Intrinsic properties of conservation-dissipation formalism of irreversible thermodynamics.

This paper proposes four fundamental requirements for establishing PDEs (partial differential equations) modelling irreversible processes. We show that the PDEs derived via the CDF (conservation-dissipation formalism) meet all the requirements. In doing so, we find useful constraints on the freedoms of CDF and point out that a shortcoming of the formalism can be remedied with the help of the Maxwell iteration. It is proved that the iteration preserves the gradient structure and strong dissipativeness of the CDF-based PDEs. A refined formulation of the second law of thermodynamics is given to characterize the strong dissipativeness, while the gradient structure corresponds to nonlinear Onsager relations. Further advantages and limitations of CDF will also be presented. This article is part of the theme issue 'Fundamental aspects of nonequilibrium thermodynamics'.

Maxwell iteration for the lattice Boltzmann method with diffusive scaling.

In this work, we present an alternative derivation of the Navier-Stokes equations from Bhatnagar-Gross-Krook models of the lattice Boltzmann method with diffusive scaling. This derivation is based on the Maxwell iteration and can expose certain important features of the lattice Boltzmann solutions. Moreover, it will be seen to be much more straightforward and logically clearer than the existing approaches including the Chapman-Enskog expansion.

Lattice Boltzmann method for convection-diffusion equations with general interfacial conditions.

In this work, we propose an interfacial scheme accompanying the lattice Boltzmann method for convection-diffusion equations with general interfacial conditions, including conjugate conditions with or without jumps in heat and mass transfer, continuity of macroscopic variables and normal fluxes in ion diffusion in porous media with different porosity, and the Kapitza resistance in heat transfer. The construction of this scheme is based on our boundary schemes [Huang and Yong, J. Comput. Phys. 300, 70 (2015)JCTPAH0021-999110.1016/j.jcp.2015.07.045] for Robin boundary conditions on straight or curved boundaries. It gives second-order accuracy for straight interfaces and first-order accuracy for curved ones. In addition, the new scheme inherits the advantage of the boundary schemes in which only the current lattice nodes are involved. Such an interfacial scheme is highly desirable for problems with complex geometries or in porous media. The interfacial scheme is numerically validated with several examples. The results show the utility of the constructed scheme and very well support our theoretical predications.

Theory of the Lattice Boltzmann method: Derivation of macroscopic equations via the Maxwell iteration.

We propose using the Maxwell iteration to derive the hydrodynamic equations from the lattice Boltzmann equation (LBE) with an external forcing term. The proposed methodology differs from existing approaches in several aspects. First, it need not explicitly introduce multiple-timescales or the Knudsen number, both of which are required in the Chapman-Enskog analysis. Second, it need not use the Hilbert expansion of the hydrodynamic variables, which is necessary in the asymptotic analysis of the LBE. The proposed methodology assumes the acoustic scaling (or the convective scaling) δ(t)∼δ(x), thus δ(t) is the only expansion parameter in the analysis of the LBE system, and it leads to the Navier-Stokes equations in compressible form. The forcing density derived in this work can reproduce existing forcing schemes by adjusting appropriate parameters. The proposed methodology also analyzes the numerical accuracy of the LBE. In particular, it shows the Mach number Ma should scale as O(δ(t)(1/3)) to maintain the truncation errors due to Ma and δ(t) in balance when δ(t)→0, so that the LBE can converge to the expected hydrodynamic equations effectively and efficiently.

Partial equilibrium approximations in apoptosis. II. The death-inducing signaling complex subsystem.

This paper is a continuation of our previous work (Huang and Yong, 2013) for simplifying the Fas signaling-induced apoptotic pathway identified by Hua et al. (2005) for human tumor T cells. The previous paper studied the downstream intracelluar-signaling subsystem, while the present one is concerned with the upstream death-inducing signaling complex (DISC) subsystem. Under the assumption that the bind of Fas-associated death domains and FLICE-inhibitory proteins to the DISC is much faster than that of the initiator procaspases, we greatly simplify the upstream subsystem from 35 reactions with 26 species to 6 reactions with 9 species by adopting the classical and recently justified partial equilibrium approximation method. Numerical simulations show that the simplified model is in an excellent agreement with the original model. Most importantly, the simplified model clearly reveals the key reactants and dominated pathways in the Fas signaling process, and thus provides new insights into the apoptosis.

