Now showing items 1-20 of 153

• Data-driven selection and parameter estimation for DNA methylation mathematical models

(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.
• Data-driven selection and parameter estimation for DNA methylation mathematical models.

(2019-01-08)
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 effective 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 define 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 identified 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. [Abstract copyright: Copyright © 2019. Published by Elsevier Ltd.]
• Bordered Constructions of Self-Dual Codes from Group Rings and New Extremal Binary Self-Dual Codes

(Elsevier, 2019)
We introduce a bordered construction over group rings for self-dual codes. We apply the constructions over the binary field and the ring $\F_2+u\F_2$, using groups of orders 9, 15, 21, 25, 27, 33 and 35 to find extremal binary self-dual codes of lengths 20, 32, 40, 44, 52, 56, 64, 68, 88 and best known binary self-dual codes of length 72. In particular we obtain 41 new binary extremal self-dual codes of length 68 from groups of orders 15 and 33 using neighboring and extensions. All the numerical results are tabulated throughout the paper.
• Optimal convergence rates for semidiscrete finite element approximations of linear space-fractional partial differential equations under minimal regularity assumptions

(Elsevier, 2018-12-17)
We consider the optimal convergence rates of the semidiscrete finite element approximations for solving linear space-fractional partial differential equations by using the regularity results for the fractional elliptic problems obtained recently by Jin et al. \cite{jinlazpasrun} and Ervin et al. \cite{ervheuroo}. The error estimates are proved by using two approaches. One approach is to apply the duality argument in Johnson \cite{joh} for the heat equation to consider the error estimates for the linear space-fractional partial differential equations. This argument allows us to obtain the optimal convergence rates under the minimal regularity assumptions for the solution. Another approach is to use the approximate solution operators of the corresponding fractional elliptic problems. This argument can be extended to consider more general linear space-fractional partial differential equations. Numerical examples are given to show that the numerical results are consistent with the theoretical results.
• Mathematical models of DNA methylation dynamics: Implications for health and ageing.

(2018-11-15)
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 paper we develop a linear and nonlinear model which captures more fully the dynamics of the key intracellular events which characterise DNA methylation. In particular the outcomes of our linear model result in gene promoter specific methylation levels which are more biologically plausible than those revealed by previous mathematical models. In addition, our nonlinear model predicts DNA methylation promoter bistability which is commonly observed experimentally. The findings from our models have implications for our current understanding of how changes to the dynamics which underpin DNA methylation affect ageing and health. We also propose how our ideas can be tested in the lab. [Abstract copyright: Copyright © 2018 Elsevier Ltd. All rights reserved.]
• A high-order scheme to approximate the Caputo fractional derivative and its application to solve the fractional diffusion wave equation

(Elsevier, 2018-10-05)
A new high-order finite difference scheme to approximate the Caputo fractional derivative $\frac{1}{2} \big ( \, _{0}^{C}D^{\alpha}_{t}f(t_{k})+ \, _{0}^{C}D^{\alpha}_{t}f(t_{k-1}) \big ), k=1, 2, \dots, N,$ with the convergence order $O(\Delta t^{4-\alpha}), \, \alpha\in(1,2)$ is obtained when $f^{\prime \prime \prime} (t_{0})=0$, where $\Delta t$ denotes the time step size. Based on this scheme we introduce a finite difference method for solving fractional diffusion wave equation with the convergence order $O(\Delta t^{4-\alpha} + h^2)$, where $h$ denotes the space step size. Numerical examples are given to show that the numerical results are consistent with the theoretical results.
• Error estimates of high-order numerical methods for solving time fractional partial differential equations

