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One of the main challenges in diffusion-based molecular communication is dealing with the non-linearity of reaction-diffusion chemical equations. While numerical methods can be used to solve these equations, a change in the input signals or…

Information Theory · Computer Science 2021-06-04 Hamidreza Abin , Amin Gohari , Masoumeh Nasiri-Kenari

The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…

Molecular Networks · Quantitative Biology 2011-05-10 Petter Holme , Mikael Huss , Sang Hoon Lee

The intermolecular interactions in the title compound are investigated using self-consistent charge density functional based tight binding molecular dynamics. Emphasis is put on the analysis of correlated motions of ion pairs using ideas of…

Chemical Physics · Physics 2016-03-22 Tobias Zentel , Oliver Kühn

We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…

Dynamical Systems · Mathematics 2017-11-22 Bernhard Brehm , Bernold Fiedler

We study the mechanisms of pattern formation for vegetation dynamics in water-limited regions. Our analysis is based on a set of two partial differential equations (PDEs) of reaction-diffusion type for the biomass and water and one ordinary…

Dynamical Systems · Mathematics 2023-03-24 Konstantinos Spiliotis , Lucia Russo , Francesco Giannino , Constantinos Siettos

Chemical kinetics mechanisms are essential for understanding, analyzing, and simulating complex combustion phenomena. In this study, a Neural Ordinary Differential Equation (Neural ODE) framework is employed to optimize kinetics parameters…

Chemical Physics · Physics 2022-09-07 Xingyu Su , Weiqi Ji , Jian An , Zhuyin Ren , Sili Deng , Chung K. Law

In general. automated farming systems make decisions based on static models built from the properties of the plant. in the contrast, irrigation decisions in our suggested method are dynamically changing environmental conditions. the model"s…

Systems and Control · Electrical Eng. & Systems 2023-04-18 Kawsalyaa Manivannan , Bharathi Sankar

Neural Ordinary Differential Equations (NODEs) use a neural network to model the instantaneous rate of change in the state of a system. However, despite their apparent suitability for dynamics-governed time-series, NODEs present a few…

Machine Learning · Computer Science 2021-08-18 Alexander Norcliffe , Cristian Bodnar , Ben Day , Jacob Moss , Pietro Liò

We study the closure problem for continuum balance equations that model mesoscale dynamics of large ODE systems. The underlying microscale model consists of classical Newton equations of particle dynamics. As a mesoscale model we use the…

Mathematical Physics · Physics 2010-10-26 Alexander Panchenko , Lyudmyla L. Barannyk , Robert P. Gilbert

Complex chemical reaction networks, which underlie many industrial and biological processes, often exhibit non-monotonic changes in chemical species concentrations, typically described using nonlinear models. Such non-monotonic dynamics are…

Adaptation and Self-Organizing Systems · Physics 2020-10-21 Zachary G. Nicolaou , Takashi Nishikawa , Schuyler B. Nicholson , Jason R. Green , Adilson E. Motter

In this paper, the applicability of the entropy method for the trend towards equilibrium for reaction-diffusion systems arising from first order chemical reaction networks is studied. In particular, we present a suitable entropy structure…

Analysis of PDEs · Mathematics 2016-12-19 Klemens Fellner , Wolfgang Prager , Bao Q. Tang

The time evolution of dynamical systems is frequently described by ordinary differential equations (ODEs), which must be solved for given initial conditions. Most standard approaches numerically integrate ODEs producing a single solution…

Machine Learning · Computer Science 2020-06-26 Cedric Flamant , Pavlos Protopapas , David Sondak

Distillation process is a complex process of conduction, mass transfer and heat conduction, which is mainly manifested as follows: The mechanism is complex and changeable with uncertainty; the process is multivariate and strong coupling;…

Chemical Physics · Physics 2021-01-05 Ningrui Zhao , Jinwei Lu

Food web topology and energy flow rates across food web linkages can influence ecosystem properties such as stability. Stability predictions from current models of energy flow are often sensitive to details in their formulation, and their…

Populations and Evolution · Quantitative Biology 2024-01-11 Zhening Li , John Harte

Understanding the hydration and diffusion of ions in water at the molecular level is a topic of widespread importance. The ammonium ion (NH$_4^+$) is an exemplar system that has received attention for decades because of its complex…

Computational Physics · Physics 2025-01-14 Jianqing Guo , Liying Zhou , Andrea Zen , Angelos Michaelides , Xifan Wu , Enge Wang , Limei Xu , Ji Chen

Fluid models are a popular formalism in the quantitative modeling of biochemical systems and analytical performance models. The main idea is to approximate a large-scale Markov chain by a compact set of ordinary differential equations…

Systems and Control · Computer Science 2019-05-02 Max Tschaikowski

A neural ordinary differential equations network (ODE-Net)-enabled reachability method (Neuro-Reachability) is devised for the dynamic verification of networked microgrids (NMs) with unidentified subsystems and heterogeneous uncertainties.…

Systems and Control · Electrical Eng. & Systems 2021-01-14 Yifan Zhou , Peng Zhang

Inferring unbiased treatment effects has received widespread attention in the machine learning community. In recent years, our community has proposed numerous solutions in standard settings, high-dimensional treatment settings, and even…

Machine Learning · Computer Science 2024-03-19 Krzysztof Kacprzyk , Samuel Holt , Jeroen Berrevoets , Zhaozhi Qian , Mihaela van der Schaar

Nonlinear model predictive control (NMPC) requires accurate and computationally efficient plant models. Our previous work has shown that the classical compartmentalization model reduction approach for distillation columns can be enhanced by…

Optimization and Control · Mathematics 2020-11-26 Jannik T. Lüthje , Jan C. Schulze , Adrian Caspari , Adel Mhamdi , Alexander Mitsos , Pascal Schäfer

Ordinary differential equations (ODEs) provide a powerful framework for modeling dynamic systems arising in a wide range of scientific domains. However, most existing ODE methods focus on a single system, and do not adequately address the…

Methodology · Statistics 2026-04-08 Shuoxun Xu , Zijian Guo , Brooke R. Staveland , Robert T. Knight , Lexin Li