A generalized Markov sampler

A recent development of the Markov chain Monte Carlo (MCMC) technique is the emergence of MCMC samplers that allow transitions between different models. Such samplers make possible a range of computational tasks involving models, including model selection, model evaluation, model averaging and hypothesis testing. An example of this type of sampler is the reversible jump MCMC sampler, which is a generalization of the Metropolis-Hastings algorithm. Here, we present a new MCMC sampler of this type. The new sampler is a generalization of the Gibbs sampler, but somewhat surprisingly, it also turns out to encompass as particular cases all of the well-known MCMC samplers, including those of Metropolis, Barker, and Hastings. Moreover, the new sampler generalizes the reversible jump MCMC. It therefore appears to be a very general framework for MCMC sampling. This paper describes the new sampler and illustrates its use in three applications in Computational Biology, specifically determination of consensus sequences, phylogenetic inference and delineation of isochores via multiple change-point analysis.

Sampling phylogenetic tree space with the generalized Gibbs sampler

The generalized Gibbs sampler (GGS) is a recently developed Markov chain Monte Carlo (MCMC) technique that enables Gibbs-like sampling of state spaces that lack a convenient representation in terms of a fixed coordinate system. This paper describes a new sampler, called the tree sampler, which uses the GGS to sample from a state space consisting of phylogenetic trees. The tree sampler is useful for a wide range of phylogenetic applications, including Bayesian, maximum likelihood, and maximum parsimony methods. A fast new algorithm to search for a maximum parsimony phylogeny is presented, using the tree sampler in the context of simulated annealing. The mathematics underlying the algorithm is explained and its time complexity is analyzed. The method is tested on two large data sets consisting of 123 sequences and 500 sequences, respectively. The new algorithm is shown to compare very favorably in terms of speed and accuracy to the program DNAPARS from the PHYLIP package.

On the temperature dependence of the absorption cross section for black holes in string theory

We study the low frequency absorption cross section of spherically symmetric nonextremal d-dimensional black holes. In the presence of α′ corrections, this quantity must have an explicit dependence on the Hawking temperature of the form 1/TH. This property of the low frequency absorption cross section is shared by the D1-D5 system from type IIB superstring theory already at the classical level, without α′ corrections. We apply our formula to the simplest example, the classical d-dimensional Reissner-Nordstr¨om solution, checking that the obtained formula for the cross section has a smooth extremal limit. We also apply it for a d-dimensional Tangherlini-like solution with α′3 corrections.

Absorption of scalars by nonextremal charged black holes in string theory

We analyze the low frequency absorption cross section of minimally coupled massless scalar fields by different kinds of charged static black holes in string theory, namely the D1–D5 system in d=5 and a four dimensional dyonic four-charged black hole. In each case we show that this cross section always has the form of some parameter of the solution divided by the black hole Hawking temperature. We also verify in each case that, despite its explicit temperature dependence, such quotient is finite in the extremal limit, giving a well defined cross section. We show that this precise explicit temperature dependence also arises in the same cross section for black holes with string \alpha' corrections: it is actually induced by them.

Design and evaluation of a solid sampler for the monitoring of airborne 1,6-hexamethylene diisocyanate (HDI) and its prepolymers in 2-component spray painting

An active, solvent-free solid sampler was developed for the collection of 1,6-hexamethylene diisocyanate (HDI) aerosol and prepolymers. The sampler was made of a filter impregnated with 1-(2-methoxyphenyl)piperazine contained in a filter holder. Interferences with HDI were observed when a set of cellulose acetate filters and a polystyrene filter holder were used; a glass fiber filter and polypropylene filter cassette gave better results. The applicability of the sampling and analytical procedure was validated with a test chamber, constructed for the dynamic generation of HDI aerosol and prepolymers in commercial two-component spray paints (Desmodur(R) N75) used in car refinishing. The particle size distribution, temporal stability, and spatial uniformity of the simulated aerosol were established in order to test the sample. The monitoring of aerosol concentrations was conducted with the solid sampler paired to the reference impinger technique (impinger flasks contained 10 mL of 0.5 mg/mL 1-(2-methoxyphenyl)piperazine in toluene) under a controlled atmosphere in the test chamber. Analyses of derivatized HDI and prepolymers were carried out by using high-performance liquid chromatography and ultraviolet detection. The correlation between the solvent-free and the impinger techniques appeared fairly good (Y = 0.979X - 0.161; R = 0.978), when the tests were conducted in the range of 0.1 to 10 times the threshold limit value (TLV) for HDI monomer and up to 60-mu-g/m3 (3 U.K. TLVs) for total -N = C = O groups.

