Thermodynamic graph-rewriting

We develop a new thermodynamic approach to stochastic graph-rewriting. The ingredients are a finite set of reversible graph-rewriting rules called generating rules, a finite set of connected graphs P called energy patterns and an energy cost function. The idea is that the generators define the qualitative dynamics, by showing which transformations are possible, while the energy patterns and cost function specify the long-term probability $\pi$ of any reachable graph. Given the generators and energy patterns, we construct a finite set of rules which (i) has the same qualitative transition system as the generators; and (ii) when equipped with suitable rates, defines a continuous-time Markov chain of which $\pi$ is the unique fixed point. The construction relies on the use of site graphs and a technique of `growth policy' for quantitative rule refinement which is of independent interest. This division of labour between the qualitative and long-term quantitative aspects of the dynamics leads to intuitive and concise descriptions for realistic models (see the examples in S4 and S5). It also guarantees thermodynamical consistency (AKA detailed balance), otherwise known to be undecidable, which is important for some applications. Finally, it leads to parsimonious parameterizations of models, again an important point in some applications

Reversing Single Sessions

Session-based communication has gained a widespread acceptance in practice as a means for developing safe communicating systems via structured interactions. In this paper, we investigate how these structured interactions are affected by reversibility, which provides a computational model allowing executed interactions to be undone. In particular, we provide a systematic study of the integration of different notions of reversibility in both binary and multiparty single sessions. The considered forms of reversibility are: one for completely reversing a given session with one backward step, and another for also restoring any intermediate state of the session with either one backward step or multiple ones. We analyse the costs of reversing a session in all these different settings. Our results show that extending binary single sessions to multiparty ones does not affect the reversibility machinery and its costs

On paths-based criteria for polynomial time complexity in proof-nets

Girard's Light linear logic (LLL) characterized polynomial time in the proof-as-program paradigm with a bound on cut elimination. This logic relied on a stratification principle and a "one-door" principle which were generalized later respectively in the systems L^4 and L^3a. Each system was brought with its own complex proof of Ptime soundness. In this paper we propose a broad sufficient criterion for Ptime soundness for linear logic subsystems, based on the study of paths inside the proof-nets, which factorizes proofs of soundness of existing systems and may be used for future systems. As an additional gain, our bound stands for any reduction strategy whereas most bounds in the literature only stand for a particular strategy.Comment: Long version of a conference pape

Which graph states are useful for quantum information processing?

Graph states are an elegant and powerful quantum resource for measurement based quantum computation (MBQC). They are also used for many quantum protocols (error correction, secret sharing, etc.). The main focus of this paper is to provide a structural characterisation of the graph states that can be used for quantum information processing. The existence of a gflow (generalized flow) is known to be a requirement for open graphs (graph, input set and output set) to perform uniformly and strongly deterministic computations. We weaken the gflow conditions to define two new more general kinds of MBQC: uniform equiprobability and constant probability. These classes can be useful from a cryptographic and information point of view because even though we cannot do a deterministic computation in general we can preserve the information and transfer it perfectly from the inputs to the outputs. We derive simple graph characterisations for these classes and prove that the deterministic and uniform equiprobability classes collapse when the cardinalities of inputs and outputs are the same. We also prove the reversibility of gflow in that case. The new graphical characterisations allow us to go from open graphs to graphs in general and to consider this question: given a graph with no inputs or outputs fixed, which vertices can be chosen as input and output for quantum information processing? We present a characterisation of the sets of possible inputs and ouputs for the equiprobability class, which is also valid for deterministic computations with inputs and ouputs of the same cardinality.Comment: 13 pages, 2 figure

A feasible algorithm for typing in Elementary Affine Logic

We give a new type inference algorithm for typing lambda-terms in Elementary Affine Logic (EAL), which is motivated by applications to complexity and optimal reduction. Following previous references on this topic, the variant of EAL type system we consider (denoted EAL*) is a variant without sharing and without polymorphism. Our algorithm improves over the ones already known in that it offers a better complexity bound: if a simple type derivation for the term t is given our algorithm performs EAL* type inference in polynomial time.Comment: 20 page

Controlling Reversibility in Reversing Petri Nets with Application to Wireless Communications

Petri nets are a formalism for modelling and reasoning about the behaviour of distributed systems. Recently, a reversible approach to Petri nets, Reversing Petri Nets (RPN), has been proposed, allowing transitions to be reversed spontaneously in or out of causal order. In this work we propose an approach for controlling the reversal of actions of an RPN, by associating transitions with conditions whose satisfaction/violation allows the execution of transitions in the forward/reversed direction, respectively. We illustrate the framework with a model of a novel, distributed algorithm for antenna selection in distributed antenna arrays.Comment: RC 201

A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation

The complexity ofmany RNA processing pathways is such that a conventional systemsmodelling approach is inadequate to represent all themolecular species involved. We demonstrate that rule-based modelling permits a detailed model of a complex RNA signalling pathway to be defined. Phosphorylation of the RNApolymerase II (RNAPII)C-terminal domain (CTD; a flexible tail-like extension of the largest subunit) couples pre-messenger RNA capping, splicing and 30 end maturation to transcriptional elongation and termination, and plays a central role in integrating these processes. The phosphorylation states of the serine residues of many heptapeptide repeats of the CTD alter along the coding region of genes as a function of distance from the promoter. From a mechanistic perspective, both the changes in phosphorylation and the location atwhich they take place on the genes are a function of the time spent byRNAPII in elongation as this interval provides the opportunity for the kinases and phosphatases to interactwith theCTD.On this basis,we synthesize the available data to create a kinetic model of the action of the known kinases and phosphatases to resolve the phosphorylation pathways and their kinetics.</p

Distribution-based bisimulation for labelled Markov processes

In this paper we propose a (sub)distribution-based bisimulation for labelled Markov processes and compare it with earlier definitions of state and event bisimulation, which both only compare states. In contrast to those state-based bisimulations, our distribution bisimulation is weaker, but corresponds more closely to linear properties. We construct a logic and a metric to describe our distribution bisimulation and discuss linearity, continuity and compositional properties.Comment: Accepted by FORMATS 201

Batalin-Vilkovisky Integrals in Finite Dimensions

The Batalin-Vilkovisky method (BV) is the most powerful method to analyze functional integrals with (infinite-dimensional) gauge symmetries presently known. It has been invented to fix gauges associated with symmetries that do not close off-shell. Homological Perturbation Theory is introduced and used to develop the integration theory behind BV and to describe the BV quantization of a Lagrangian system with symmetries. Localization (illustrated in terms of Duistermaat-Heckman localization) as well as anomalous symmetries are discussed in the framework of BV.Comment: 35 page