Positive equilibria of a class of power-law kinetics

This paper studies a class of power-law kinetics, PL-ILK, for whose subset, PL-TIK, analogues of the Deficiency Zero Theorem and the Deficiency One Theorem (DOT) for mass action systems are valid. The DOT also includes the necessary and sufficient condition of Boros for uniqueness in the non-weakly reversible case. To our knowledge, this is the first set of kinetics beyond mass action kinetics (MAK) for which the DOT has been shown to be valid. A further interesting property of PL-TIK is a certain “robustness” relative to dependence of linkage classes: existence of a positive equilibrium for each linkage class implies the existence of a positive equilibrium for the whole network. For MAK systems, the PL-ILK property is equivalent to the reactant deficiency of the linkage class containing the zero complex being one, and zero for all other linkage classes. As shown in the Supplementary Materials, an initial survey of MAK and BST systems already reveals numerous examples with PL-ILK kinetics.     

Multiple rate-determining steps for nonideal and fractal kinetics

We show that the kinetic model of a single rate-determining step in a reaction mechanism can be extended to systems with multiple overall reactions for which the elementary reactions obey nonideal or fractal kinetics. The following assumptions are necessary: (1) The system studied is either closed or open, but no constraints exist preventing the evolution toward equilibrium. (2) Elementary reactions occur in pairs of forward and backward steps. (3) The kinetics of the elementary steps are either nonideal or fractal and are compatible with equilibrium thermodynamics. (4) The number of reaction routes is identical with the number of rate-determining steps. If these hypotheses are valid, then the overall reaction rates can be explicitly evaluated: they have a form similar to the kinetic equations for the elementary reactions and the apparent reaction orders and fractal coefficients can be expressed analytically in terms of the kinetic parameters of the elementary reactions. We derive a set of relationships which connect the equilibrium constants of the reaction routes, the corresponding overall rate coefficients, and the stoichiometric numbers of the rate-determining steps. We also derive a set of generalized Boreskov relations among the apparent activation energies of the forward and backward overall processes, the corresponding reaction enthalpies, and the stoichiometric coefficients of the rate-determining steps. If the elementary reactions obey fractal kinetics, the same is true for the rate-determining steps. The fractal exponents of the forward and backward overall reactions are linear combinations of the fractal exponents of the fractal elementary reactions. Similar to the theory of single rate-determining steps, our approach can be used for selecting suitable reaction mechanisms from experimental data.     

Stability of Surface Mechanisms with Three Species and Mass-Action Kinetics

The linear stability problem for surface mechanisms with free sites and two adsorbed species is investigated under the assumptions of mass action (Langmuir) surface kinetics, fast mass transport to and from the surface, and a conservation condition. The results also apply to enzyme kinetics for systems with a single enzyme occurring in the free form and two combined forms, and with fast mass transport of the substrates and products. Mechanisms are classified according to their stability and the presence or absence of complex eigenvalues, and specific reactions with numerical values of the rate constants and surface concentrations are given to illustrate the results. Some mechanisms, e.g., proportionate reactions, are shown to be stable for all values of the rate constants and stoichiometric coefficients. The two most common types of mechanisms, namely sequential mechanisms and the simple Langmuir–Hinshelwood mechanism (one adsorbate per site), are always stable. The possibility of complex eigenvalues arises for sequential mechanisms (providing a counterexample to a condition for real eigenvalues given previously in the literature). More general Langmuir–Hinshelwood mechanisms can be unstable (e.g., those in which one adsorbate occupies two sites). Some results are generalized to mechanisms with three or more adsorbed species, and global stability is investigated using monotone dynamical systems theory.     

Model hysteresis dimer molecule II: deductions from probability profile due to system coordinates

