Related papers: Computing the Frequency Response of Biochemical Ne…
In most natural sciences there is currently the insight that it is necessary to bridge gaps between different processes which can be observed on different scales. This is especially true in the field of chemical reactions where the…
We study the current response to periodic driving of a crucial biochemical reaction network, namely, substrate inhibition. We focus on the conversion rate of substrate into product under time-varying metabolic conditions, modeled by a…
The online estimation of the derivative of an input signal is widespread in control theory and engineering. In the realm of chemical reaction networks (CRN), this raises however a number of specific issues on the different ways to achieve…
Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their…
This paper introduces a frequency response characteristic (FRC) curve and its application in high renewable power systems. In addition, the paper presents a method for fast frequency response assessment and frequency nadir prediction…
The Frequency Response Functions (FRFs) are the most widely used functions to characterise the dynamic behaviour of structures. The natural frequencies and damping behaviour can be easily and quickly detected from a Bode diagram. The modal…
Reliability on complex biological networks reconstructions remains a concern. Although observations are getting more and more precise, the data collection process is yet error prone and the proofs display uneven certitude. In the case of…
Stochastic models for chemical reaction networks have become very popular in recent years. For such models, the estimation of parameter sensitivities is an important and challenging problem. Sensitivity values help in analyzing the network,…
We consider the problem of estimating parameter sensitivity for Markovian models of reaction networks. Sensitivity values measure the responsiveness of an output to the model parameters. They help in analyzing the network, understanding its…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
We present a simple method for determining the exact noise power spectra in linear chemical reaction networks. We apply the method to networks which are representative of biochemical processes such as gene expression and signal detection.…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…
Models of biochemical networks are frequently high-dimensional and complex. Reduction methods that preserve important dynamical properties are therefore essential in their study. Interactions between the nodes in such networks are…
Engineering systems modelling and analysis based on the bond graph approach has been applied to biomolecular systems. In this context, the notion of a Faraday-equivalent chemical potential is introduced which allows chemical potential to be…
Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses. Results: We have developed SimPlot++, an open-source multiplatform application implemented in Python,…
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.…
Understanding cell function requires an accurate description of how noise is transmitted through biochemical networks. We present an analytical result for the power spectrum of the output signal of a biochemical network that takes into…
According to the chemical reaction network theory, the topology of a certain class of chemical reaction networks, regardless of the kinetic details, sets a limit on the dynamical properties that a particular network can potentially admit;…
Biochemical reaction networks frequently consist of species evolving on multiple timescales. Stochastic simulations of such networks are often computationally challenging and therefore various methods have been developed to obtain sensible…