Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userPropagation of Fluctuations in Biochemical Systems, I: Linear SSC Networks
93
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
We investigate the propagation of random fluctuations through biochemical networks in which the concentrations of species are large enough so that the unperturbed problem is well-described by ordinary differential equation. We characterize the behavior of variance as fluctuations propagate down chains, study the effect of side chains and feedback loops, and investigate the asymptotic behavior as one rate constant gets large. We also describe how the ideas can be applied to the study of methionine metabolism.
rate research
Read More
The linear noise approximation is commonly used to obtain intrinsic noise statistics for biochemical networks. These estimates are accurate for networks with large numbers of molecules. However it is well known that many biochemical networks are characterized by at least one species with a small number of molecules. We here describe version 0.3 of the software intrinsic Noise Analyzer (iNA) which allows for accurate computation of noise statistics over wide ranges of molecule numbers. This is achieved by calculating the next order corrections to the linear noise approximations estimates of variance and covariance of concentration fluctuations. The efficiency of the methods is significantly improved by automated just-in-time compilation using the LLVM framework leading to a fluctuation analysis which typically outperforms that obtained by means of exact stochastic simulations. iNA is hence particularly well suited for the needs of the computational biology community.
This paper addresses the problem of model reduction for dynamical system models that describe biochemical reaction networks. Inherent in such models are properties such as stability, positivity and network structure. Ideally these properties should be preserved by model reduction procedures, although traditional projection based approaches struggle to do this. We propose a projection based model reduction algorithm which uses generalised block diagonal Gramians to preserve structure and positivity. Two algorithms are presented, one provides more accurate reduced order models, the second provides easier to simulate reduced order models. The results are illustrated through numerical examples.
We consider a class of continuous-time stochastic growth models on $d$-dimensional lattice with non-negative real numbers as possible values per site. The class contains examples such as binary contact path process and potlatch process. We show the equivalence between the slow population growth and localization property that the time integral of the replica overlap diverges. We also prove, under reasonable assumptions, a localization property in a stronger form that the spatial distribution of the population does not decay uniformly in space.
We consider a dynamical model of distress propagation on complex networks, which we apply to the study of financial contagion in networks of banks connected to each other by direct exposures. The model that we consider is an extension of the DebtRank algorithm, recently introduced in the literature. The mechanics of distress propagation is very simple: When a bank suffers a loss, distress propagates to its creditors, who in turn suffer losses, and so on. The original DebtRank assumes that losses are propagated linearly between connected banks. Here we relax this assumption and introduce a one-parameter family of non-linear propagation functions. As a case study, we apply this algorithm to a data-set of 183 European banks, and we study how the stability of the system depends on the non-linearity parameter under different stress-test scenarios. We find that the system is characterized by a transition between a regime where small shocks can be amplified and a regime where shocks do not propagate, and that the overall stability of the system increases between 2008 and 2013.
We consider a class of interacting particle systems with values in $[0,8)^{zd}$, of which the binary contact path process is an example. For $d ge 3$ and under a certain square integrability condition on the total number of the particles, we prove a central limit theorem for the density of the particles, together with upper bounds for the density of the most populated site and the replica overlap.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