The hysteresis dimer reaction of the first sequel is applied to test the Gibbs density-in-phase hypothesis for a canonical distribution at equilibrium. The probability distribution of variously defined internal and external variables is probed using the algorithms described, in particular the novel probing of the energy states of a labeled particle where it is found that there is compliance with the Gibbs’ hypothesis for the stated equilibrium condition and where the probability data strongly suggests that an extended equipartition principle may be formulated for some specific molecular coordinates, whose equipartition temperature does not equal the mean system temperature and a conjecture concerning which coordinates may be suitable is provided. Evidence of violations to the mesoscopic nonequilibrium thermodynamics (MNET) assumptions used without clear qualifications for a canonical distribution for internal variables are described, and possible reasons outlined, where it is found that the free dimer and atom particle kinetic energy distributions agree fully with Maxwell–Boltzmann statistics but the distribution for the relative kinetic energy of bonded atoms does not. The principle of local equilibrium (PLE) commonly used in nonequilibrium theories to model irreversible systems is investigated through NEMD simulation at extreme conditions of bond formation and breakup at the reservoir ends in the presence of a temperature gradient, where for this study a simple and novel difference equation algorithm to test the divergence theorem for mass conservation is utilized, where mass is found to be conserved from the algorithm in the presence of flux currents, in contradiction to at least one aspect of PLE in the linear domain. It is concluded therefore that this principle can be a good approximation at best, corroborating previous purely theoretical results derived from the generalized Clausius Inequality, which proved that the PLE cannot be an exact principle for nonequilibrium systems.      

Multistationarity is neither necessary nor sufficient to oscillations

The existence of more than one stationary point for certain parameter values is generally considered to be a necessary condition of the emergence of oscillatory solutions for some parameter values in reaction kinetics. Examples taken from both physics and chemical kinetics show that the condition is neither necessary nor sufficient. This revised version was published online in July 2006 with corrections to the Cover Date.     

Review of non-reactive and reactive wetting of liquids on surfaces

Wettability is a tendency for a liquid to spread on a solid substrate and is generally measured in terms of the angle (contact angle) between the tangent drawn at the triple point between the three phases (solid, liquid and vapour) and the substrate surface. A liquid spreading on a substrate with no reaction/absorption of the liquid by substrate material is known as non-reactive or inert wetting whereas the wetting process influenced by reaction between the spreading liquid and substrate material is known as reactive wetting. Young's equation gives the equilibrium contact angle in terms of interfacial tensions existing at the three-phase interface. The derivation of Young's equation is made under the assumptions of spreading of non-reactive liquid on an ideal (physically and chemically inert, smooth, homogeneous and rigid) solid, a condition that is rarely met in practical situations. Nevertheless Young's equation is the most fundamental starting point for understanding of the complex field of wetting. Reliable and reproducible measurements of contact angle from the experiments are important in order to analyze the wetting behaviour. Various methods have been developed over the years to evaluate wettability of a solid by a liquid. Among these, sessile drop and wetting balance techniques are versatile, popular and provide reliable data. Wetting is affected by large number of factors including liquid properties, substrate properties and system conditions. The effect of these factors on wettability is discussed. Thermodynamic treatment of wetting in inert systems is simple and based on free energy minimization where as that in reactive systems is quite complex. Surface energetics has to be considered while determining the driving force for spreading. Similar is the case of spreading kinetics. Inert systems follow definite flow pattern and in most cases a single function is sufficient to describe the whole kinetics. Theoretical models successfully describe the spreading in inert systems. However, it is difficult to determine the exact mechanism that controls the kinetics since reactive wetting is affected by a number of factors like interfacial reactions, diffusion of constituents, dissolution of the substrate, etc. The quantification of the effect of these interrelated factors on wettability would be useful to build a predictive model of wetting kinetics for reactive systems.     

The wonderful world of micelles

This review is focused on the most unique and paradoxical properties of micelles, which require special consideration. Six properties have been noted. (1) Micelle formation in the absence of attraction between monomers. Under the action of the hydrophobic effect, ionic micelles can be formed even in the presence of repulsion between similarly charged ions. (2) Despite small sizes, micelles are not nuclei of any phase and have no macroscopic analogs. (3) Solid-liquid duality. Micelles are liquidlike in the tangential direction and solidlike in the normal (radial) direction. This rigidity is sufficient for the development of polymorphism. (4) The suddenness of micelle formation and instantaneous emergence of large molecular aggregates. The quasi-chemical and phase approaches explain the abrupt transition through the mass action law by large aggregation numbers and the possible existence of a metastable state during the microphase transition, respectively. (5) Abnormal solubility. Micelles do not obey the Kelvin equation and exhibit symbate variations in sizes and solubility. The paradox can be solved using the theory of aggregative equilibrium. (6) When an ionic surfactant is added to a micellar solution, the concentration of one of its ions decreases. This postulate can be strictly proved based on combined consideration of the electrical neutrality condition and the mass action law.     

