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At least 73 records · Page 4

A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws

Theoretical analysis of signaling pathways can provide a substantial amount of insight into their function. One particular area of research considers signaling pathways capable of assuming two or more stable states given the same amount of signaling ligand. This phenomenon of bistability can give rise to switch-like behavior, a mechanism that governs cellular decision making. Investigation of whether or not a signaling pathway can confer bistability and switch-like behavior, without knowledge of specific kinetic rate constant values, is a mathematically challenging problem. Recently a technique based on optimization has been introduced, which is capable of finding example parameter values that confer switch-like behavior for a given pathway. Although this approach has made it possible to analyze moderately sized pathways, it is limited to reaction networks that presume a uniterminal structure. It is this limited structure we address by developing a general technique that applies to any mass action reaction network with conservation laws. In this paper we developed a generalized method for detecting switch-like bistable behavior in any mass action reaction network with conservation laws. The method involves (1) construction of a constrained optimization problem using the determinant of the Jacobian of the underlying rate equations, (2) minimization of the objective function to search for conditions resulting in a zero eigenvalue, (3) computation of a confidence level that describes if the global minimum has been found and (4) evaluation of optimization values, using either numerical continuation or directly simulating the ODE system, to verify that a bistability region exists. The generalized method has been tested on three motifs known to be capable of bistability. We have developed a variation of an optimization-based method for the discovery of bistability, which is not limited to uniterminal chemical reaction networks. Successful completion of the method provides an S-shaped bifurcation diagram, which indicates that the network acts as a bistable switch for the given optimization parameters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Non-oscillatory central differencing for hyperbolic conservation laws

Many of the recently developed high resolution schemes for hyperbolic conservation laws are based on upwind differencing. The building block for these schemes is the averaging of an appropriate Godunov solver; its time consuming part involves the field-by-field decomposition which is required in order to identify the direction of the wind. Instead, the use of the more robust Lax-Friedrichs (LxF) solver is proposed. The main advantage is simplicity: no Riemann problems are solved and hence field-by-field decompositions are avoided. The main disadvantage is the excessive numerical viscosity typical to the LxF solver. This is compensated for by using high-resolution MUSCL-type interpolants. Numerical experiments show that the quality of results obtained by such convenient central differencing is comparable with those of the upwind schemes.

Nessyahu, Haim↗

Some observations on boundary conditions for numerical conservation laws

Four choices of outflow boundary conditions are considered for numerical conservation laws. All four methods are stable for linear problems, for which examples are presented where either a boundary layer forms or the numerical scheme, together with the boundary condition, is unstable due to the formation of a reflected shock. A simple heuristic argument is presented for determining the suitability of the boundary condition.

Kamowitz, David↗

High order filtering methods for approximating hyberbolic systems of conservation laws

In the computation of discontinuous solutions of hyperbolic systems of conservation laws, the recently developed essentially non-oscillatory (ENO) schemes appear to be very useful. However, they are computationally costly compared to simple central difference methods. A filtering method which is developed uses simple central differencing of arbitrarily high order accuracy, except when a novel local test indicates the development of spurious oscillations. At these points, the full ENO apparatus is used, maintaining the high order of accuracy, but removing spurious oscillations. Numerical results indicate the success of the method. High order of accuracy was obtained in regions of smooth flow without spurious oscillations for a wide range of problems and a significant speed up of generally a factor of almost three over the full ENO method.

Lafon, F.↗

Non-oscillatory central differencing for hyperbolic conservation laws

Many of the recently developed high resolution schemes for hyperbolic conservation laws are based on upwind differencing. The building block for these schemes is the averaging of an appropriate Godunov solver; its time consuming part involves the field-by-field decomposition which is required in order to identify the direction of the wind. Instead, the use of the more robust Lax-Friedrichs (LxF) solver is proposed. The main advantage is simplicity: no Riemann problems are solved and hence field-by-field decompositions are avoided. The main disadvantage is the excessive numerical viscosity typical to the LxF solver. This is compensated for by using high-resolution MUSCL-type interpolants. Numerical experiments show that the quality of results obtained by such convenient central differencing is comparable with those of the upwind schemes.

