A Krylov-based finite state projection algorithm for solving the chemical master equation arising in the discrete modelling of biological systems

Biochemical reactions underlying genetic regulation are often modelled as a continuous-time, discrete-state, Markov process, and the evolution of the associated probability density is described by the so-called chemical master equation (CME). However the CME is typically difficult to solve, since the state-space involved can be very large or even countably infinite. Recently a finite state projection method (FSP) that truncates the state-space was suggested and shown to be effective in an example of a model of the Pap-pili epigenetic switch. However in this example, both the model and the final time at which the solution was computed, were relatively small. Presented here is a Krylov FSP algorithm based on a combination of state-space truncation and inexact matrix-vector product routines. This allows larger-scale models to be studied and solutions for larger final times to be computed in a realistic execution time. Additionally the new method computes the solution at intermediate times at virtually no extra cost, since it is derived from Krylov-type methods for computing matrix exponentials. For the purpose of comparison the new algorithm is applied to the model of the Pap-pili epigenetic switch, where the original FSP was first demonstrated. Also the method is applied to a more sophisticated model of regulated transcription. Numerical results indicate that the new approach is significantly faster and extendable to larger biological models.

Finite element modelling of load bearing cold-formed steel wall systems under fire conditions

Light Gauge Steel Framing (LSF) walls are made of cold-formed, thin-walled steel lipped channel studs with plasterboard linings on both sides. However, these thin-walled steel sections heat up quickly and lose their strength under fire conditions despite the protection provided by plasterboards. A new composite wall panel was recently proposed to improve the fire resistance rating of LSF walls, where an insulation layer was used externally between the plasterboards on both sides of the wall frame instead of using it in the cavity. A research study using both fire tests and numerical studies was undertaken to investigate the structural and thermal behaviour of load bearing LSF walls made of both conventional and the new composite panels under standard fire conditions and to determine their fire resistance rating. This paper presents the details of finite element models of LSF wall studs developed to simulate the structural performance of LSF wall panels under standard fire conditions. Finite element analyses were conducted under both steady and transient state conditions using the time-temperature profiles measured during the fire tests. The developed models were validated using the fire test results of 11 LSF wall panels with various plasterboard/insulation configurations and load ratios. They were able to predict the fire resistance rating within five minutes. The use of accurate numerical models allowed the inclusion of various complex structural and thermal effects such as local buckling, thermal bowing and neutral axis shift that occurred in thin-walled steel studs under non-uniform elevated temperature conditions. Finite element analyses also demonstrated the improvements offered by the new composite panel system over the conventional cavity insulated system.

A finite volume method with linearisation in time for the solution of advection-reaction-diffusion systems

The numerical solution in one space dimension of advection--reaction--diffusion systems with nonlinear source terms may invoke a high computational cost when the presently available methods are used. Numerous examples of finite volume schemes with high order spatial discretisations together with various techniques for the approximation of the advection term can be found in the literature. Almost all such techniques result in a nonlinear system of equations as a consequence of the finite volume discretisation especially when there are nonlinear source terms in the associated partial differential equation models. This work introduces a new technique that avoids having such nonlinear systems of equations generated by the spatial discretisation process when nonlinear source terms in the model equations can be expanded in positive powers of the dependent function of interest. The basis of this method is a new linearisation technique for the temporal integration of the nonlinear source terms as a supplementation of a more typical finite volume method. The resulting linear system of equations is shown to be both accurate and significantly faster than methods that necessitate the use of solvers for nonlinear system of equations.

A finite element modelling method for thin layer mortared masonry systems

This paper deals with a finite element modelling method for thin layer mortared masonry systems. In this method, the mortar layers including the interfaces are represented using a zero thickness interface element and the masonry units are modelled using an elasto-plastic, damaging solid element. The interface element is formulated using two regimes; i) shear-tension and ii) shearcompression. In the shear-tension regime, the failure of joint is consiedered through an eliptical failure criteria and in shear-compression it is considered through Mohr Coulomb type failure criterion. An explicit integration scheme is used in an implicit finite element framework for the formulation of the interface element. The model is calibrated with an experimental dataset from thin layer mortared masonry prism subjected to uniaxial compression, a triplet subjected to shear loads a beam subjected to flexural loads and used to predict the response of thin layer mortared masonry wallettes under orthotropic loading. The model is found to simulate the behaviour of a thin layer mortated masonry shear wall tested under pre-compression and inplane shear quite adequately. The model is shown to reproduce the failure of masonry panels under uniform biaxial state of stresses.