Phase-equilibrium calculations for n-alkane + alkanol systems using continuous thermodynamics

A new association model based on continuous thermodynamics is introduced and applied to six systems of the type n-alkane (n-hexane, n-heptane, n-octane) + alkanol (methanol, ethanol). The alkanol is considered to be a mixture of chain associates with the composition described by a continuous distribution function. This distribution function is derived as an analytical expression from the mass action law applied to the association equilibrium. To consider the entropic contribution originating from the size differences of the molecules (associates) activity coefficients based on Flory–Huggins model are included in the mass action law. Unlike the molecular-mass distribution of a polymer the chain-length distribution of the associates depends on the temperature and on the mole fraction of the alkanol. The treatment of vapor–liquid equilibrium and liquid–liquid equilibrium is similar to that of an oil system or of a polymer solution using continuous thermodynamics. Different to other chemical models of association there is no additive split into a physical and a chemical contribution. The equilibrium constants of association were fitted to vapor-pressure data of methanol and ethanol. The model needs only one interaction parameter being independent of temperature and taking the same value for all systems studied. Considering the simplicity of the model, both the liquid–liquid equilibrium of the three methanol systems and the vapor–liquid equilibrium of all six systems are predicted with reasonable accuracy.     

Computing minimal entropy production trajectories: an approach to model reduction in chemical kinetics

Advanced experimental techniques in chemistry and physics provide increasing access to detailed deterministic mass action models for chemical reaction kinetics. Especially in complex technical or biochemical systems the huge amount of species and reaction pathways involved in a detailed modeling approach call for efficient methods of model reduction. These should be automatic and based on a firm mathematical analysis of the ordinary differential equations underlying the chemical kinetics in deterministic models. A main purpose of model reduction is to enable accurate numerical simulations of even high dimensional and spatially extended reaction systems. The latter include physical transport mechanisms and are modeled by partial differential equations. Their numerical solution for hundreds or thousands of species within a reasonable time will exceed computer capacities available now and in a foreseeable future. The central idea of model reduction is to replace the high dimensional dynamics by a low dimensional approximation with an appropriate degree of accuracy. Here I present a global approach to model reduction based on the concept of minimal entropy production and its numerical implementation. For given values of a single species concentration in a chemical system all other species concentrations are computed under the assumption that the system is as close as possible to its attractor, the thermodynamic equilibrium, in the sense that all modes of thermodynamic forces are maximally relaxed except the one, which drives the remaining system dynamics. This relaxation is expressed in terms of minimal entropy production for single reaction steps along phase space trajectories.     

Kinetics of autocatalysis in small systems

Autocatalysis is a ubiquitous chemical process that drives a plethora of biological phenomena, including the self-propagation of prions etiological to the Creutzfeldt-Jakob disease and bovine spongiform encephalopathy. To explain the dynamics of these systems, we have solved the chemical master equation for the irreversible autocatalytic reaction A+B-->2A. This solution comprises the first closed form expression describing the probabilistic time evolution of the populations of autocatalytic and noncatalytic molecules from an arbitrary initial state. Grand probability distributions are likewise presented for autocatalysis in the equilibrium limit (A+B <==>2A), allowing for the first mechanistic comparison of this process with chemical isomerization (B<==>A) in small systems. Although the average population of autocatalytic (i.e., prion) molecules largely conforms to the predictions of the classical "rate law" approach in time and the law of mass action at equilibrium, thermodynamic differences between the entropies of isomerization and autocatalysis are revealed, suggesting a "mechanism dependence" of state variables for chemical reaction processes. These results demonstrate the importance of chemical mechanism and molecularity in the development of stochastic processes for chemical systems and the relationship between the stochastic approach to chemical kinetics and nonequilibrium thermodynamics.     

Kinetic pathways of sheared block copolymer systems derived from Minkowski functionals

We employ Minkowski functionals to analyze the kinetics of pattern formation under an applied external shear flow. The considered pattern formation model describes the dynamics of phase separating block copolymer systems. For our purpose, we have chosen two block copolymer systems (a melt and a solution) that exhibit a hexagonal cylindrical morphology as an equilibrium structure. Our main objective is the determination of efficient choices for the treshold values that are required for the calculation of the Minkowski functionals. We find that a minimal set of two treshold values (one from which should be equal to an average density value and another to a higher density value) is sufficient to unraffle the phase separation kinetics. Given these choices, we focus on the influence of the degree of phase separation, and the instance at which the shear is applied, on the kinetic pathways. We also found a remarkable similarity of the time evolution of Euler characteristic and the segregation parameter for the average density choice.     