(De Gruyter, 2018-07-12)
Error estimates of some high-order numerical methods for solving time fractional partial differential equations are studied in this paper. We first provide the detailed error estimate of a high-order numerical method proposed recently by Li et al. \cite{liwudin} for solving time fractional partial differential equation. We prove that this method has the convergence order $O(\tau^{3- \alpha})$ for all $\alpha \in (0, 1)$ when the first and second derivatives of the solution are vanish at $t=0$, where $\tau$ is the time step size and $\alpha$ is the fractional order in the Caputo sense. We then introduce a new time discretization method for solving time fractional partial differential equations, which has no requirements for the initial values as imposed in Li et al. \cite{liwudin}. We show that this new method also has the convergence order $O(\tau^{3- \alpha})$ for all $\alpha \in (0, 1)$. The proofs of the error estimates are based on the energy method developed recently by Lv and Xu \cite{lvxu}. We also consider the space discretization by using the finite element method. Error estimates with convergence order $O(\tau^{3- \alpha} + h^2)$ are proved in the fully discrete case, where $h$ is the space step size. Numerical examples in both one- and two-dimensional cases are given to show that the numerical results are consistent with the theoretical results.
• Theoretical and numerical analysis of unsteady fractional viscoelastic flows in simple geometries.

(Elsevier, 2018-07-12)
In this work we discuss the connection between classical and fractional viscoelastic Maxwell models, presenting the basic theory supporting these constitutive equations, and establishing some background on the admissibility of the fractional Maxwell model. We then develop a numerical method for the solution of two coupled fractional differential equations (one for the velocity and the other for the stress), that appear in the pure tangential annular ow of fractional viscoelastic fluids. The numerical method is based on finite differences, with the approximation of fractional derivatives of the velocity and stress being inspired by the method proposed by Sun and Wu for the fractional diffusion-wave equation [ Z.Z. Sun, X. Wu, A fully discrete difference scheme for a diffusion-wave system, Applied Numerical Mathematics 56 (2006) 193-209]. We prove solvability, study numerical convergence of the method, and also discuss the applicability of this method for simulating the rheological response of complex fluids in a real concentric cylinder rheometer. By imposing a torsional step-strain, we observe the different rates of stress relaxation obtained with different values of \alpha and \beta (the fractional order exponents that regulate the viscoelastic response of the complex fluids).
• Malliavin Calculus for the stochastic Cahn- Hilliard/Allen-Cahn equation with unbounded noise diffusion

(Elsevier, 2018-05-08)
The stochastic partial di erential equation analyzed in this work, is motivated by a simplified mesoscopic physical model for phase separation. It describes pattern formation due to adsorption and desorption mechanisms involved in surface processes, in the presence of a stochastic driving force. This equation is a combination of Cahn-Hilliard and Allen-Cahn type operators with a multiplicative, white, space-time noise of unbounded di usion. We apply Malliavin calculus, in order to investigate the existence of a density for the stochastic solution u. In dimension one, according to the regularity result in [5], u admits continuous paths a.s. Using this property, and inspired by a method proposed in [8], we construct a modi ed approximating sequence for u, which properly treats the new second order Allen-Cahn operator. Under a localization argument, we prove that the Malliavin derivative of u exists locally, and that the law of u is absolutely continuous, establishing thus that a density exists.
• A posteriori error estimates for fully discrete schemes for the time dependent Stokes problem

(Springer, 2018-05-02)
This work is devoted to a posteriori error analysis of fully discrete finite element approximations to the time dependent Stokes system. The space discretization is based on popular stable spaces, including Crouzeix–Raviart and Taylor–Hood finite element methods. Implicit Euler is applied for the time discretization. The finite element spaces are allowed to change with time steps and the projection steps include alternatives that is hoped to cope with possible numerical artifices and the loss of the discrete incompressibility of the schemes. The final estimates are of optimal order in L∞(L2) for the velocity error.
• The sharp interface limit for the stochastic Cahn-Hilliard Equation

