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At least 73 records · Page 4

Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws

In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks “in a box”, whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = s{sup Y} between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats s{sup Y}. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Implicit TVD schemes for hyperbolic conservation laws in curvilinear coordinates

The Harten (1983, 1984) total variation-diminishing (TVD) schemes, constituting a one-parameter explicit and implicit, second-order-accurate family, have the property of not generating spurious oscillations when applied to one-dimensional, nonlinear scalar hyperbolic conservation laws and constant coefficient hyperbolic systems. These methods are presently extended to the multidimensional hyperbolic conservation laws in curvilinear coordinates. Means by which to linearize the implicit operator and solution strategies, in order to improve the computation efficiency of the implicit algorithm, are discussed. Numerical experiments with steady state airfoil calculations indicate that the proposed linearized implicit TVD schemes are accurate and robust.

Yee, H. C.↗

A High-Order Finite Spectral Volume Method for Conservation Laws on Unstructured Grids

A time accurate, high-order, conservative, yet efficient method named Finite Spectral Volume (FSV) is developed for conservation laws on unstructured grids. The concept of a 'spectral volume' is introduced to achieve high-order accuracy in an efficient manner similar to spectral element and multi-domain spectral methods. In addition, each spectral volume is further sub-divided into control volumes (CVs), and cell-averaged data from these control volumes is used to reconstruct a high-order approximation in the spectral volume. Riemann solvers are used to compute the fluxes at spectral volume boundaries. Then cell-averaged state variables in the control volumes are updated independently. Furthermore, TVD (Total Variation Diminishing) and TVB (Total Variation Bounded) limiters are introduced in the FSV method to remove/reduce spurious oscillations near discontinuities. A very desirable feature of the FSV method is that the reconstruction is carried out only once, and analytically, and is the same for all cells of the same type, and that the reconstruction stencil is always non-singular, in contrast to the memory and CPU-intensive reconstruction in a high-order finite volume (FV) method. Discussions are made concerning why the FSV method is significantly more efficient than high-order finite volume and the Discontinuous Galerkin (DG) methods. Fundamental properties of the FSV method are studied and high-order accuracy is demonstrated for several model problems with and without discontinuities.

Wang, Z. J.↗

Similarity considerations and conservation laws for magneto-static atmospheres

The equations of magnetohydrostatic equilibria for a plasma in a gravitational field are investigated analytically. For equilibria with one ignorable spatial coordinate, the equations reduce to a single nonlinear elliptic equation for the magnetic potential. Similarity solutions of the elliptic equation are obtained for the case of an isothermal atmosphere in a uniform gravitational field. The solutions are obtained from a consideration of the invariance group of the elliptic equation. The importance of symmetries of the elliptic equation also appears in the determination of conservation laws. It turns out that the elliptic equation can be written as a variational principle, and the symmetries of the variational functional lead (via Noether's theorem) to conservation laws for the equation. As an example of the application of the similarity solutions, a model magnetostatic atmosphere is constructed in which the current density J is proportional to the cube of the magnetic potential, and falls off exponentially with distance vertical to the base, with an 'e-folding' distance equal to the gravitational scale height. The solutions show the interplay between the gravitational force, the J x B force (B, magnetic field induction) and the gas pressure gradient.

Webb, G. M.↗

Axial magnetic field and toroidally streaming fast ions in the dense plasma focus are natural consequences of conservation laws in the curved axisymmetric geometry of the current sheath

Direct measurement of axial magnetic field in the PF-1000 dense plasma focus (DPF), and its reported correlation with neutron emission, call for a fresh look at previous reports of existence of axial magnetic field component in the DPF from other laboratories, and associated data suggesting toroidal directionality of fast ions participating in fusion reactions, with a view to understand the underlying physics. In this context, recent work dealing with application of the hyperbolic conservation law formalism to the DPF is extended in this paper to a curvilinear coordinate system, which reflects the shape of the DPF current sheath. Locally unidirectional shock propagation in this coordinate system enables construction of a system of 7 one-dimensional hyperbolic conservation law equations with geometric source terms, taking into account all the components of magnetic field and flow velocity. Rankine-Hugoniot jump conditions for this system lead to expressions for the axial magnetic field and three components of fluid velocity having high ion kinetic energy.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Discretely Conservative Finite-Difference Formulations for Nonlinear Conservation Laws in Split Form: Theory and Boundary Conditions

Simulations of nonlinear conservation laws that admit discontinuous solutions are typically restricted to discretizations of equations that are explicitly written in divergence form. This restriction is, however, unnecessary. Herein, linear combinations of divergence and product rule forms that have been discretized using diagonal-norm skew-symmetric summation-by-parts (SBP) operators, are shown to satisfy the sufficient conditions of the Lax-Wendroff theorem and thus are appropriate for simulations of discontinuous physical phenomena. Furthermore, special treatments are not required at the points that are near physical boundaries (i.e., discrete conservation is achieved throughout the entire computational domain, including the boundaries). Examples are presented of a fourth-order, SBP finite-difference operator with second-order boundary closures. Sixth- and eighth-order constructions are derived, and included in E. Narrow-stencil difference operators for linear viscous terms are also derived; these guarantee the conservative form of the combined operator.

Fisher, Travis C.↗

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↗

On a regularization of a scalar conservation law with discontinuous coefficients

This paper is devoted to a scalar conservation law with a linear flux function involving discontinuous coefficients. It is clear that the delta standing wave should be introduced into the Riemann solution in some nonclassical situation. In order to study the formation of delta standing wave, we consider a regularization of the discontinuous coefficient with the Helmholtz mollifier and then obtain a regularized system which depends on a regularization parameter ε > 0. The regularization mechanism is a nonlinear bending of characteristic curves that prevents their finite-time intersection. It is proved rigorously that the solutions of regularized system converge to the delta standing wave solution in the ε → 0 limit. Compared with the classical method of vanishing viscosity, here it is clear to see how the delta standing wave forms naturally along the characteristics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

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↗