Positive equilibria of weakly reversible power law kinetic systems with linear independent interactions

In this paper, we extend our study of power law kinetic systems whose kinetic order vectors (which we call “interactions”) are reactant-determined (i.e. reactions with the same reactant complex have identical vectors) and are linear independent per linkage class. In particular, we consider PL-TLK systems, i.e. such whose T-matrix (the matrix with the interactions as columns indexed by the reactant complexes), when augmented with the rows of characteristic vectors of the linkage classes, has maximal column rank. Our main result states that any weakly reversible PL-TLK system has a complex balanced equilibrium. On the one hand, we consider this result as a “Higher Deficiency Theorem” for such systems since in our previous work, we derived analogues of the Deficiency Zero and the Deficiency One Theorems for mass action kinetics (MAK) systems for them, thus covering the “Low Deficiency” case. On the other hand, our result can also be viewed as a “Weak Reversibility Theorem” (WRT) in the sense that the statement “any weakly reversible system with a kinetics from the given set has a positive equilibrium” holds. According to the work of Deng et al. and more recently of Boros, such a WRT holds for MAK systems. However, we show that a WRT does not hold for two proper MAK supersets: the set PL-NIK of non-inhibitory power law kinetics (i.e. all kinetic orders are non-negative) and the set PL-FSK of factor span surjective power law kinetics (i.e. different reactants imply different interactions).     

On the origin of Turing instability

A reaction–diffusion system consisting of one, two or three chemical species and taking place in an arbitrary number of spatial dimensions cannot exhibit Turing instability if none of the reaction steps express cross‐inhibition. A corollary of this result – obtained by elementary calculations – underlines the importance of nonlinearity in the formation of stationary structures, a kind of self‐organization on a chemical basis. Relations to global stability of reaction–diffusion systems, and results on multispecies systems are also mentioned. The statements are not restricted to mass action type models. As a by‐product, the solution of a basic inverse problem of formal kinetics is also presented which extends a previous result by Hárs and Tóth (1981) to models with arbitrary – including rational – functions as reaction rates so often occurring, e.g., in enzyme kinetics.     

On the dependence of the existence of the positive steady states on the rate coefficients for deficiency-one mass action systems: single linkage class

The Deficiency-One Theorem states that there exists a unique positive steady state in each positive stoichiometric class for weakly reversible deficiency-one mass action systems with one linkage class (regardless of the values of the rate coefficients). The non-emptiness of the set of positive steady states does not remain valid if we omit the weak reversibility. A recently published paper provided an equivalent condition to the existence of a positive steady state for deficiency-one mass action systems that are not weakly reversible, but still has only one linkage class. Based on that result, we characterise in this paper those of these mass action systems for which the non-emptiness of the set of positive steady states holds regardless of the values of the rate coefficients. Also, we provide an equivalent condition to the existence of rate coefficients such that the set of positive steady states is nonempty for the resulting mass action system.     

Modeling of Coesterification Process for Biodegradable Poly(Butylene Succinate‐co‐Butylene Terephthalate) Copolyesters

Comprehensive mathematical model based on the kinetics and thermodynamic equations is developed to examine a coesterification concept of biodegradable aliphatic‐aromatic copolyesters, poly(butylene succinate‐co‐butylene terephthalate) (PBST). The simulation results for batch process are validated with pilot experimental data. The continuous process is further studied to figure out the coesterification performance of succinic acid (SA) and terephthalic acid (TPA) with different reaction activities and thermodynamic properties in terms of reaction efficiency, small molecular evaporation and product quality. There is a compromise between the operating conditions of the two systems of SA/1,4‐butanediol (BDO) and TPA/BDO. Proper pressure reduction is beneficial to reaction efficiency and product quality. The way to increase reaction efficiency by raising temperature is limited due to the serious evaporation of reactants. Influenced by the solid–liquid equilibrium and the slow reaction rate of TPA, the esterification of acid needs sufficient residence time to complete.     

Polynomial time algorithms to determine weakly reversible realizations of chemical reaction networks

Weak reversibility is a crucial structural property of chemical reaction networks (CRNs) with mass action kinetics, because it has major implications related to the existence, uniqueness and stability of equilibrium points and to the boundedness of solutions. In this paper, we present two new algorithms to find dynamically equivalent weakly reversible realizations of a given CRN. They are based on linear programming and thus have polynomial time-complexity. Hence, these algorithms can deal with large-scale biochemical reaction networks, too. Furthermore, one of the methods is able to deal with linearly conjugate networks, too.