@inbook{3573,
abstract = {Given a finite point set in R, the surface reconstruction problem asks for a surface that passes through many but not necessarily all points. We describe an unambigu- ous definition of such a surface in geometric and topological terms, and sketch a fast algorithm for constructing it. Our solution overcomes past limitations to special point distributions and heuristic design decisions.},
author = {Herbert Edelsbrunner},
booktitle = {Discrete & Computational Geometry},
pages = {379 -- 404},
publisher = {Springer},
title = {{Surface reconstruction by wrapping finite sets in space}},
doi = {10.1007/978-3-642-55566-4_17},
year = {2003},
}
@article{3584,
abstract = {We develop fast algorithms for computing the linking number of a simplicial complex within a filtration.We give experimental results in applying our work toward the detection of non-trivial tangling in biomolecules, modeled as alpha complexes.},
author = {Edelsbrunner, Herbert and Zomorodian, Afra},
journal = {Homology, Homotopy and Applications},
number = {2},
pages = {19 -- 37},
publisher = {International Press},
title = {{Computing linking numbers of a filtration}},
volume = {5},
year = {2003},
}
@article{3593,
abstract = {Temporal logics such as Computation Tree Logic (CTL) and Linear Temporal Logic (LTL) have become popular for specifying temporal properties over a wide variety of planning and verification problems. In this paper we work towards building a generalized framework for automated reasoning based on temporal logics. We present a powerful extension of CTL with first-order quantification over the set of reachable states for reasoning about extremal properties of weighted labeled transition systems in general. The proposed logic, which we call Weighted Quantified Computation Tree Logic (WQCTL), captures the essential elements common to the domain of planning and verification problems and can thereby be used as an effective specification language in both domains. We show that in spite of the rich, expressive power of the logic, we are able to evaluate WQCTL formulas in time polynomial in the size of the state space times the length of the formula. Wepresent experimental results on the WQCTL verifier.},
author = {Krishnendu Chatterjee and Dasgupta, Pallab and Chakrabarti, Partha P},
journal = {Journal of Automated Reasoning},
number = {2},
pages = {205 -- 232},
publisher = {Springer},
title = {{A branching time temporal framework for quantitative reasoning}},
doi = {10.1023/A:1023217515688},
volume = {30},
year = {2003},
}
@article{3618,
abstract = {There are several analyses in evolutionary ecology which assume that a family of offspring has come from only two parents. Here, we present a simple test for detecting when a batch involves two or more subfamilies. It is based on the fact that the mixing of families generates associations amongst unlinked marker loci. We also present simulations illustrating the power of our method for varying numbers of loci, alleles per locus and genotyped individuals.},
author = {Vines, Timothy H and Nicholas Barton},
journal = {Molecular Ecology},
number = {7},
pages = {1999 -- 2002},
publisher = {Wiley-Blackwell},
title = {{A new approach to detecting mixed families}},
doi = {10.1046/j.1365-294X.2003.01867.x},
volume = {12},
year = {2003},
}
@article{3619,
abstract = {What is the chance that some part of a stretch of genome will survive? In a population of constant size, and with no selection, the probability of survival of some part of a stretch of map length y<1 approaches View the MathML source for View the MathML source. Thus, the whole genome is certain to be lost, but the rate of loss is extremely slow. This solution extends to give the whole distribution of surviving block sizes as a function of time. We show that the expected number of blocks at time t is 1+yt and give expressions for the moments of the number of blocks and the total amount of genome that survives for a given time. The solution is based on a branching process and assumes complete interference between crossovers, so that each descendant carries only a single block of ancestral material. We consider cases where most individuals carry multiple blocks, either because there are multiple crossovers in a long genetic map, or because enough time has passed that most individuals in the population are related to each other. For species such as ours, which have a long genetic map, the genome of any individual which leaves descendants (∼80% of the population for a Poisson offspring number with mean two) is likely to persist for an extremely long time, in the form of a few short blocks of genome.},
