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In this paper we envisage building Probabilistic Boolean Networks (PBNs) from a prescribed stationary distribution. This is an inverse problem of huge size that can be subdivided into two parts — viz. (i) construction of a transition probability matrix from a given stationary distribution (Problem ST), and (ii) construction of a PBN from a given transition probability matrix (Problem TP). A generalized entropy approach has been proposed for Problem ST and a maximum entropy rate approach for Problem TP respectively. Here we propose to improve both methods, by considering a new objective function based on the entropy rate with an additional term of La-norm that can help in getting a sparse solution. A sparse solution is useful in identifying the major component Boolean networks (BNs) from the constructed PBN. These major BNs can simplify the identification of the network structure and the design of control policy, and neglecting non-major BNs does not change the dynamics of the constructed PBN to a large extent. Numerical experiments indicate that our new objective function is effective in finding a better sparse solution.
The GMRES(m) method proposed by Saad and Schultz is one of the most successful Krylov subspace methods for solving nonsymmetric linear systems. In this paper, we investigate how to update the initial guess to make it converge faster, and in particular propose an efficient variant of the method that exploits an unfixed update. The mathematical background of the unfixed update variant is based on the error equations, and its potential for efficient convergence is explored in some numerical experiments.
This paper discusses the development of an invariant finite difference scheme to simulate the microphase separation of copolymers in one-dimensional thin liquid films. The film phenomena are modelled using two-phase shallow water equations and the Ohta-Kawasaki potential, which governs the phase separation of the copolymer. Non-positive volume fractions and spurious oscillations are eventually eliminated, in simulating the one-dimensional phase separation lamellar pattern.
This paper considers the effect of a hard-wall beach on the downstream side of submerged parallel bars in a breakwater. In previous research, it was assumed that the beach can absorb all of the transmitted wave energy, when an optimal dimension for a submerged parallel bar is obtained and the wave amplitude is reduced as more bars are installed. However, for a hard-wall beach there are waves reflected from the beach that change the long-term wave interaction. We adopt the linear shallow water equations in Riemann invariant form and use the method of characteristics, in a procedure applicable to various formations of submerged rectangular bars. The distance from the parallel bar (or bars) to the beach determines the phase differences between right running waves in the beach basin and whether they superpose destructively or constructively before hitting the beach, to define the safest and the most dangerous cases. Our numerical calculations for one bar, two bars and for periodic rectangular bars confirm the analytical formulae obtained.
This paper discusses a new fourth-order compact off-step discretization for the solution of a system of two-dimensional nonlinear elliptic partial differential equations subject to Dirichlet boundary conditions. New methods to obtain the fourth-order accurate numerical solution of the first order normal derivatives of the solution are also derived. In all cases, we use only nine grid points to compute the solution. The proposed methods are directly applicable to singular problems and problems in polar coordinates, which is a main attraction. The convergence analysis of the derived method is discussed in detail. Several physical problems are solved to demonstrate the usefulness of the proposed methods.