Dagstuhl Reports : Volume 1, Issue 2, February 2011

Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn

Fast optimization algorithms and the cosmological constant

Denef and Douglas have observed that in certain landscape models the problem of finding small values of the cosmological constant is a large instance of an NP-hard problem. The number of elementary operations (quantum gates) needed to solve this problem by brute force search exceeds the estimated computational capacity of the observable universe. Here we describe a way out of this puzzling circumstance: despite being NP-hard, the problem of finding a small cosmological constant can be attacked by more sophisticated algorithms whose performance vastly exceeds brute force search. In fact, in some parameter regimes the average-case complexity is polynomial. We demonstrate this by explicitly finding a cosmological constant of order $10^{-120}$ in a randomly generated $10^9$-dimensional ADK landscape.Comment: 19 pages, 5 figure

Epistemic virtues, metavirtues, and computational complexity

I argue that considerations about computational complexity show that all finite agents need characteristics like those that have been called epistemic virtues. The necessity of these virtues follows in part from the nonexistence of shortcuts, or efficient ways of finding shortcuts, to cognitively expensive routines. It follows that agents must possess the capacities – metavirtues –of developing in advance the cognitive virtues they will need when time and memory are at a premium

Single-machine scheduling with stepwise tardiness costs and release times

We study a scheduling problem that belongs to the yard operations component of the railroad planning problems, namely the hump sequencing problem. The scheduling problem is characterized as a single-machine problem with stepwise tardiness cost objectives. This is a new scheduling criterion which is also relevant in the context of traditional machine scheduling problems. We produce complexity results that characterize some cases of the problem as pseudo-polynomially solvable. For the difficult-to-solve cases of the problem, we develop mathematical programming formulations, and propose heuristic algorithms. We test the formulations and heuristic algorithms on randomly generated single-machine scheduling problems and real-life datasets for the hump sequencing problem. Our experiments show promising results for both sets of problems

Between anaphora and deixis...the resolution of the demonstrative noun-phrase ‘that N’

Three experiments examined the hypothesis that the demonstrative noun phrase (NP) that N, as an anadeictic expression, preferentially refers to the less salient referent in a discourse representation when used anaphorically, whereas the anaphoric pronoun he or she preferentially refers to the highly-focused referent. The findings, from a sentence completion task and two reading time experiments that used gender to create ambiguous and unambiguous coreference, reveal that the demonstrative NP specifically orients processing toward a less salient referent when there is no gender cue discriminating between different possible referents. These findings show the importance of taking into account the discourse function of the anaphor itself and its influence on the process of searching for the referent

Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential

Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a long DNA molecule and then strongly binds this site. Here we aim to find a mechanism that can provide both a fast search (1-10 sec) and high stability of the specific protein-DNA complex ($K_d=10^{-15}-10^{-8}$ M). Earlier studies have suggested that rapid search involves the sliding of a protein along the DNA. Here we consider sliding as a one-dimensional (1D) diffusion in a sequence-dependent rough energy landscape. We demonstrate that, in spite of the landscape's roughness, rapid search can be achieved if 1D sliding is accompanied by 3D diffusion. We estimate the range of the specific and non-specific DNA-binding energy required for rapid search and suggest experiments that can test our mechanism. We show that optimal search requires a protein to spend half of time sliding along the DNA and half diffusing in 3D. We also establish that, paradoxically, realistic energy functions cannot provide both rapid search and strong binding of a rigid protein. To reconcile these two fundamental requirements we propose a search-and-fold mechanism that involves the coupling of protein binding and partial protein folding. Proposed mechanism has several important biological implications for search in the presence of other proteins and nucleosomes, simultaneous search by several proteins etc. Proposed mechanism also provides a new framework for interpretation of experimental and structural data on protein-DNA interactions

Competent genetic-evolutionary optimization of water distribution systems

A genetic algorithm has been applied to the optimal design and rehabilitation of a water distribution system. Many of the previous applications have been limited to small water distribution systems, where the computer time used for solving the problem has been relatively small. In order to apply genetic and evolutionary optimization technique to a large-scale water distribution system, this paper employs one of competent genetic-evolutionary algorithms - a messy genetic algorithm to enhance the efficiency of an optimization procedure. A maximum flexibility is ensured by the formulation of a string and solution representation scheme, a fitness definition, and the integration of a well-developed hydraulic network solver that facilitate the application of a genetic algorithm to the optimization of a water distribution system. Two benchmark problems of water pipeline design and a real water distribution system are presented to demonstrate the application of the improved technique. The results obtained show that the number of the design trials required by the messy genetic algorithm is consistently fewer than the other genetic algorithms

Communication between therapists and nurses working in inpatient interprofessional teams: Systematic review and meta-ethnography

Purpose: The aim of the synthesis was to develop new understanding about the influences on communication in interprofessional teams from therapist and nurse perspectives. Methods: Six electronic databases were searched, combined with citation tracking and hand searching, yielding 3994 papers. Three researchers were involved in screening and quality appraisal, resulting in 18 papers for synthesis, using the process of meta-ethnography. Concepts were identified, compared and translated under five category headings. Two researchers mapped interpretative summaries and a line of argument was created. Results: The line of argument is that four inter-related contingences underpin effective communication between therapists and nurses. Effective communication depends on there being a genuine need to give and receive information for patient care, the capacity to attend to, hold, and use information, and opportunities to share space to enable communication to occur. The fourth contingency is good quality relationships and this is the glue that holds the contingencies together. Conclusion: This synthesis has provided an opportunity to illuminate how therapists and nurses accomplish interprofessional work through communication. The contingencies of need, capacity, opportunity and quality of relationships create a new structure for understanding what underpins communication between these two groups .Peer reviewedFinal Accepted Versio