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

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

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

A Signature of Cosmic Strings Wakes in the CMB Polarization

We calculate a signature of cosmic strings in the polarization of the cosmic microwave background (CMB). We find that ionization in the wakes behind moving strings gives rise to extra polarization in a set of rectangular patches in the sky whose length distribution is scale-invariant. The length of an individual patch is set by the co-moving Hubble radius at the time the string is perturbing the CMB. The polarization signal is largest for string wakes produced at the earliest post-recombination time, and for an alignment in which the photons cross the wake close to the time the wake is created. The maximal amplitude of the polarization relative to the temperature quadrupole is set by the overdensity of free electrons inside a wake which depends on the ionization fraction $f$ inside the wake. The signal can be as high as $0.06 {\rm \mu K}$ in degree scale polarization for a string at high redshift (near recombination) and a string tension $\mu$ given by $G \mu = 10^{-7}$.Comment: 8 pages, 3 figure

Canny Algorithm: A New Estimator for Primordial Non-Gaussianities

We utilize the Canny edge detection algorithm as an estimator for primordial non-Gaussianities. In preliminary tests on simulated sky patches with a window size of 57 degrees and multipole moments $l$ up to 1024, we find a $3\sigma$ distinction between maps with local non-Gaussianity $f_{NL}=350$ (or $f_{NL}=-700$) and Gaussian maps. We present evidence that high resolution CMB studies will strongly enhance the sensitivity of the Canny algorithm to non-Gaussianity, making it a promising technique to estimate primordial non-Gaussianity.Comment: 4 pages, 4 figures; v2. 5pp, as submitted to PRD; v3. 5pp, minor clarifications and added discussion of negative fNL value

A lambda calculus for quantum computation with classical control

The objective of this paper is to develop a functional programming language for quantum computers. We develop a lambda calculus for the classical control model, following the first author's work on quantum flow-charts. We define a call-by-value operational semantics, and we give a type system using affine intuitionistic linear logic. The main results of this paper are the safety properties of the language and the development of a type inference algorithm.Comment: 15 pages, submitted to TLCA'05. Note: this is basically the work done during the first author master, his thesis can be found on his webpage. Modifications: almost everything reformulated; recursion removed since the way it was stated didn't satisfy lemma 11; type inference algorithm added; example of an implementation of quantum teleportation adde

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