Related papers: Computing the Frequency Response of Biochemical Ne…
Populations of heterogeneous cells play an important role in many biological systems. In this paper we consider systems where each cell can be modelled by an ordinary differential equation. To account for heterogeneity, parameter values are…
We present PyOECP, a Python-based flexible open-source software for estimating and modeling the complex permittivity obtained from the open-ended coaxial probe (OECP) technique. The transformation of the measured reflection coefficient to…
Frequency tagging is a powerful approach to investigate the neural processing of sensory features, and is recently adapted to study the neural correlates of superordinate structures, i.e., chunks, in complex sequences such as speech and…
We describe a novel, interdisciplinary, computational methods course that uses Python and associated numerical and visualization libraries to enable students to implement simulations for a number of different course modules. Problems in…
The validity of a complex reaction pathway proposed to treat Inflammatory Bowel Disease (IBD) was verified by a comprehensive time and frequency domain analysis. The model was taken to the frequency domain to study the effect and the…
This paper develops the concept of decomposition for chemical reaction networks, based on which a network decomposition technique is proposed to capture the stability of large-scale networks characterized by a high number of species, high…
We present a method for estimating parameters in stochastic models of biochemical reaction networks by fitting steady-state distributions using Wasserstein distances. We simulate a reaction network at different parameter settings and train…
Signal transduction in biological cells is effected by signaling pathways that typically include multiple feedback loops. Here we analyze information transfer through a prototypical signaling module with biochemical feedback. The module…
Biochemical oscillations are ubiquitous in nature and allow organisms to properly time their biological functions. In this paper, we consider minimal Markov state models of nonequilibrium biochemical networks that support oscillations. We…
We present a detailed kinetic model for the Polymerase Chain Reaction, and model the probability of replication in terms of the physical parameters of the problem. Applying the theory of branching processes, we show the existance of a new…
Information processing relying on biochemical interactions in the cellular environment is essential for biological organisms. The implementation of molecular computational systems holds significant interest and potential in the fields of…
The problem of calculating the frequencies of network motifs on three and four nodes in large networks is considered. Telecommunications networks, cell molecular networks are investigated. The sizes of the investigated networks are hundreds…
In this paper we survey recent work on the use of statistical model checking techniques for biological applications. We begin with an overview of the basic modelling techniques for biochemical reactions and their corresponding stochastic…
An exact linear response expression is obtained for the heat current in a classical Hamiltonian system coupled to heat baths with time-dependent temperatures. The expression is equally valid at zero and finite frequencies. We present…
In chemical processing and bioprocessing, conventional online sensors are limited to measure only basic process variables like pressure and temperature, pH, dissolved O and CO$_2$ and viable cell density (VCD). The concentration of other…
The means to obtain the rate constants of a chemical reaction is a fundamental open problem in both science and the industry. Traditional techniques for finding rate constants require either chemical modifications of the reactants or…
A coarse-grained computational procedure based on the Finite Element Method is proposed to calculate the normal modes and mechanical response of proteins and their supramolecular assemblies. Motivated by the elastic network model, proteins…
The nonlinearities found in molecular networks usually prevent mathematical analysis of network behaviour, which has largely been studied by numerical simulation. This can lead to difficult problems of parameter determination. However,…
We describe PyRaTE, a new, non-local thermodynamic equilibrium (non-LTE) line radiative transfer code developed specifically for post-processing astrochemical simulations. Population densities are estimated using the escape probability…
radioactivedecay is a Python package for radioactive decay modelling. It contains functions to fetch decay data, define inventories of nuclides and perform decay calculations. The default nuclear decay dataset supplied with radioactivedecay…