On the zeros of the Abelian integrals for a class of Liénard systems

A planar polynomial differential system has a finite number of limit cycles. However, finding the upper bound of the number of limit cycles is an open problem for the general nonlinear dynamical systems. In this paper, we investigated a class of Liénard systems of the form x'=y, y'=f(x)+y g(x) with deg f=5 and deg g=4. We proved that the related elliptic integrals of the Liénard systems have at most three zeros including multiple zeros, which implies that the number of limit cycles bifurcated from the periodic orbits of the unperturbed system is less than or equal to 3.

Communication Architecture Design for Real-Time Networked Control Systems

Networked control over data networks has received increasing attention in recent years. Among many problems in networked control systems (NCSs) is the need to reduce control latency and jitter and to deal with packet dropouts. This paper introduces our recent progress on a queuing communication architecture for real-time NCS applications, and simple strategies for dealing with packet dropouts. Case studies for a middle-scale process or multiple small-scale processes are presented for TCP/IP based real-time NCSs. Variations of network architecture design are modelled, simulated, and analysed for evaluation of control latency and jitter performance. It is shown that a simple bandwidth upgrade or adding hierarchy does not necessarily bring benefits for performance improvement of control latency and jitter. A co-design of network and control is necessary to maximise the real-time control performance of NCSs

A bridging transition technique for the combination of meshfree method with finite element method in 2D solids and structures

For certain continuum problems, it is desirable and beneficial to combine two different methods together in order to exploit their advantages while evading their disadvantages. In this paper, a bridging transition algorithm is developed for the combination of the meshfree method (MM) with the finite element method (FEM). In this coupled method, the meshfree method is used in the sub-domain where the MM is required to obtain high accuracy, and the finite element method is employed in other sub-domains where FEM is required to improve the computational efficiency. The MM domain and the FEM domain are connected by a transition (bridging) region. A modified variational formulation and the Lagrange multiplier method are used to ensure the compatibility of displacements and their gradients. To improve the computational efficiency and reduce the meshing cost in the transition region, regularly distributed transition particles, which are independent of either the meshfree nodes or the FE nodes, can be inserted into the transition region. The newly developed coupled method is applied to the stress analysis of 2D solids and structures in order to investigate its’ performance and study parameters. Numerical results show that the present coupled method is convergent, accurate and stable. The coupled method has a promising potential for practical applications, because it can take advantages of both the meshfree method and FEM when overcome their shortcomings.

Determination of elastic modulus of thin coating materials using nanoindentation and finite element analysis

A deconvolution method that combines nanoindentation and finite element analysis was developed to determine elastic modulus of thin coating layer in a coating-substrate bilayer system. In this method, the nanoindentation experiments were conducted to obtain the modulus of both the bilayer system and the substrate. The finite element analysis was then applied to deconvolve the elastic modulus of the coating. The results demonstrated that the elastic modulus obtained using the developed method was in good agreement with that reported in literature.

Improvements to the fire performance of light gauge steel floor systems

Light gauge steel frame (LSF) structures are increasingly used in commercial and residential buildings because of their non-combustibility, dimensional stability and ease of installation. A common application is in floor-ceiling systems. The LSF floor-ceiling systems must be designed to serve as fire compartment boundaries and provide adequate fire resistance. Fire-rated floor-ceiling assemblies have been increasingly used in buildings. However, limited research has been undertaken in the past and hence a thorough understanding of their fire resistance behaviour is not available. Recently a new composite floor-ceiling system has been developed to provide higher fire rating. But its increased fire rating could not be determined using the currently available design methods. Therefore a research project was conducted to investigate its structural and fire resistance behaviour under standard fire conditions. This paper presents the results of full scale experimental investigations into the structural and fire behaviour of the new LSF floor system protected by the composite ceiling unit. Both the conventional and the new floor systems were tested under structural and fire loads. It demonstrates the improvements provided by the new composite panel system in comparison to conventional floor systems. Numerical studies were also undertaken using the finite element program ABAQUS. Measured temperature profiles of floors were used in the numerical analyses and their results were compared with fire test results. Tests and numerical studies provided a good understanding of the fire behaviour of the LSF floor-ceiling systems and confirmed the superior performance of the new composite system.

