1,627 research outputs found
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
Enzyme Replacement Therapy In Different Clinical Phenotypes Of Hypophosphatasia – A Presentation Of Two Cases
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 -dimensional incarnations. We are also given
bin types, each with its own cost and -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 times the optimum. For the running time to be polynomial we
require and . 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
Hypophosphatasia: Enzyme Replacement Therapy (Asfotase Alfa) Decreases TNSALP Substrate Accumulation And Improves Functional Outcomes In Affected Adolescents And Adults
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
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