اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدOn Projection-Based Model Reduction of Biochemical Networks-- Part II: The Stochastic Case
203
0
0.0
(
0
)
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
In this paper, we consider the problem of model order reduction of stochastic biochemical networks. In particular, we reduce the order of (the number of equations in) the Linear Noise Approximation of the Chemical Master Equation, which is often used to describe biochemical networks. In contrast to other biochemical network reduction methods, the presented one is projection-based. Projection-based methods are powerful tools, but the cost of their use is the loss of physical interpretation of the nodes in the network. In order alleviate this drawback, we employ structured projectors, which means that some nodes in the network will keep their physical interpretation. For many models in engineering, finding structured projectors is not always feasible; however, in the context of biochemical networks it is much more likely as the networks are often (almost) monotonic. To summarise, the method can serve as a trade-off between approximation quality and physical interpretation, which is illustrated on numerical examples.
قيم البحث
اقرأ أيضاً
The Chemical Master Equation (CME) is well known to provide the highest resolution models of a biochemical reaction network. Unfortunately, even simulating the CME can be a challenging task. For this reason more simple approximations to the CME have
been proposed. In this work we focus on one such model, the Linear Noise Approximation. Specifically, we consider implications of a recently proposed LNA time-scale separation method. We show that the reduced order LNA converges to the full order model in the mean square sense. Using this as motivation we derive a network structure preserving reduction algorithm based on structured projections. We present convex optimisation algorithms that describe how such projections can be computed and we discuss when structured solutions exits. We also show that for a certain class of systems, structured projections can be found using basic linear algebra and no optimisation is necessary. The algorithms are then applied to a linearised stochastic LNA model of the yeast glycolysis pathway.
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 b
e 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.
This paper presents a model reduction method for the class of linear quantum stochastic systems often encountered in quantum optics and their related fields. The approach is proposed on the basis of an interpolatory projection ensuring that specific
input-output responses of the original and the reduced-order systems are matched at multiple selected points (or frequencies). Importantly, the physical realizability property of the original quantum system imposed by the law of quantum mechanics is preserved under our tangential interpolatory projection. An error bound is established for the proposed model reduction method and an avenue to select interpolation points is proposed. A passivity preserving model reduction method is also presented. Examples of both active and passive systems are provided to illustrate the merits of our proposed approach.
Leaping methods show great promise for significantly accelerating stochastic simulations of complex biochemical reaction networks. However, few practical applications of leaping have appeared in the literature to date. Here, we address this issue usi
ng the partitioned leaping algorithm (PLA) [L.A. Harris and P. Clancy, J. Chem. Phys. 125, 144107 (2006)], a recently-introduced multiscale leaping approach. We use the PLA to investigate stochastic effects in two model biochemical reaction networks. The networks that we consider are simple enough so as to be accessible to our intuition but sufficiently complex so as to be generally representative of real biological systems. We demonstrate how the PLA allows us to quantify subtle effects of stochasticity in these systems that would be difficult to ascertain otherwise as well as not-so-subtle behaviors that would strain commonly-used exact stochastic methods. We also illustrate bottlenecks that can hinder the approach and exemplify and discuss possible strategies for overcoming them. Overall, our aim is to aid and motivate future applications of leaping by providing stark illustrations of the benefits of the method while at the same time elucidating obstacles that are often encountered in practice.
This paper investigates a model reduction problem for linear directed network systems, in which the interconnections among the vertices are described by general weakly connected digraphs. First, the definitions of pseudo controllability and observabi
lity Gramians are proposed for semistable systems, and their solutions are characterized by Lyapunov-like equations. Then, we introduce a concept of vertex clusterability to guarantee the boundedness of the approximation error and use the newly proposed Gramians to facilitate the evaluation of the dissimilarity of each pair of vertices. An clustering algorithm is thereto provided to generate an appropriate graph clustering, whose characteristic matrix is employed as the projections in the Petrov-Galerkin reduction framework. The obtained reduced-order system preserves the weakly connected directed network structure, and the approximation error is computed by the pseudo Gramians. Finally, the efficiency of the proposed approach is illustrated by numerical examples.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
