Related papers: Computing the Frequency Response of Biochemical Ne…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
The frequency response analysis describes the steady-state responses of a system to sinusoidal inputs at different frequencies, providing control engineers with an effective tool for designing control systems in the frequency domain.…
Understanding the function of network motifs in an attempt to gain insight into how their combinations create larger reaction networks that drive cellular functions, has been a longstanding pursuit of systems biology. One specific objective…
Feedback circuits in biochemical networks which underly cellular signaling pathways are important elements in creating complex behavior. A specific aspect thereof is how stability of equilibrium points depends on model parameters. For…
A detailed understanding of biochemical networks at the molecular level is essential for studying complex cellular processes. In this paper, we provide a comprehensive description of biochemical networks by considering individual atoms and…
Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps…
Computer algebra methods for analyzing reaction networks often rely on the assumption of mass-action kinetics, which transform the governing ODEs into polynomial systems amenable to techniques such as Gr\"obner basis computation and related…
Antimony is a high-level, human-readable text-based language designed for defining and sharing models in the systems biology community. It enables scientists to describe biochemical networks and systems using a simple and intuitive syntax.…
Simplified stochastic models are widely used in the study of frequency-resolved noise propagation in biochemical reaction networks, a common measure being the coherence between random fluctuations in molecule number trajectories. Such…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
Dynamical system models of complex biochemical reaction networks are usually high-dimensional, nonlinear, and contain many unknown parameters. In some cases the reaction network structure dictates that positive equilibria must be unique for…
A powerful tool in control and systems engineering is represented by Nyquist plots, for which a qualitative representation often gives a clearer visualization of the frequency response function that is typically not given by computer…
In this paper, we propose a new method to identify biochemical reaction networks (i.e. both reactions and kinetic parameters) from heterogeneous datasets. Such datasets can contain (a) data from several replicates of an experiment performed…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…
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…
Motivation: An essential step in developing computational tools for the inference, optimization, and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks.…
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but also allows fluctuation measurements which may reveal the structure and dynamics of the underlying biochemical network.…
Oscillatory chemical reactions often serve as a timing clock of cellular processes in living cells. The temporal dynamics of protein concentration levels is thus of great interest in biology. Here we propose a theoretical framework to…
Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…