Related papers: A semi-quantitative equivalence for abstracting fr…
We study, from a purely quantitative point of view, the quasi-steady-state assumption for the fundamental mathematical model of the general enzymatic reaction: we re-establish, on a rigorous basis, certain already known results and we…
This paper introduces the counterpart of strong bisimilarity for labelled transition systems extended with time-out transitions. It supports this concept through a modal characterisation, congruence results for a standard process algebra…
In biochemical networks, reactions often occur on disparate timescales and can be characterized as either "fast" or "slow." The quasi-steady state approximation (QSSA) utilizes timescale separation to project models of biochemical networks…
The quasi-steady-state approximation (or stochastic averaging principle) is a useful tool in the study of multiscale stochastic systems, giving a practical method by which to reduce the number of degrees of freedom in a model. The method is…
Analysis of large continuous-time stochastic systems is a computationally intensive task. In this work we focus on population models arising from chemical reaction networks (CRNs), which play a fundamental role in analysis and design of…
The computer algebra routines documented here empower you to reproduce and check many of the details described by an article on large deviations for slow-fast stochastic systems [abs:1001.4826]. We consider a 'small' spatial domain with two…
From molecular, cellular, to ecological systems, the modeling of biological processes often stands on the assumption that fast components immediately reach the equilibrium at each moment (quasi-steady state) and only slow components govern…
Answer Set Programming (ASP) is a well-established formalism for nonmonotonic reasoning. An ASP program can have no answer set due to cyclic default negation. In this case, it is not possible to draw any conclusion, even if this is not…
We propose a variant of the CCS process algebra with new features aiming at allowing multiscale modelling of biological systems. In the usual semantics of process algebras for modelling biological systems actions are instantaneous. When…
In this paper we derive several quasi steady-state approximations (QSSAs) to the stochastic reaction network describing the Michaelis-Menten enzyme kinetics. We show how the different assumptions about chemical species abundance and…
Stochastic HYPE is a novel process algebra that models stochastic, instantaneous and continuous behaviour. It develops the flow-based approach of the hybrid process algebra HYPE by replacing non-urgent events with events with…
Apoptosis is one of the most basic biological processes. In apoptosis, tens of species are involved in many biochemical reactions with times scales of widely differing orders of magnitude. By the law of mass action, the process is…
It has recently been shown that structural conditions on the reaction network, rather than a 'fine-tuning' of system parameters, often suffice to impart 'absolute concentration robustness' on a wide class of biologically relevant,…
Recent works have shown that defining a behavioural equivalence that matches the observational properties of a quantum-capable, concurrent, non-deterministic system is a surprisingly difficult task. We explore coalgebras over distributions…
We introduce an algebra qCCS of pure quantum processes in which no classical data is involved, communications by moving quantum states physically are allowed, and computations is modeled by super-operators. An operational semantics of qCCS…
Several application domains require formal but flexible approaches to the comparison problem. Different process models that cannot be related by behavioral equivalences should be compared via a quantitative notion of similarity, which is…
This paper provides an adaptation of branching bisimilarity to reactive systems with time-outs. Multiple equivalent definitions are procured, along with a modal characterisation and a proof of its congruence property for a standard process…
We study transient patterns appearing in a class of SPDE using the framework of quasi-stationary and quasi-ergodic measures. In particular, we prove the existence and uniqueness of quasi-stationary and quasi-ergodic measures for a class of…
We consider nonsynchronous sampling of parameterized stochastic regression models, which contain stochastic differential equations. Constructing a quasi-likelihood function, we prove that the quasi-maximum likelihood estimator and the Bayes…
It is well known that the theory of coalgebras provides an abstract definition of behavioural equivalence that coincides with strong bisimulation across a wide variety of state-based systems. Unfortunately, the theory in the presence of…