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Register a new userAsymptotology of Chemical Reaction Networks
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The concept of the limiting step is extended to the asymptotology of multiscale reaction networks. Complete theory for linear networks with well separated reaction rate constants is developed. We present algorithms for explicit approximations of eigenvalues and eigenvectors of kinetic matrix. Accuracy of estimates is proven. Performance of the algorithms is demonstrated on simple examples. Application of algorithms to nonlinear systems is discussed.
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A variety of natural phenomena comprises a huge number of competing reactions and short-lived intermediates. Any study of such processes requires the discovery and accurate modeling of their underlying reaction network. However, this task is challenging due to the complexity in exploring all the possible pathways and the high computational cost in accurately modeling a large number of reactions. Fortunately, very often these processes are dominated by only a limited subset of the networks reaction pathways. In this work we propose a novel computationally inexpensive method to identify and select the key pathways of complex reaction networks, so that high-level ab-initio calculations can be more efficiently targeted at these critical reactions. The method estimates the relative importance of the reaction pathways for given reactants by analyzing the accelerated evolution of hundreds of replicas of the system and detecting products formation. This acceleration-detection method is able to tremendously speed up the reactivity of uni- and bimolecular reactions, without requiring any previous knowledge of products or transition states. Importantly, the method is efficiently iterative, as it can be straightforwardly applied for the most frequently observed products, therefore providing an efficient algorithm to identify the key reactions of extended chemical networks. We verified the validity of our approach on three different systems, including the reactivity of t-decalin with a methyl radical, and in all cases the expected behavior was recovered within statistical error.
We develop a thermodynamic framework for closed and open chemical networks applicable to non-elementary reactions that do not need to obey mass action kinetics. It only requires the knowledge of the kinetics and of the standard chemical potentials, and makes use of the topological properties of the network (conservation laws and cycles). Our approach is proven to be exact if the network results from a bigger network of elementary reactions where the fast-evolving species have been coarse grained. Our work should be particularly relevant for energetic considerations in biosystems where the characterization of the elementary dynamics is seldomly achieved.
Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a Grand-Canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work we propose the Constant Chemical Potential Molecular Dynamics (C$mu$MD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the C$mu$MD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions, and to extract growth rates and free-energy barriers.
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems of polynomial ordinary differential equations. The steady states of these mass action systems have been analysed via a variety of techniques, including elementary flux mode analysis, algebraic techniques (e.g. Groebner bases), and deficiency theory. In this paper, we present a novel method for characterizing the steady states of mass action systems. Our method explicitly links a networks capacity to permit a particular class of steady states, called toric steady states, to topological properties of a related network called a translated chemical reaction network. These networks share their reaction stoichiometries with their source network but are permitted to have different complex stoichiometries and different network topologies. We apply the results to examples drawn from the biochemical literature.
The numerical computation of chemical potential in dense, non-homogeneous fluids is a key problem in the study of confined fluids thermodynamics. To this day several methods have been proposed, however there is still need for a robust technique, capable of obtaining accurate estimates at large average densities. A widely established technique is the Widom insertion method, that computes the chemical potential by sampling the energy of insertion of a test particle. Non-homogeneity is accounted for by assigning a density dependent weight to the insertion points. However, in dense systems, the poor sampling of the insertion energy is a source of inefficiency, hampering a reliable convergence. We have recently presented a new technique for the chemical potential calculation in homogeneous fluids. This novel method enhances the sampling of the insertion energy via Well-Tempered Metadynamics, reaching accurate estimates at very large densities. In this paper we extend the technique to the case of non-homogeneous fluids. The method is successfully tested on a confined Lennard-Jones fluid. In particular we show that, thanks to the improved sampling, our technique does not suffer from a systematic error that affects the classic Widom method for non-homogeneous fluids, providing a precise and accurate result.
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