathematical models

      Larson, Karen; Zagkos, Loukas; Mc Auley, Mark T.; Roberts, Jason A.; Kavallaris, Nikos I.; Matzavinos, Anastasios; Brown University; University of Chester (Elsevier, 2019-01-10)
      Epigenetics is coming to the fore as a key process which underpins health. In particular emerging experimental evidence has associated alterations to DNA methylation status with healthspan and aging. Mammalian DNA methylation status is maintained by an intricate array of biochemical and molecular processes. It can be argued changes to these fundamental cellular processes ultimately drive the formation of aberrant DNA methylation patterns, which are a hallmark of diseases, such as cancer, Alzheimer's disease and cardiovascular disease. In recent years mathematical models have been used as e ective tools to help advance our understanding of the dynamics which underpin DNA methylation. In this paper we present linear and nonlinear models which encapsulate the dynamics of the molecular mechanisms which de ne DNA methylation. Applying a recently developed Bayesian algorithm for parameter estimation and model selection, we are able to estimate distributions of parameters which include nominal parameter values. Using limited noisy observations, the method also identifed which methylation model the observations originated from, signaling that our method has practical applications in identifying what models best match the biological data for DNA methylation.
    • Detailed error analysis for a fractional Adams method

      Diethelm, Kai; Ford, Neville J.; Freed, Alan D. (Springer, 2004-05)
      This preprint discusses a method for a numerical solution of a nonlinear fractional differential equation, which can be seen as a generalisation of the Adams–Bashforth–Moulton scheme.
    • Detailed error analysis for a fractional adams method with graded meshes

      Liu, Yanzhi; Roberts, Jason A.; Yan, Yubin; Lvliang University; University of Chester; (Springer, 2017-09-21)
      We consider a fractional Adams method for solving the nonlinear fractional differential equation $\, ^{C}_{0}D^{\alpha}_{t} y(t) = f(t, y(t)), \, \alpha >0$, equipped with the initial conditions $y^{(k)} (0) = y_{0}^{(k)}, k=0, 1, \dots, \lceil \alpha \rceil -1$. Here $\alpha$ may be an arbitrary positive number and $ \lceil \alpha \rceil$ denotes the smallest integer no less than $\alpha$ and the differential operator is the Caputo derivative. Under the assumption $\, ^{C}_{0}D^{\alpha}_{t} y \in C^{2}[0, T]$, Diethelm et al. \cite[Theorem 3.2]{dieforfre} introduced a fractional Adams method with the uniform meshes $t_{n}= T (n/N), n=0, 1, 2, \dots, N$ and proved that this method has the optimal convergence order uniformly in $t_{n}$, that is $O(N^{-2})$ if $\alpha > 1$ and $O(N^{-1-\alpha})$ if $\alpha \leq 1$. They also showed that if $\, ^{C}_{0}D^{\alpha}_{t} y(t) \notin C^{2}[0, T]$, the optimal convergence order of this method cannot be obtained with the uniform meshes. However, it is well known that for $y \in C^{m} [0, T]$ for some $m \in \mathbb{N}$ and $ 0 < \alpha 1$, we show that the optimal convergence order of this method can be recovered uniformly in $t_{n}$ even if $\, ^{C}_{0}D^{\alpha}_{t} y$ behaves as $t^{\sigma}, 0< \sigma <1$. Numerical examples are given to show that the numerical results are consistent with the theoretical results.
    • Determining control parameters for dendritic cell-cytotoxic T lymphocyte interaction

      Ludewig, Burkhard; Krebs, Philippe; Junt, Tobias; Metters, Helen; Ford, Neville J.; Anderson, Roy M.; Bocharov, Gennady; University of Zürich ; University of Zürich ; University of Zürich ; University of Zürich ; University College Chester ; Imperial College, University of London ; Institute of Numerical Mathematics, Russian Academy of Sciences (WILEY-VCH Verlag GmbH & Co. KGaA, 2004-08-05)
      Dendritic cells (DC) are potent immunostimulatory cells facilitating antigen transport to lymphoid tissues and providing efficient stimulation of T cells. A series of experimental studies in mice demonstrated that cytotoxic T lymphocytes (CTL) can be efficiently induced by adoptive transfer of antigen-presenting DC. However, the success of DC-based immunotherapeutic treatment of human cancer, for example, is still limited because the details of the regulation and kinetics of the DC-CTL interaction are not yet completely understood. Using a combination of experimental mouse studies, mathematical modeling, and nonlinear parameter estimation, we analyzed the population dynamics of DC-induced CTL responses. The model integrates a predator-prey-type interaction of DC and CTL with the non-linear compartmental dynamics of T cells. We found that T cell receptor avidity, the half-life of DC, and the rate of CTL-mediated DC-elimination are the major control parameters for optimal DC-induced CTL responses. For induction of high avidity CTL, the number of adoptively transferred DC was of minor importance once a minimal threshold of approximately 200 cells per spleen had been reached. Taken together, our study indicates that the availability of high avidity T cells in the recipient in combination with the optimal application regimen is of prime importance for successful DC-based immunotherapy.