Novel analytical and numerical methods for solving fractional dynamical systems

During the past three decades, the subject of fractional calculus (that is, calculus of integrals and derivatives of arbitrary order) has gained considerable popularity and importance, mainly due to its demonstrated applications in numerous diverse and widespread fields in science and engineering. For example, fractional calculus has been successfully applied to problems in system biology, physics, chemistry and biochemistry, hydrology, medicine, and finance. In many cases these new fractional-order models are more adequate than the previously used integer-order models, because fractional derivatives and integrals enable the description of the memory and hereditary properties inherent in various materials and processes that are governed by anomalous diffusion. Hence, there is a growing need to find the solution behaviour of these fractional differential equations. However, the analytic solutions of most fractional differential equations generally cannot be obtained. As a consequence, approximate and numerical techniques are playing an important role in identifying the solution behaviour of such fractional equations and exploring their applications. The main objective of this thesis is to develop new effective numerical methods and supporting analysis, based on the finite difference and finite element methods, for solving time, space and time-space fractional dynamical systems involving fractional derivatives in one and two spatial dimensions. A series of five published papers and one manuscript in preparation will be presented on the solution of the space fractional diffusion equation, space fractional advectiondispersion equation, time and space fractional diffusion equation, time and space fractional Fokker-Planck equation with a linear or non-linear source term, and fractional cable equation involving two time fractional derivatives, respectively. One important contribution of this thesis is the demonstration of how to choose different approximation techniques for different fractional derivatives. Special attention has been paid to the Riesz space fractional derivative, due to its important application in the field of groundwater flow, system biology and finance. We present three numerical methods to approximate the Riesz space fractional derivative, namely the L1/ L2-approximation method, the standard/shifted Gr¨unwald method, and the matrix transform method (MTM). The first two methods are based on the finite difference method, while the MTM allows discretisation in space using either the finite difference or finite element methods. Furthermore, we prove the equivalence of the Riesz fractional derivative and the fractional Laplacian operator under homogeneous Dirichlet boundary conditions – a result that had not previously been established. This result justifies the aforementioned use of the MTM to approximate the Riesz fractional derivative. After spatial discretisation, the time-space fractional partial differential equation is transformed into a system of fractional-in-time differential equations. We then investigate numerical methods to handle time fractional derivatives, be they Caputo type or Riemann-Liouville type. This leads to new methods utilising either finite difference strategies or the Laplace transform method for advancing the solution in time. The stability and convergence of our proposed numerical methods are also investigated. Numerical experiments are carried out in support of our theoretical analysis. We also emphasise that the numerical methods we develop are applicable for many other types of fractional partial differential equations.

Fair flow control of ABR service by per-VC virtual queuing

In this paper, a rate-based flow control scheme based upon per-VC virtual queuing is proposed for the Available Bit Rate (ABR) service in ATM. In this scheme, each VC in a shared buffer is assigned a virtual queue, which is a counter. To achieve a specific kind of fairness, an appropriate scheduler is applied to the virtual queues. Each VC's bottleneck rate (fair share) is derived from its virtual cell departure rate. This approach of deriving a VC's fair share is simple and accurate. By controlling each VC with respect to its virtual queue and queue build-up in the shared buffer, network congestion is avoided. The principle of the control scheme is first illustrated by max–min flow control, which is realised by scheduling the virtual queues in round-robin. Further application of the control scheme is demonstrated with the achievement of weighted fairness through weighted round robin scheduling. Simulation results show that with a simple computation, the proposed scheme achieves the desired fairness exactly and controls network congestion effectively.