Related papers: Mapping dynamical systems into chemical reactions

The catalytic reaction system (CRS) formalism by Hordijk and Steel is a versatile method to model autocatalytic biochemical reaction networks. It is particularly suited, and has been widely used, to study self-sustainment and…

Chemical reaction networks in living cells maintain precise control over thousands of metabolites despite operating far from equilibrium under constant perturbations. While mass action kinetics accurately describe the underlying dynamics,…

Complex systems can be advantageously modeled by formal reaction systems (RS), a.k.a. chemical reaction networks in chemistry. Reaction-based models can indeed be interpreted in a hierarchy of semantics, depending on the question at hand,…

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,…

We propose the use of partial dynamical symmetry (PDS) as a selection criterion for higher-order terms in situations when a prescribed symmetry is obeyed by some states and is strongly broken in others. The procedure is demonstrated in a…

We consider the dynamics of a droplet on a vibrating fluid bath. This hydrodynamic quantum analog system is shown to elicit the canonical behavior of damped-driven systems, including a period doubling route to chaos. By approximating the…

In this paper, a novel computational technique for finite discrete approximation of continuous dynamical systems suitable for a significant class of biochemical dynamical systems is introduced. The method is parameterized in order to affect…

Multidimensional coherent spectroscopy (MDCS) has been established in quantum chemistry as a powerful tool for studying the nonlinear response and nonequilibrium dynamics of molecular systems. More recently, the technique has also been…

The goal of the paper is to derive a revised condition of global equilibrium in complex chemical systems as variational principle in formalism of recently developed discrete thermodynamics (DTD) of chemical equilibria. In classical approach…

We exploit the rich algebraic structure of the interacting boson model to explain the notion of partial dynamical symmetry (PDS), and present a procedure for constructing Hamiltonians with this property. We demonstrate the relevance of PDS…

We consider the basic features of complex dynamical and control systems. Special attention is paid to the problems of synthesis of dynamical models of complex systems, construction of efficient control models, and to the development of…

Polynomial dynamical systems describing interacting particles in the plane are studied. A method replacing integration of a polynomial multi--particle dynamical system by finding polynomial solutions of a partial differential equations is…

We critically explore the applicability of a recently proposed framework to sample the quantum dynamics of a many-body quantum system interacting with light by stochastic trajectories, applying it to the closed and open Tavis-Cummings model…

The dynamics of one species chemical kinetics is studied. Chemical reactions are modelled by means of continuous time Markov processes whose probability distribution obeys a suitable master equation. A large deviation theory is formally…

Dynamical systems with quadratic or polynomial drift exhibit complex dynamics, yet compared to nonlinear systems in general form, are often easier to analyze, simulate, control, and learn. Results going back over a century have shown that…

It is increasingly realized that taking stochastic effects into account is important in order to study biological cells. However, the corresponding mathematical formulation, the chemical master equation (CME), suffers from the curse of…

Complex balanced mass-action systems (CBMASs) are of great importance in the filed of biochemical reaction networks. However analyzing the persistence of these networks with high dimensions and time delays poses significant challenges. To…

The Distributed Cooperative Modeling System (DCMS) solves complex decision problems involving a lot of participants with different viewpoints by network based distributed modeling and multi-template aggregation. This thesis aims at…

Convergent Cross Mapping (CCM) is a powerful method for detecting causality in coupled nonlinear dynamical systems, providing a model-free approach to capture dynamic causal interactions. Partial Cross Mapping (PCM) was introduced as an…

It is a challenge to obtain an accurate model of the state-to-state dynamics of a complex biological system from molecular dynamics (MD) simulations. In recent years, Markov State Models have gained immense popularity for computing…