In the area of Natural Computing, Reaction Systems (RSs) are a qualitative abstraction inspired by the functioning of living cells, suitable to model the main mechanisms of biochemical reactions. RSs interact with a context, and pose challenges for modularity, compositionality, extendibility and behavioural equivalence. In this paper we define a modular encoding of RSs as processes in the chained Core Network Algebra (cCNA), which is a new variant of the link-calculus. The encoding represents the behaviour of each entity separately and preserves faithfully their features, and we prove its correctness and completeness. Our encoding provides a Labelled Transition System (LTS) semantics for RSs. Based on the LTS semantics, we adapt the classical notion of bisimulation to define a novel equivalence, called bio-similarity, for studying properties of RSs. In particular, we define a new assertion language based on regular expressions, which allows us to specify the properties of interest, and use it to extend Hennessy-Milner logic to our setting. We prove that our bio-similarity relation and the logical equivalence, that are defined parametrically on some assertion of interest, coincide. Finally, we claim that our encoding contributes to increase the expressiveness of RSs, by exploiting the interaction among different RSs.

在自然计算领域，反应系统（RSs）是受活细胞功能启发的定性抽象，适合于模拟生化反应的主要机制。RS与上下文交互，并在模块化，组合性，可扩展性和行为等效性方面提出挑战。在本文中，我们将RS的模块化编码定义为链式核心网络代数（cCNA）中的过程，它是链接的新变体-结石。编码分别表示每个实体的行为，并忠实地保留其特征，我们证明了其正确性和完整性。我们的编码为RS提供了标记过渡系统（LTS）语义。基于LTS语义，我们采用双仿真的经典概念来定义一种新的等价物，称为生物相似性，用于研究RS的特性。特别是，我们基于正则表达式定义了一种新的断言语言，它使我们能够指定感兴趣的属性，并使用它将Hennessy-Milner逻辑扩展到我们的设置。我们证明我们的生物相似性关系和逻辑等价关系（在某些利益主张中通过参数定义）是​​一致的。最后，我们声称我们的编码有助于提高RS的表达力，