Nessyahu, Haim↗

The origin of the energy–momentum conservation law

The interplay between the action–reaction principle and the energy–momentum conservation law is revealed by the examples of the Maxwell–Lorentz and Yang–Mills–Wong theories, and general relativity. These two statements are shown to be equivalent in the sense that both hold or fail together. Their mutual agreement is demonstrated most clearly in the self-interaction problem by taking account of the rearrangement of degrees of freedom appearing in the action of the Maxwell–Lorentz and Yang–Mills–Wong theories. The failure of energy–momentum conservation in general relativity is attributed to the fact that this theory allows solutions having nontrivial topologies. The total energy and momentum of a system with nontrivial topological content prove to be ambiguous, coordinatization-dependent quantities. For example, the energy of a Schwarzschild black hole may take any positive value greater than, or equal to, the mass of the body whose collapse is responsible for forming this black hole. We draw the analogy to the paradoxial Banach–Tarski theorem; the measure becomes a poorly defined concept if initial three-dimensional bounded sets are rearranged in topologically nontrivial ways through the action of free non-Abelian isometry groups. - Highlights: • The action–reaction principle and energy–momentum conservation hold or fail together. • Nontrivial topology is the reason for energy–momentum nonconservation in gravity. • The total energy of a black hole is an ambiguous coordinatization-dependent quantity. • This affair closely parallels that in the paradoxical Banach–Tarski theorem.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

On the construction and application of implicit factored schemes for conservation laws

Efficient, noniterative, implicit finite difference algorithms are systematically developed for nonlinear conservation laws including purely hyperbolic systems and mixed hyperbolic parabolic systems. Utilization of a rational fraction or Pade time differencing formulas, yields a direct and natural derivation of an implicit scheme in a delta form. Attention is given to advantages of the delta formation and to various properties of one- and two-dimensional algorithms.

Warming, R. F.↗

Parallel, adaptive finite element methods for conservation laws

We construct parallel finite element methods for the solution of hyperbolic conservation laws in one and two dimensions. Spatial discretization is performed by a discontinuous Galerkin finite element method using a basis of piecewise Legendre polynomials. Temporal discretization utilizes a Runge-Kutta method. Dissipative fluxes and projection limiting prevent oscillations near solution discontinuities. A posteriori estimates of spatial errors are obtained by a p-refinement technique using superconvergence at Radau points. The resulting method is of high order and may be parallelized efficiently on MIMD computers. We compare results using different limiting schemes and demonstrate parallel efficiency through computations on an NCUBE/2 hypercube. We also present results using adaptive h- and p-refinement to reduce the computational cost of the method.

Biswas, Rupak↗

Error estimates to smooth solutions of semi-discrete discontinuous Galerkin methods with quadrature rules for scalar conservation laws

Here, we focus on error estimates to smooth solutions of semi-discrete discontinuous Galerkin (DG) methods with quadrature rules for scalar conservation laws. The main techniques we use are energy estimate and Taylor expansion first introduced by Zhang and Shu in (Zhang and Shu, SIAM J Num Anal 42 (2004), 641–666). We show that, with p K (piecewise polynomials of degree k) finite elements in 1D problems, if the quadrature over elements is exact for polynomials of degree (2k) error estimates of O(h k+1/2 ) are obtained for general monotone fluxes, and optimal estimates of O(h k+1 ) are obtained for upwind fluxes. For multidimensional problems, if in addition quadrature over edges is exact for polynomials of degree (2k+1), error estimates of O(h k ) are obtained for general monotone fluxes, and O(h k+1/2 ) are obtained for monotone and sufficiently smooth numerical fluxes. Numerical results validate our analysis.

97 MATHEMATICS AND COMPUTING↗

Cone-grid scheme for solving hyperbolic systems of conservation laws and one application

In this work, we introduce a new numerical method, the so-called cone-grid scheme for solving hyperbolic systems of conservation laws. The formulation and the theoretical analysis for this scheme are slightly simpler than other algorithms. Simultaneously, our technique leads to a more efficacious numerical scheme. The Riemann solution is the basic ingredient for this scheme. We also give the main application of this technique, namely the global weak solutions for the one-dimensional model prescribes heat conduction in solids at low temperature, which called phonon–Bose model. This system consists of a conservation equation for the energy density and the heat flux. The scheme also satisfies positivity. The cone-grid scheme was compared with exact solution by three numerical examples, where explicit solutions are known. These numerical results verify the accuracy of the proposed scheme qualitatively and quantitatively.

