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.

Finite field computation technique for exact solution of systems of linear equations and interval linear programming problems

An error-free computational approach is employed for finding the integer solution to a system of linear equations, using finite-field arithmetic. This approach is also extended to find the optimum solution for linear inequalities such as those arising in interval linear programming probloms.

An operator-splitting finite element method for the efficient parallel solution of multidimensional population balance systems

A finite element method for solving multidimensional population balance systems is proposed where the balance of fluid velocity, temperature and solute partial density is considered as a two-dimensional system and the balance of particle size distribution as a three-dimensional one. The method is based on a dimensional splitting into physical space and internal property variables. In addition, the operator splitting allows to decouple the equations for temperature, solute partial density and particle size distribution. Further, a nodal point based parallel finite element algorithm for multi-dimensional population balance systems is presented. The method is applied to study a crystallization process assuming, for simplicity, a size independent growth rate and neglecting agglomeration and breakage of particles. Simulations for different wall temperatures are performed to show the effect of cooling on the crystal growth. Although the method is described in detail only for the case of d=2 space and s=1 internal property variables it has the potential to be extendable to d+s variables, d=2, 3 and s >= 1. (C) 2011 Elsevier Ltd. All rights reserved.

The time finite element as a robust general scheme for solving nonlinear dynamic equations including chaotic systems

Schemes that can be proven to be unconditionally stable in the linear context can yield unstable solutions when used to solve nonlinear dynamical problems. Hence, the formulation of numerical strategies for nonlinear dynamical problems can be particularly challenging. In this work, we show that time finite element methods because of their inherent energy momentum conserving property (in the case of linear and nonlinear elastodynamics), provide a robust time-stepping method for nonlinear dynamic equations (including chaotic systems). We also show that most of the existing schemes that are known to be robust for parabolic or hyperbolic problems can be derived within the time finite element framework; thus, the time finite element provides a unification of time-stepping schemes used in diverse disciplines. We demonstrate the robust performance of the time finite element method on several challenging examples from the literature where the solution behavior is known to be chaotic. (C) 2015 Elsevier Inc. All rights reserved.

The time finite element as a robust general scheme for solving nonlinear dynamic equations including chaotic systems

Schemes that can be proven to be unconditionally stable in the linear context can yield unstable solutions when used to solve nonlinear dynamical problems. Hence, the formulation of numerical strategies for nonlinear dynamical problems can be particularly challenging. In this work, we show that time finite element methods because of their inherent energy momentum conserving property (in the case of linear and nonlinear elastodynamics), provide a robust time-stepping method for nonlinear dynamic equations (including chaotic systems). We also show that most of the existing schemes that are known to be robust for parabolic or hyperbolic problems can be derived within the time finite element framework; thus, the time finite element provides a unification of time-stepping schemes used in diverse disciplines. We demonstrate the robust performance of the time finite element method on several challenging examples from the literature where the solution behavior is known to be chaotic. (C) 2015 Elsevier Inc. All rights reserved.

Trading the stability of finite zeros for global stabilization of nonlinear cascade systems

This note analyzes the stabilizability properties of nonlinear cascades in which a nonminimum phase linear system is interconnected through its output to a Stable nonlinear system. It is shown that the instability of the zeros of the linear System can be traded with the stability of the nonlinear system up to a limit fixed by the growth properties of the cascade interconnection term. Below this limit, global stabilization is achieved by smooth static-state feedback. Beyond this limit, various examples illustrate that controllability of the cascade may be lost, making it impossible to achieve large regions of attractions.