Algorithmic aspects of bio-inspired string operations

We present building blocks for algorithms for the efficient reduction of square factor, i.e. direct repetitions in strings. So the basic problem is this: given a string, compute all strings that can be obtained by reducing factors of the form zz to z. Two types of algorithms are treated: an offline algorithm is one that can compute a data structure on the given string in advance before the actual search for the square begins; in contrast, online algorithms receive all input only at the time when a request is made. For offline algorithms we treat the following problem: Let u and w be two strings such that w is obtained from u by reducing a square factor zz to only z. If we further are given the suffix table of u, how can we derive the suffix table for w without computing it from scratch? As the suffix table plays a key role in online algorithms for the detection of squares in a string, this derivation can make the iterated reduction of squares more efficient. On the other hand, we also show how a suffix array, used for the offline detection of squares, can be adapted to the new string resulting from the deletion of a square. Because the deletion is a very local change, this adaption is more eficient than the computation of the new suffix array from scratch.

Un nuevo muestreador de huevos de peces pelagicos a bordo del BIC Jose Olaya Balandra: CUFES (Continuous Underway y Fish egg Sampler)

El IMARPE cuenta con un nuevo muestreador de huevos de peces pelágicos, con características diferentes aquéllas de las redes convencionales.

Derivation of the gauge-invariant action for open and closed free bosonic string field theories

The gauge-invariant actions for open and closed free bosonic string field theories are obtained from the string field equations in the conformal gauge using the cohomology operations of Banks and Peskin. For the closed-string theory no restrictions are imposed on the gauge parameters.

Hamiltonian and Lagrangian constraints of the bosonic string

We study the Hamiltonian and Lagrangian constraints of the Polyakov string. The gauge fixing at the Hamiltonian and Lagrangian level is also studied.

Exotic nonrelativistic string

We construct a classical nonrelativistic string model in 3+1 dimensions. The model contains a spurion tensor field that is responsible for the noncommutative structure of the model. Under double-dimensional reduction the model reduces to the exotic nonrelativistic particle in 2+1 dimensions.

D-String on near horizon geometries and infinite conformal symmetry

We show that the symmetries of effective D-string actions in constant dilaton backgrounds are directly related to homothetic motions of the background metric. In the presence of such motions, there are infinitely many nonlinearly realized rigid symmetries forming a loop (or looplike) algebra. Near horizon (antideSitter) D3 and D1+D5 backgrounds are discussed in detail and shown to provide 2D interacting field theories with infinite conformal symmetry.

Noether's theorem and gauge transformations. Application to the bosonic string and CP(2,n-1) model

New results on the theory of constrained systems are applied to characterize the generators of Noethers symmetry transformations. As a byproduct, an algorithm to construct gauge transformations in Hamiltonian formalism is derived. This is illustrated with two relevant examples.

Semiclassical back reaction in the formation of a straight cosmic string

We derive the back reaction on the gravitational field of a straight cosmic string during its formation due to the gravitational coupling of the string to quantum matter fields. A very simple model of string formation is considered. The gravitational field of the string is computed in the linear approximation. The vacuum expectation value of the stress tensor of a massless scalar quantum field coupled to the string gravitational field is computed to one loop order. Finally, the back-reaction effect is obtained by solving perturbatively the semiclassical Einsteins equations.