(IMS Journals, 2018-02-19)
We study the two and three dimensional stochastic Cahn-Hilliard equation in the sharp interface limit, where the positive parameter \eps tends to zero, which measures the width of transition layers generated during phase separation. We also couple the noise strength to this parameter. Using formal asymptotic expansions, we identify the limit. In the right scaling we indicate that the solutions of stochastic Cahn-Hilliard converge to a solution of a Hele-Shaw problem with stochastic forcing. In the case when the noise is sufficiently small, we rigorously prove that the limit is a deterministic Hele-Shaw problem. Finally, we discuss which estimates are necessary in order to extend the rigorous result to larger noise strength.
• Constructions for Self-Dual Codes Induced from Group Rings

(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.
• Fourier spectral methods for stochastic space fractional partial differential equations driven by special additive noises

(Springer, 2018-02)
Fourier spectral methods for solving stochastic space fractional partial differential equations driven by special additive noises in one-dimensional case are introduced and analyzed. The space fractional derivative is defined by using the eigenvalues and eigenfunctions of Laplacian subject to some boundary conditions. The space-time noise is approximated by the piecewise constant functions in the time direction and by some appropriate approximations in the space direction. The approximated stochastic space fractional partial differential equations are then solved by using Fourier spectral methods. For the linear problem, we obtain the precise error estimates in the $L_{2}$ norm and find the relations between the error bounds and the fractional powers. For the nonlinear problem, we introduce the numerical algorithms and MATLAB codes based on the FFT transforms. Our numerical algorithms can be adapted easily to solve other stochastic space fractional partial differential equations with multiplicative noises. Numerical examples for the semilinear stochastic space fractional partial differential equations are given.
• An analysis of the modified L1 scheme for time-fractional partial differential equations with nonsmooth data

(Society for Industrial and Applied Mathematics, 2018-01-11)
We introduce a modified L1 scheme for solving time fractional partial differential equations and obtain error estimates for smooth and nonsmooth initial data in both homogeneous and inhomogeneous cases. Jin \et (2016, An analysis of the L1 scheme for the subdiffusion equation with nonsmooth data, IMA J. of Numer. Anal., 36, 197-221) established an $O(k)$ convergence rate for the L1 scheme for smooth and nonsmooth initial data for the homogeneous problem, where $k$ denotes the time step size. We show that the modified L1 scheme has convergence rate $O(k^{2-\alpha}), 0< \alpha <1$ for smooth and nonsmooth initial data in both homogeneous and inhomogeneous cases. Numerical examples are given to show that the numerical results are consistent with the theoretical results.
• A novel high-order algorithm for the numerical estimation of fractional differential equations

(Elsevier, 2018-01-09)
This paper uses polynomial interpolation to design a novel high-order algorithm for the numerical estimation of fractional differential equations. The Riemann-Liouville fractional derivative is expressed by using the Hadamard finite-part integral and the piecewise cubic interpolation polynomial is utilized to approximate the integral. The detailed error analysis is presented and it is established that the convergence order of the algorithm is O(h4−a). Asymptotic expansion of the error for the presented algorithm is also investigated. Some numerical examples are provided and compared with the exact solution to show that the numerical results are in well agreement with the theoretical ones and also to illustrate the accuracy and efficiency of the proposed algorithm.
• A higher order numerical method for time fractional partial differential equations with nonsmooth data

