Model-Driven Parallel and Distributed Stochastic Simulation of Chemical Reaction Networks
2025 29th International Symposium on Distributed Simulation and Real Time Applications (DS-RT)Biochemical systems are characterized by rich stochastic behaviors and complex interaction patterns, often modeled through rule-based frameworks such as BioNetGen. Despite the expressiveness of such high-level specifications, simulating large-scale models remains computationally prohibitive.
Bauco, Simone +4 more
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Biochemical Reaction Network Modeling: Predicting Metabolism of Organic Chemical Mixtures
Environmental Science & Technology, 2005All organisms are exposed to multiple xenobiotics, through food, environmental contamination, and drugs. These xenobiotics often undergo biotransformation, a complex process that plays a critical role in xenobiotic elimination or bioactivation to toxic metabolites.
Arthur N, Mayeno +2 more
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Dynamic Modeling of Chemical Reaction Systems with Neural Networks and Hybrid Models
Chemical Engineering & Technology, 1999A common problem in kinetic modeling of complex chemical reactions is that a rigorous description of the reaction system, e.g., based on elementary reactions, is not possible. This is because either the reaction involves too many reactions and intermediates or the reaction mechanism is not known in sufficient detail. Alternative data-driven modeling, e.
Hans-Jörg Zander +2 more
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Hawkes process modelling for chemical reaction networks in a random environment
2023Abstract Cellular processes are open systems, situated in a heterogeneous context, rather than operating in isolation. Chemical reaction networks (CRNs) whose reaction rates are modelled as external stochastic processes account for the heterogeneous environment when describing the embedded process. A marginal description of the embedded
Mark Sinzger-D’Angelo, Heinz Koeppl
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The differentiable manifold model of quantum-chemical reaction networks
International Journal of Quantum Chemistry, 2009The methods of general and differential topology (topology ≈ “rubber geometry”) are particularly suitable for the quantum-mechanical description of nonrigid molecular systems. The concept of nuclear configuration space 3NR is replaced by a metric space M and subsequently by a topological space (M, TC) where points of nuclear geometries, as fundamental ...
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Advances in Chemical Reaction Network Theory for the Identification of Kinetic Models
IFAC Proceedings Volumes, 2012Abstract In this work, we illustrate the potential of Chemical Reaction Network Theory for model identification of kinetic models, setting up the basis for a novel method of inverse bifurcation analysis of bistable biochemical systems. The method exploits the structural properties of biochemical networks to infer the kinetic parameters from dose ...
Irene Otero-Muras +2 more
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P System Models of Bistable, Enzyme Driven Chemical Reaction Networks
2007In certain classes of chemical reaction networks (CRN), there may be two stable states. The challenge is to find a model of the CRN such that the stability properties can be predicted. In this paper we consider the problem of building a P-system designed to simulate the CRN in an attempt to determine if the CRN is stable or bistable.
Stanley M. Dunn, Peter Stivers
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Kinetic modeling of CL-20 decomposition by a chemical reaction neural network
Journal of Analytical and Applied Pyrolysis, 2023Shi Yan, Mingjie Wen, Qingzhao Chu
exaly
Multi-fidelity neural network for uncertainty quantification of chemical reaction models
Combustion and Flame, 2023Bin Yang, Yiru Wang, Keli Lin
exaly
Robust Model Invalidation for Chemical Reaction Networks Using Generalized Moments
2023 62nd IEEE Conference on Decision and Control (CDC), 2023Theodore W. Grunberg +1 more
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