97 MATHEMATICS AND COMPUTING↗

A convergent series expansion for hyperbolic systems of conservation laws

The discontinuities piecewise analytic initial value problem for a wide class of conservation laws is considered which includes the full three-dimensional Euler equations. The initial interaction at an arbitrary curved surface is resolved in time by a convergent series. Among other features the solution exhibits shock, contact, and expansion waves as well as sound waves propagating on characteristic surfaces. The expansion waves correspond to he one-dimensional rarefactions but have a more complicated structure. The sound waves are generated in place of zero strength shocks, and they are caused by mismatches in derivatives.

Harabetian, E.↗

Asymptotic-induced numerical methods for conservation laws

Asymptotic-induced methods are presented for the numerical solution of hyperbolic conservation laws with or without viscosity. The methods consist of multiple stages. The first stage is to obtain a first approximation by using a first-order method, such as the Godunov scheme. Subsequent stages of the method involve solving internal-layer problems identified by using techniques derived via asymptotics. Finally, a residual correction increases the accuracy of the scheme. The method is derived and justified with singular perturbation techniques.

Garbey, Marc↗

The convergence rate of approximate solutions for nonlinear scalar conservation laws

The convergence rate is discussed of approximate solutions for the nonlinear scalar conservation law. The linear convergence theory is extended into a weak regime. The extension is based on the usual two ingredients of stability and consistency. On the one hand, the counterexamples show that one must strengthen the linearized L(sup 2)-stability requirement. It is assumed that the approximate solutions are Lip(sup +)-stable in the sense that they satisfy a one-sided Lipschitz condition, in agreement with Oleinik's E-condition for the entropy solution. On the other hand, the lack of smoothness requires to weaken the consistency requirement, which is measured in the Lip'-(semi)norm. It is proved for Lip(sup +)-stable approximate solutions, that their Lip'convergence rate to the entropy solution is of the same order as their Lip'-consistency. The Lip'-convergence rate is then converted into stronger L(sup p) convergence rate estimates.

Nessyahu, Haim↗

Second-order accurate nonoscillatory schemes for scalar conservation laws

Explicit finite difference schemes for the computation of weak solutions of nonlinear scalar conservation laws is presented and analyzed. These schemes are uniformly second-order accurate and nonoscillatory in the sense that the number of extrema of the discrete solution is not increasing in time.

Huynh, Hung T.↗

Solution of steady-state one-dimensional conservation laws by mathematical programming

Solution techniques for a class of steady-state scalar conservation laws are developed analytically. Discretization by finite-volume formulas is employed to obtain an overdetermined system of algebraic equations, which are then perturbed nonsingularly (with perturbation coefficient = epsilon) and solved using the l(1) mathematical-programming algorithm of Seneta and Steiger (1984); this approach limits the matrix bandwidth to two, so that an explicit solution can be found efficiently. It is shown that, for small values of epsilon, the l(1) solutions exhibit sharp correctly located shocks and are nonoscillatory O(epsilon) approximations of the physically relevant solutions.

Lavery, J. E.↗

Second-order accurate nonoscillatory schemes for scalar conservation laws

Explicit finite difference schemes for the computation of weak solutions of nonlinear scalar conservation laws is presented and analyzed. These schemes are uniformly second-order accurate and nonoscillatory in the sense that the number of extrema of the discrete solution is not increasing in time.

Huynh, Hung T.↗

An hp-adaptivity and error estimation for hyperbolic conservation laws

This paper presents an hp-adaptive discontinuous Galerkin method for linear hyperbolic conservation laws. A priori and a posteriori error estimates are derived in mesh-dependent norms which reflect the dependence of the approximate solution on the element size (h) and the degree (p) of the local polynomial approximation. The a posteriori error estimate, based on the element residual method, provides bounds on the actual global error in the approximate solution. The adaptive strategy is designed to deliver an approximate solution with the specified level of error in three steps. The a posteriori estimate is used to assess the accuracy of a given approximate solution and the a priori estimate is used to predict the mesh refinements and polynomial enrichment needed to deliver the desired solution. Numerical examples demonstrate the reliability of the a posteriori error estimates and the effectiveness of the hp-adaptive strategy.

Bey, Kim S.↗