(Elsevier, 2018-01-02)
Gao et al. (2014) introduced a numerical scheme to approximate the Caputo fractional derivative with the convergence rate $O(k^{3-\alpha}), 0< \alpha <1$ by directly approximating the integer-order derivative with some finite difference quotients in the definition of the Caputo fractional derivative, see also Lv and Xu (2016), where $k$ is the time step size. Under the assumption that the solution of the time fractional partial differential equation is sufficiently smooth, Lv and Xu (2016) proved by using energy method that the corresponding numerical method for solving time fractional partial differential equation has the convergence rate $O(k^{3-\alpha}), 0< \alpha <1$ uniformly with respect to the time variable $t$. However, in general the solution of the time fractional partial differential equation has low regularity and in this case the numerical method fails to have the convergence rate $O(k^{3- \alpha}), 0 < \alpha <1$ uniformly with respect to the time variable $t$. In this paper, we first obtain a similar approximation scheme to the Riemann-Liouville fractional derivative with the convergence rate $O(k^{3- \alpha}), 0 < \alpha <1$ as in Gao \et \cite{gaosunzha} (2014) by approximating the Hadamard finite-part integral with the piecewise quadratic interpolation polynomials. Based on this scheme, we introduce a time discretization scheme to approximate the time fractional partial differential equation and show by using Laplace transform methods that the time discretization scheme has the convergence rate $O(k^{3- \alpha}), 0 < \alpha <1$ for any fixed $t_{n}>0$ for smooth and nonsmooth data in both homogeneous and inhomogeneous cases. Numerical examples are given to show that the theoretical results are consistent with the numerical results.
• Units of the group algebra of the group $C_n\times D_6$ over any finite field of characteristic $3$

(International Electronic Journal of Algebra, 2018)
In this paper, we establish the structure of the unit group of the group algebra ${\FF}_{3^t}(C_n\times D_6)$ for $n \geq 1$.
• A Posteriori Analysis for Space-Time, discontinuous in time Galerkin approximations for parabolic equations in a variable domain

(ECP sciences, 2018)
This paper presents an a posteriori error analysis for the discontinuous in time space-time scheme proposed by Jamet for the heat equation in multi-dimensional, non-cylindrical domains [25]. Using a Cl ement-type interpolant, we prove abstract a posteriori error bounds for the numerical error. Furthermore, in the case of two-dimensional spatial domains we transform the problem into an equivalent one, of parabolic type, with space-time dependent coe cients but posed on a cylindrical domain. We formulate a discontinuous in time space{time scheme and prove a posteriori error bounds of optimal order. The a priori estimates of [19] for general parabolic initial and boundary value problems are used in the derivation of the upper bound. Our lower bound coincides with that of Picasso [36], proposed for adaptive, Runge-Kutta finite element methods for linear parabolic problems. Our theoretical results are verified by numerical experiments.
• Mathematical models of DNA methylation dynamics: Implications for health and ageing

(Elsevier, 2018)
DNA methylation status 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, Alzheimers 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 paper we develop a linear and nonlinear model which captures more fully the dynamics of the key intracellular events which characterise DNA methylation. In particular the outcomes of our linear model result in gene promoter specific methylation levels which are more biologically plausible than those revealed by previous mathematical models. In addition, our non-linear model predicts DNA methylation promoter bistability which is commonly observed experimentally. The findings from our models have implications for our current understanding of how changes to the dynamics which underpin DNA methylation affect ageing and health.
• Non-Local Partial Differential Equations for Engineering and Biology: Mathematical Modeling and Analysis

(Springer, 2017-12-31)
This book presents new developments in non-local mathematical modeling and mathematical analysis on the behavior of solutions with novel technical tools. Theoretical backgrounds in mechanics, thermo-dynamics, game theory, and theoretical biology are examined in details. It starts off with a review and summary of the basic ideas of mathematical modeling frequently used in the sciences and engineering. The authors then employ a number of models in bio-science and material science to demonstrate applications, and provide recent advanced studies, both on deterministic non-local partial differential equations and on some of their stochastic counterparts used in engineering. Mathematical models applied in engineering, chemistry, and biology are subject to conservation laws. For instance, decrease or increase in thermodynamic quantities and non-local partial differential equations, associated with the conserved physical quantities as parameters. These present novel mathematical objects are engaged with rich mathematical structures, in accordance with the interactions between species or individuals, self-organization, pattern formation, hysteresis. These models are based on various laws of physics, such as mechanics of continuum, electro-magnetic theory, and thermodynamics. This is why many areas of mathematics, calculus of variation, dynamical systems, integrable systems, blow-up analysis, and energy methods are indispensable in understanding and analyzing these phenomena. This book aims for researchers and upper grades students in mathematics, engineering, physics, economics, and biology.