author = {Baird, Stuart J and Nicholas Barton and Etheridge, Alison M},
journal = {Theoretical Population Biology},
number = {4},
pages = {451 -- 471},
publisher = {Academic Press},
title = {{The distribution of surviving blocks of an ancestral genome}},
doi = {10.1016/S0040-5809(03)00098-4},
volume = {64},
year = {2003},
}
@article{3620,
abstract = {Stable hybrid zones in which ecologically divergent taxa give rise to a range of recombinants are natural laboratories in which the genetic basis of adaptation and reproductive isolation can be unraveled. One such hybrid zone is formed by the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae). Adaptations to permanent and ephemeral breeding habitats, respectively, have shaped numerous phenotypic differences between the taxa. All of these are, in principle, candidates for a genetic dissection via QTL mapping. We present here a linkage map of 28 codominant and 10 dominant markers in the Bombina genome. In an F2 cross, markers that were mainly microsatellites, SSCPs or allozymes were mapped to 20 linkage groups. Among the 40 isolated CA microsatellites, we noted a preponderance of compound and frequently interleaved CA-TA repeats as well as a striking polarity at the 5′ end of the repeats.},
author = {Nürnberger, Beate and Hofman, Sebastian and Förg-Brey, Bqruni and Praetzel, Gabriele and Maclean, Alan W and Szymura, Jacek M and Abbott, Catherine M and Nicholas Barton},
journal = {Heredity},
number = {2},
pages = {136 -- 142},
publisher = {Nature Publishing Group},
title = {{A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae)}},
doi = {10.1038/sj.hdy.6800291},
volume = {91},
year = {2003},
}
@phdthesis{3678,
author = {Christoph Lampert},
booktitle = {Bonner Mathematische Schriften},
pages = {1 -- 165},
publisher = {Universität Bonn, Fachbibliothek Mathematik},
title = {{The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric }},
volume = {356},
year = {2003},
}
@article{3725,
abstract = {The combination of high-resolution atomic force microscopy (AFM) imaging and single-molecule force-spectroscopy was employed to unfold single bacteriorhodopsins (BR) from native purple membrane patches at various physiologically relevant temperatures. The unfolding spectra reveal detailed insight into the stability of individual structural elements of BR against mechanical unfolding. Intermittent states in the unfolding process are associated with the stepwise unfolding of alpha-helices, whereas other states are associated with the unfolding of polypeptide loops connecting the alpha-helices. It was found that the unfolding forces of the secondary structures considerably decreased upon increasing the temperature from 8 to 52°C. Associated with this effect, the probability of individual unfolding pathways of BR was significantly influenced by the temperature. At lower temperatures, transmembrane alpha-helices and extracellular polypeptide loops exhibited sufficient stability to individually establish potential barriers against unfolding, whereas they predominantly unfolded collectively at elevated temperatures. This suggests that increasing the temperature decreases the mechanical stability of secondary structural elements and changes molecular interactions between secondary structures, thereby forcing them to act as grouped structures.},
author = {Harald Janovjak and Kessler, Max and Oesterhelt, Dieter and Gaub, Hermann and Mueller, Daniel J},
journal = {EMBO Journal},
number = {19},
pages = {5220 -- 5229},
publisher = {Wiley-Blackwell},
title = {{Unfolding pathways of native bacteriorhodopsin depend on temperature}},
doi = {10.1093/emboj/cdg509},
volume = {22},
year = {2003},
}
@article{3752,
abstract = {We use the lac operon in Escherichia coli as a prototype system to illustrate the current state, applicability, and limitations of modeling the dynamics of cellular networks. We integrate three different levels of description (molecular, cellular, and that of cell population) into a single model, which seems to capture many experimental aspects of the system.},
author = {Vilar,Jose M and Calin Guet and Leibler, Stanislas},
journal = {Journal of Cell Biology},
number = {3},
pages = {471 -- 476},
publisher = {Rockefeller University Press},
title = {{Modeling network dynamics: the lac operon, a case study}},
doi = {10.1083/jcb.200301125},
volume = {161},
year = {2003},
}
@article{3797,
author = {Bauer, Wolfgang and Kleine-Berkenbusch, Marco and Bollenbach, Tobias},
journal = {Revista Mexicana De Fisica},
number = {4},
pages = {1 -- 6},
publisher = {Sociedad Mexicana de Física},
title = {{Breaking atomic nuclei into little pieces: evidence for a phase transition}},
volume = {49},
year = {2003},
}