A Kinetic Model for Cell Damage Caused by Oligomer Formation.

It is well known that the formation of amyloid fiber may cause invertible damage to cells, although the underlying mechanism has not been fully understood. In this article, a microscopic model considering the detailed processes of amyloid formation and cell damage is constructed based on four simple assumptions, one of which is that cell damage is raised by oligomers rather than mature fibrils. By taking the maximum entropy principle, this microscopic model in the form of infinite mass-action equations together with two reaction-convection partial differential equations (PDEs) has been greatly coarse-grained into a macroscopic system consisting of only five ordinary differential equations (ODEs). With this simple model, the effects of primary nucleation, elongation, fragmentation, and protein and seeds concentration on amyloid formation and cell damage have been extensively explored and compared with experiments. We hope that our results will provide new insights into the quantitative linkage between amyloid formation and cell damage.

Partial equilibrium approximations in apoptosis. I. The intracellular-signaling subsystem.

Apoptosis is one of the most basic biological processes. In apoptosis, tens of species are involved in many biochemical reactions with times scales of widely differing orders of magnitude. By the law of mass action, the process is mathematically described with a large and stiff system of ODEs (ordinary differential equations). The goal of this work is to simplify such systems of ODEs with the PEA (partial equilibrium approximation) method. In doing so, we propose a general framework of the PEA method together with some conditions, under which the PEA method can be justified rigorously. The main condition is the principle of detailed balance for fast reactions as a whole and the framework provides some meaningful physical insights of the full chemical kinetics. With the justified method as a tool, we simplify the Fas-signaling pathway model due to Hua et al. [6] under the empirical assumption that nine reactions therein can be well regarded as relatively fast. This paper reports our simplification, together with numerical results which confirm the reliability of both our simplified model and the empirical assumption.

Simple moment-closure model for the self-assembly of breakable amyloid filaments.

In this work, we derive a simple mathematical model from mass-action equations for amyloid fiber formation that takes into account the primary nucleation, elongation, and length-dependent fragmentation. The derivation is based on the principle of minimum free energy under certain constraints and is mathematically related to the partial equilibrium approximation. Direct numerical comparisons confirm the usefulness of our simple model. We further explore its basic kinetic and equilibrium properties, and show that the current model is a straightforward generalization of that with constant fragmentation rates.

Accuracy of the viscous stress in the lattice Boltzmann equation with simple boundary conditions.

Based on the theory of asymptotic analysis, we prove that the viscous stress tensor computed with the lattice Boltzmann equation (LBE) in a two-dimensional domain is indeed second-order accurate in space. We only consider simple bounce-back boundary conditions which can be reduced to the periodic boundary conditions by using the method of image. While the LBE with nine velocities on two-dimensional square lattice (i.e., the D2Q9 model) and with the Bhatnagar-Gross-Krook collision model is used as an example in this work, our proof can be extended to the LBE with any linear relaxation collision models in both two and three dimensions.

Conservation-dissipation structure of chemical reaction systems.

In this Brief Report, we show that balanced chemical reaction systems governed by the law of mass action have an elegant conservation-dissipation structure. From this structure a number of important conclusions can be easily deduced. In particular, with the help of this structure we can rigorously justify the classical partial equilibrium approximation in chemical kinetics.

Nonexistence of H theorems for the athermal lattice Boltzmann models with polynomial equilibria.

We prove that no H theorem exists for the athermal lattice Boltzmann equation with polynomial equilibria satisfying the conservation laws exactly and explicitly. The proof is demonstrated by using the seven-velocity model in a triangular lattice in two dimensions, and can be readily extended to other lattice Boltzmann models in two and three dimensions. Some issues pertinent to the numerical instabilities of the lattice Boltzmann method are discussed.