相关论文: BlenX-based compositional modeling of complex reac…

Compositionality is a key feature of process algebras which is often cited as one of their advantages as a modelling technique. It is certainly true that in biochemical systems, as in many other systems, model construction is made easier in…

Gillespie's direct method for stochastic simulation of chemical kinetics is a staple of computational systems biology research. However, the algorithm requires explicit enumeration of all reactions and all chemical species that may arise in…

Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…

We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…

Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed,…

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…

Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from…

The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…

Large complexes of classical particles play central roles in biology, in polymer physics, and in other disciplines. However, physics currently lacks mathematical methods for describing such complexes in terms of component particles,…

Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…

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…

Efforts toward a comprehensive description of behavior have indeed facilitated the development of representation-based approaches that utilize deep learning to capture behavioral information. As behavior complexity increases, the expressive…

Complex behaviour in many systems arises from the stochastic interactions of spatially distributed particles or agents. Stochastic reaction-diffusion processes are widely used to model such behaviour in disciplines ranging from biology to…

This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…

Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from…

Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory…

We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…

Due to the increased complexity of software development projects more and more systems are described by models. The sheer size makes it impractical to describe these systems by a single model. Instead many models are developed that provide…

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…

Biochemical reactions involving three or more reactants, called higher-molecular reactions, play an important role in theoretical systems and synthetic biology. In particular, such reactions underpin a variety of important bio-dynamical…