Reactive Turing Machines

We propose reactive Turing machines (RTMs), extending classical Turing machines with a process-theoretical notion of interaction, and use it to define a notion of executable transition system. We show that every computable transition system with a bounded branching degree is simulated modulo divergence-preserving branching bisimilarity by an RTM, and that every effective transition system is simulated modulo the variant of branching bisimilarity that does not require divergence preservation. We conclude from these results that the parallel composition of (communicating) RTMs can be simulated by a single RTM. We prove that there exist universal RTMs modulo branching bisimilarity, but these essentially employ divergence to be able to simulate an RTM of arbitrary branching degree. We also prove that modulo divergence-preserving branching bisimilarity there are RTMs that are universal up to their own branching degree. Finally, we establish a correspondence between executability and finite definability in a simple process calculus

Parallel Pushdown Automata and Commutative Context-Free Grammars in Bisimulation Semantics (Extended Abstract)

A classical theorem states that the set of languages given by a pushdown automaton coincides with the set of languages given by a context-free grammar. In previous work, we proved the pendant of this theorem in a setting with interaction: the set of processes given by a pushdown automaton coincides with the set of processes given by a finite guarded recursive specification over a process algebra with actions, choice, sequencing and guarded recursion, if and only if we add sequential value passing. In this paper, we look what happens if we consider parallel pushdown automata instead of pushdown automata, and a process algebra with parallelism instead of sequencing.Comment: In Proceedings EXPRESS/SOS2023, arXiv:2309.05788. arXiv admin note: text overlap with arXiv:2203.0171

Pushdown Automata and Context-Free Grammars in Bisimulation Semantics

The Turing machine models an old-fashioned computer, that does not interact with the user or with other computers, and only does batch processing. Therefore, we came up with a Reactive Turing Machine that does not have these shortcomings. In the Reactive Turing Machine, transitions have labels to give a notion of interactivity. In the resulting process graph, we use bisimilarity instead of language equivalence. Subsequently, we considered other classical theorems and notions from automata theory and formal languages theory. In this paper, we consider the classical theorem of the correspondence between pushdown automata and context-free grammars. By changing the process operator of sequential composition to a sequencing operator with intermediate acceptance, we get a better correspondence in our setting. We find that the missing ingredient to recover the full correspondence is the addition of a notion of state awareness

Linearization of CIF Through SOS

Linearization is the procedure of rewriting a process term into a linear form, which consist only of basic operators of the process language. This procedure is interesting both from a theoretical and a practical point of view. In particular, a linearization algorithm is needed for the Compositional Interchange Format (CIF), an automaton based modeling language. The problem of devising efficient linearization algorithms is not trivial, and has been already addressed in literature. However, the linearization algorithms obtained are the result of an inventive process, and the proof of correctness comes as an afterthought. Furthermore, the semantic specification of the language does not play an important role on the design of the algorithm. In this work we present a method for obtaining an efficient linearization algorithm, through a step-wise refinement of the SOS rules of CIF. As a result, we show how the semantic specification of the language can guide the implementation of such a procedure, yielding a simple proof of correctness.Comment: In Proceedings EXPRESS 2011, arXiv:1108.407

Pushdown Automata and Context-Free Grammars in Bisimulation Semantics

The Turing machine models an old-fashioned computer, that does not interact with the user or with other computers, and only does batch processing. Therefore, we came up with a Reactive Turing Machine that does not have these shortcomings. In the Reactive Turing Machine, transitions have labels to give a notion of interactivity. In the resulting process graph, we use bisimilarity instead of language equivalence. Subsequently, we considered other classical theorems and notions from automata theory and formal languages theory. In this paper, we consider the classical theorem of the correspondence between pushdown automata and context-free grammars. By changing the process operator of sequential composition to a sequencing operator with intermediate acceptance, we get a better correspondence in our setting. We find that the missing ingredient to recover the full correspondence is the addition of a notion of state awareness

Operational semantics for signal handling

Signals are a lightweight form of interprocess communication in Unix. When a process receives a signal, the control flow is interrupted and a previously installed signal handler is run. Signal handling is reminiscent both of exception handling and concurrent interleaving of processes. In this paper, we investigate different approaches to formalizing signal handling in operational semantics, and compare them in a series of examples. We find the big-step style of operational semantics to be well suited to modelling signal handling. We integrate exception handling with our big-step semantics of signal handling, by adopting the exception convention as defined in the Definition of Standard ML. The semantics needs to capture the complex interactions between signal handling and exception handling.Comment: In Proceedings EXPRESS/SOS 2012, arXiv:1208.244

Expressiveness modulo Bisimilarity of Regular Expressions with Parallel Composition (Extended Abstract)

The languages accepted by finite automata are precisely the languages denoted by regular expressions. In contrast, finite automata may exhibit behaviours that cannot be described by regular expressions up to bisimilarity. In this paper, we consider extensions of the theory of regular expressions with various forms of parallel composition and study the effect on expressiveness. First we prove that adding pure interleaving to the theory of regular expressions strictly increases its expressiveness up to bisimilarity. Then, we prove that replacing the operation for pure interleaving by ACP-style parallel composition gives a further increase in expressiveness. Finally, we prove that the theory of regular expressions with ACP-style parallel composition and encapsulation is expressive enough to express all finite automata up to bisimilarity. Our results extend the expressiveness results obtained by Bergstra, Bethke and Ponse for process algebras with (the binary variant of) Kleene's star operation.Comment: In Proceedings EXPRESS'10, arXiv:1011.601

A Logic with Reverse Modalities for History-preserving Bisimulations

We introduce event identifier logic (EIL) which extends Hennessy-Milner logic by the addition of (1) reverse as well as forward modalities, and (2) identifiers to keep track of events. We show that this logic corresponds to hereditary history-preserving (HH) bisimulation equivalence within a particular true-concurrency model, namely stable configuration structures. We furthermore show how natural sublogics of EIL correspond to coarser equivalences. In particular we provide logical characterisations of weak history-preserving (WH) and history-preserving (H) bisimulation. Logics corresponding to HH and H bisimulation have been given previously, but not to WH bisimulation (when autoconcurrency is allowed), as far as we are aware. We also present characteristic formulas which characterise individual structures with respect to history-preserving equivalences.Comment: In Proceedings EXPRESS 2011, arXiv:1108.407

Full humanization of the glycolytic pathway in Saccharomyces cerevisiae

Although transplantation of single genes in yeast plays a key role in elucidating gene functionality in metazoans, technical challenges hamper humanization of full pathways and processes. Empowered by advances in synthetic biology, this study demonstrates the feasibility and implementation of full humanization of glycolysis in yeast. Single gene and full pathway transplantation revealed the remarkable conservation of glycolytic and moonlighting functions and, combined with evolutionary strategies, brought to light context-dependent responses. Human hexokinase 1 and 2, but not 4, required mutations in their catalytic or allosteric sites for functionality in yeast, whereas hexokinase 3 was unable to complement its yeast ortholog. Comparison with human tissues cultures showed preservation of turnover numbers of human glycolytic enzymes in yeast and human cell cultures. This demonstration of transplantation of an entire essential pathway paves the way for establishment of species-, tissue-, and disease-specific metazoan models