Algebras for parameterised monads

Parameterised monads have the same relationship to adjunctions with parameters as monads do to adjunctions. In this paper, we investigate algebras for parameterised monads. We identify the Eilenberg-Moore category of algebras for parameterised monads and prove a generalisation of Beck’s theorem characterising this category. We demonstrate an application of this theory to the semantics of type and effect systems

Hilbert-Post completeness for the state and the exception effects

In this paper, we present a novel framework for studying the syntactic completeness of computational effects and we apply it to the exception effect. When applied to the states effect, our framework can be seen as a generalization of Pretnar's work on this subject. We first introduce a relative notion of Hilbert-Post completeness, well-suited to the composition of effects. Then we prove that the exception effect is relatively Hilbert-Post complete, as well as the "core" language which may be used for implementing it; these proofs have been formalized and checked with the proof assistant Coq.Comment: Siegfried Rump (Hamburg University of Technology), Chee Yap (Courant Institute, NYU). Sixth International Conference on Mathematical Aspects of Computer and Information Sciences , Nov 2015, Berlin, Germany. 2015, LNC

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

Non-Markovian Configurational Diffusion and Reaction Coordinates for Protein Folding

The non-Markovian nature of polymer motions is accounted for in folding kinetics, using frequency-dependent friction. Folding, like many other problems in the physics of disordered systems, involves barrier crossing on a correlated energy landscape. A variational transition state theory (VTST) that reduces to the usual Bryngelson-Wolynes Kramers approach when the non-Markovian aspects are neglected is used to obtain the rate, without making any assumptions regarding the size of the barrier, or the memory time of the friction. The transformation to collective variables dependent on the dynamics of the system allows the theory to address the controversial issue of what are ``good'' reaction coordinates for folding.Comment: 9 pages RevTeX, 3 eps-figures included, submitted to PR

Examining Hydrogen Transitions.

This report describes the results of an effort to identify key analytic issues associated with modeling a transition to hydrogen as a fuel for light duty vehicles, and using insights gained from this effort to suggest ways to improve ongoing modeling efforts. The study reported on here examined multiple hydrogen scenarios reported in the literature, identified modeling issues associated with those scenario analyses, and examined three DOE-sponsored hydrogen transition models in the context of those modeling issues. The three hydrogen transition models are HyTrans (contractor: Oak Ridge National Laboratory), MARKAL/DOE* (Brookhaven National Laboratory), and NEMS-H2 (OnLocation, Inc). The goals of these models are (1) to help DOE improve its R&D effort by identifying key technology and other roadblocks to a transition and testing its technical program goals to determine whether they are likely to lead to the market success of hydrogen technologies, (2) to evaluate alternative policies to promote a transition, and (3) to estimate the costs and benefits of alternative pathways to hydrogen development

Human cytomegalovirus induces stage-specific embryonic antigen 1 in differentiating human teratocarcinoma cells and fibroblasts.

Cell surface expression of stage specific embryonic antigen 1 (SSEA-1), or Lex (III3 FucnLC4), was induced in differentiated human teratocarcinoma cells and in human diploid fibroblasts 3-6 d after infection with human cytomegalovirus (HCMV). In parallel, fucosylated lactoseries glycolipids bearing the SSEA-1/Lex epitope were readily detected in the infected cells but not in the uninfected cells. HCMV infection also results in altered expression of several glycosyltransferases. SSEA-1/Lex induction is probably a consequence of both increased expression of beta 1----3N-acetylglucosaminyltransferase, which catalyzes the rate-limiting step in lactoseries core chain synthesis, and subtle alterations in the relative competition for common precursor structures at key points in the biosynthetic pathway. Since SSEA-1 has been suggested to play a role in some morphogenetic cell-cell interactions during embryonic development, the induction of this antigen at inappropriate times might provide one mechanism whereby intrauterine infection with HCMV can damage the developing fetal nervous system

Layer by layer - Combining Monads

We develop a method to incrementally construct programming languages. Our approach is categorical: each layer of the language is described as a monad. Our method either (i) concretely builds a distributive law between two monads, i.e. layers of the language, which then provides a monad structure to the composition of layers, or (ii) identifies precisely the algebraic obstacles to the existence of a distributive law and gives a best approximant language. The running example will involve three layers: a basic imperative language enriched first by adding non-determinism and then probabilistic choice. The first extension works seamlessly, but the second encounters an obstacle, which results in a best approximant language structurally very similar to the probabilistic network specification language ProbNetKAT

On the construction of model Hamiltonians for adiabatic quantum computation and its application to finding low energy conformations of lattice protein models

In this report, we explore the use of a quantum optimization algorithm for obtaining low energy conformations of protein models. We discuss mappings between protein models and optimization variables, which are in turn mapped to a system of coupled quantum bits. General strategies are given for constructing Hamiltonians to be used to solve optimization problems of physical/chemical/biological interest via quantum computation by adiabatic evolution. As an example, we implement the Hamiltonian corresponding to the Hydrophobic-Polar (HP) model for protein folding. Furthermore, we present an approach to reduce the resulting Hamiltonian to two-body terms gearing towards an experimental realization.Comment: 35 pages, 8 figure