Related papers: Computing the Frequency Response of Biochemical Ne…
Recently, molecular communication (MC) has been studied as a micro-scale communication between cells or molecular robots. In previous works, the MC channels in unbounded environment was analyzed. However, many of the experimentally…
Sensitivity studies the network response to perturbations. We consider local perturbations of the concentrations of metabolites at an equilibrium. We investigate the responses in the network, both of the metabolite concentrations and of the…
The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction…
Bayesian Networks (BNs) are used in various fields for modeling, prediction, and decision making. pgmpy is a python package that provides a collection of algorithms and tools to work with BNs and related models. It implements algorithms for…
Stochastic modeling and simulation provide powerful predictive methods for the intrinsic understanding of fundamental mechanisms in complex biochemical networks. Typically, such mathematical models involve networks of coupled jump…
This paper introduces a closed-loop frequency analysis tool for reset control systems. To begin with sufficient conditions for the existence of the steady-state response for a closed-loop system with a reset element and driven by periodic…
Characterization of the frequency response of coherent radiometric receivers is a key element in estimating the flux of astrophysical emissions, since the measured signal depends on the convolution of the source spectral emission with the…
A recombination reaction model for high-temperature chemical kinetics is derived from ab initio simulations data. A kinetic recombination rate model is derived using a recently developed ab initio state-specific dissociation model and the…
Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
Analyzing qualitative behaviors of biochemical reactions using its associated network structure has proven useful in diverse branches of biology. As an extension of our previous work, we introduce a graph-based framework to calculate steady…
The automated inference of physically interpretable (bio)chemical reaction network models from measured experimental data is a challenging problem whose solution has significant commercial and academic ramifications. It is demonstrated,…
bayesian_pyhf is a Python package that allows for the parallel Bayesian and frequentist evaluation of multi-channel binned statistical models. The Python library pyhf is used to build such models according to the HistFactory framework and…
I present a fast Python tool, SpectRes, for carrying out the resampling of spectral flux densities and their associated uncertainties onto different wavelength grids. The function works with any grid of wavelength values, including…
Heterogeneity in gene expression across isogenic cell populations can give rise to phenotypic diversity, even when cells are in homogenous environments. This diversity arises from the discrete, stochastic nature of biochemical reactions,…
Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about…
The relationship between components of biochemical network and the resulting dynamics of the overall system is a key focus of computational biology. However, as these networks and resulting mathematical models are inherently complex and…
We consider the general problem of describing the dynamics of subnetworks of larger biochemical reaction networks, e.g. protein interaction networks involving complex formation and dissociation reactions. We propose the use of model…
The binomial acceptance correction procedure is studied for particle number distributions detected in high energy reactions in finite regions of the momentum space. We present acceptance correction formulas for scaled variance, skewness,…
Boolean networks have long been used as models of molecular networks and play an increasingly important role in systems biology. This paper describes a software package, Polynome, offered as a web service, that helps users construct Boolean…