相关论文: Complexity reduction of astrochemical networks
Chemistry has a key role in the evolution of the interstellar medium (ISM), so it is highly desirable to follow its evolution in numerical simulations. However, it may easily dominate the computational cost when applied to large systems. In…
We present a new method to analyse and reduce chemical networks and apply this technique to the chemistry in molecular clouds. Using the technique, we investigated the possibility of reducing the number of chemical reactions and species in…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
Astrochemical simulations are a powerful tool for revealing chemical evolution in the interstellar medium. Astrochemical calculations require efficient processing of large matrices for the chemical networks. The large chemical reaction…
We discuss a method of approximate model reduction for networks of biochemical reactions. This method can be applied to networks with polynomial or rational reaction rates and whose parameters are given by their orders of magnitude. In…
In many astrophysical applications, the cost of solving a chemical network represented by a system of ordinary differential equations (ODEs) grows significantly with the size of the network, and can often represent a significant…
Databases of gas and surface chemical reactions are a key tool for scientists working in a wide range of physical sciences. In Astrochemistry, databases of chemical reactions are used as inputs to chemical models to determine the abundances…
Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…
With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an…
Network systems consist of subsystems and their interconnections, and provide a powerful framework for analysis, modeling and control of complex systems. However, subsystems may have high-dimensional dynamics, and the amount and nature of…
Recent years have witnessed the detection of an increasing number of complex organic molecules in interstellar space, some of them being of prebiotic interest. Disentangling the origin of interstellar prebiotic chemistry and its connection…
Astrochemical models can be greatly simplified, with obvious computational advantages, if the reaction networks for key species can be reduced to a bare minimum. In addition, if chemical equilibrium holds, then simple analytical solutions…
In this paper, we consider the problem of model order reduction of stochastic biochemical networks. In particular, we reduce the order of (the number of equations in) the Linear Noise Approximation of the Chemical Master Equation, which is…
Complex systems often have features that can be modeled by advanced mathematical tools [1]. Of special interests are the features of complex systems that have a network structure as such systems are important for modeling technological and…
Complex networks have acquired a great popularity in recent years, since the graph representation of many natural, social and technological systems is often very helpful to characterize and model their phenomenology. Additionally, the…
The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…
Large-scale network systems describe a wide class of complex dynamical systems composed of many interacting subsystems. A large number of subsystems and their high-dimensional dynamics often result in highly complex topology and dynamics,…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…
The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…
Simulating chemical reaction networks is often computationally demanding, in particular due to stiffness. We propose a novel simulation scheme where long runs are not simulated as a whole but assembled from shorter precomputed segments of…