A Syntactic Model of Mutation and Aliasing

Traditionally, semantic models of imperative languages use an auxiliary structure which mimics memory. In this way, ownership and other encapsulation properties need to be reconstructed from the graph structure of such global memory. We present an alternative "syntactic" model where memory is encoded as part of the program rather than as a separate resource. This means that execution can be modelled by just rewriting source code terms, as in semantic models for functional programs. Formally, this is achieved by the block construct, introducing local variable declarations, which play the role of memory when their initializing expressions have been evaluated. In this way, we obtain a language semantics which directly represents at the syntactic level constraints on aliasing, allowing simpler reasoning about related properties. To illustrate this advantage, we consider the issue, widely studied in the literature, of characterizing an isolated portion of memory, which cannot be reached through external references. In the syntactic model, closed block values, called "capsules", provide a simple representation of isolated portions of memory, and capsules can be safely moved to another location in the memory, without introducing sharing, by means of "affine' variables. We prove that the syntactic model can be encoded in the conventional one, hence efficiently implemented.Comment: In Proceedings DCM 2018 and ITRS 2018 , arXiv:1904.0956

A Calculus of Looping Sequences with Local Rules

In this paper we present a variant of the Calculus of Looping Sequences (CLS for short) with global and local rewrite rules. While global rules, as in CLS, are applied anywhere in a given term, local rules can only be applied in the compartment on which they are defined. Local rules are dynamic: they can be added, moved and erased. We enrich the new calculus with a parallel semantics where a reduction step is lead by any number of global and local rules that could be performed in parallel. A type system is developed to enforce the property that a compartment must contain only local rules with specific features. As a running example we model some interactions happening in a cell starting from its nucleus and moving towards its mitochondria.Comment: In Proceedings DCM 2011, arXiv:1207.682

A Type System for a Stochastic CLS

The Stochastic Calculus of Looping Sequences is suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities. We propose a type system for this calculus that models how the presence of positive and negative catalysers can modify these speeds. We claim that types are the right abstraction in order to represent the interaction between elements without specifying exactly the element positions. Our claim is supported through an example modelling the lactose operon

Alias types for "environment-aware" computations

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Constrained Polymorphic Types for a Calculus with Name Variables

We extend the simply-typed lambda-calculus with a mechanism for dynamic rebinding of code based on parametric nominal interfaces. That is, we introduce values which represent single fragments, or families of named fragments, of open code, where free variables are associated with names which do not obey alpha-equivalence. In this way, code fragments can be passed as function arguments and manipulated, through their nominal interface, by operators such as rebinding, overriding and renaming. Moreover, by using name variables, it is possible to write terms which are parametric in their nominal interface and/or in the way it is adapted, greatly enhancing expressivity. However, in order to prevent conflicts when instantiating name variables, the name-polymorphic types of such terms need to be equipped with simple {inequality} constraints. We show soundness of the type system

Parallel BioScape: A Stochastic and Parallel Language for Mobile and Spatial Interactions

BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials. It has been motivated by the need to model antibacterial surfaces, biofilm formation, and the effect of DNAse in treating and preventing biofilm infections. As its predecessor, SPiM, BioScape has a sequential semantics based on Gillespie's algorithm, and its implementation does not scale beyond 1000 agents. However, in order to model larger and more realistic systems, a semantics that may take advantage of the new multi-core and GPU architectures is needed. This motivates the introduction of parallel semantics, which is the contribution of this paper: Parallel BioScape, an extension with fully parallel semantics.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347

Formal Attributes Traceability in Modular Language Development Frameworks

AbstractModularization and component reuse are concepts that can speed up the design and implementation of domain specific languages. Several modular development frameworks have been developed that rely on attributes to share information among components. Unfortunately, modularization also fosters development in isolation and attributes could be undefined or used inconsistently due to a lack of coordination. This work presents 1) a type system that permits to trace attributes and statically validate the composition against attributes lack or misuse and 2) a correct and complete type inference algorithm for this type system. The type system and inference are based on the Neverlang development framework but it is also discussed how it can be used with different frameworks