Introducing a Calculus of Effects and Handlers for Natural Language Semantics

In compositional model-theoretic semantics, researchers assemble truth-conditions or other kinds of denotations using the lambda calculus. It was previously observed that the lambda terms and/or the denotations studied tend to follow the same pattern: they are instances of a monad. In this paper, we present an extension of the simply-typed lambda calculus that exploits this uniformity using the recently discovered technique of effect handlers. We prove that our calculus exhibits some of the key formal properties of the lambda calculus and we use it to construct a modular semantics for a small fragment that involves multiple distinct semantic phenomena

A systematically coarse-grained model for DNA, and its predictions for persistence length, stacking, twist, and chirality

We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with minimal phenomenology. Persistence length, degree of stacking, and twist are studied by molecular dynamics simulation as functions of temperature, salt concentration, sequence, interaction potential strength, and local position along the chain, for both single- and double-stranded DNA where appropriate. The model of DNA shows several phase transitions and crossover regimes in addition to dehybridization, including unstacking, untwisting, and collapse which affect mechanical properties such as rigidity and persistence length. The model also exhibits chirality with a stable right-handed and metastable left-handed helix.Comment: 30 pages, 20 figures, Supplementary Material available at http://www.physics.ubc.ca/~steve/publications.htm

Cataclysmic Variables and Other Compact Binaries in the Globular Cluster NGC 362: Candidates from Chandra and HST

Highly sensitive and precise X-ray imaging from Chandra, combined with the superb spatial resolution of HST optical images, dramatically enhances our empirical understanding of compact binaries such as cataclysmic variables and low mass X-ray binaries, their progeny, and other stellar X-ray source populations deep into the cores of globular clusters. Our Chandra X-ray images of the globular cluster NGC 362 reveal 100 X-ray sources, the bulk of which are likely cluster members. Using HST color-magnitude and color-color diagrams, we quantitatively consider the optical content of the NGC 362 Chandra X-ray error circles, especially to assess and identify the compact binary population in this condensed-core globular cluster. Despite residual significant crowding in both X-rays and optical, we identify an excess population of H{\alpha}-emitting objects that is statistically associated with the Chandra X-ray sources. The X-ray and optical characteristics suggest that these are mainly cataclysmic variables, but we also identify a candidate quiescent low mass X-ray binary. A potentially interesting and largely unanticipated use of observations such as these may be to help constrain the macroscopic dynamic state of globular clusters.Comment: 6 pages, 6 figures, to appear in the proceedings of the conference "Binary Star Evolution: Mass Loss, Accretion, and Mergers," Mykonos, Greece, June 22-25, 201

Extended Initiality for Typed Abstract Syntax

Initial Semantics aims at interpreting the syntax associated to a signature as the initial object of some category of 'models', yielding induction and recursion principles for abstract syntax. Zsid\'o proves an initiality result for simply-typed syntax: given a signature S, the abstract syntax associated to S constitutes the initial object in a category of models of S in monads. However, the iteration principle her theorem provides only accounts for translations between two languages over a fixed set of object types. We generalize Zsid\'o's notion of model such that object types may vary, yielding a larger category, while preserving initiality of the syntax therein. Thus we obtain an extended initiality theorem for typed abstract syntax, in which translations between terms over different types can be specified via the associated category-theoretic iteration operator as an initial morphism. Our definitions ensure that translations specified via initiality are type-safe, i.e. compatible with the typing in the source and target language in the obvious sense. Our main example is given via the propositions-as-types paradigm: we specify propositions and inference rules of classical and intuitionistic propositional logics through their respective typed signatures. Afterwards we use the category--theoretic iteration operator to specify a double negation translation from the former to the latter. A second example is given by the signature of PCF. For this particular case, we formalize the theorem in the proof assistant Coq. Afterwards we specify, via the category-theoretic iteration operator, translations from PCF to the untyped lambda calculus

Vector Bin Packing with Multiple-Choice

We consider a variant of bin packing called multiple-choice vector bin packing. In this problem we are given a set of items, where each item can be selected in one of several $D$-dimensional incarnations. We are also given $T$ bin types, each with its own cost and $D$-dimensional size. Our goal is to pack the items in a set of bins of minimum overall cost. The problem is motivated by scheduling in networks with guaranteed quality of service (QoS), but due to its general formulation it has many other applications as well. We present an approximation algorithm that is guaranteed to produce a solution whose cost is about $\ln D$ times the optimum. For the running time to be polynomial we require $D=O(1)$ and $T=O(\log n)$. This extends previous results for vector bin packing, in which each item has a single incarnation and there is only one bin type. To obtain our result we also present a PTAS for the multiple-choice version of multidimensional knapsack, where we are given only one bin and the goal is to pack a maximum weight set of (incarnations of) items in that bin

Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.Comment: 4 pages, 2 figure

Introduction to protein folding for physicists

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of flexible molecules is nothing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them powerful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the first steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day status of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we physically define the problem stating the assumptions behind this (commonly implicit) definition. Finally, we review the 'special flavor' of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.Comment: 53 pages, 18 figures, the figures are at a low resolution due to arXiv restrictions, for high-res figures, go to http://www.pabloechenique.co

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