IEAD: A Novel One-Line Interface to Query Astronomical Science Archives

In this article I present IEAD, a new interface for astronomical science databases. It is based on a powerful, yet simple, syntax designed to completely abstract the user from the structure of the underlying database. The programming language chosen for its implementation, JavaScript, makes it possible to interact directly with the user and to provide real-time information on the parsing process, error messages, and the name resolution of targets; additionally, the same parsing engine is used for context-sensitive autocompletion. Ultimately, this product should significantly simplify the use of astronomical archives, inspire more advanced uses of them, and allow the user to focus on what scientific research to perform, instead of on how to instruct the computer to do it.Comment: 13 pages, PASP in pres

Field-control, phase-transitions, and life's emergence

Instances of critical-like characteristics in living systems at each organizational level as well as the spontaneous emergence of computation (Langton), indicate the relevance of self-organized criticality (SOC). But extrapolating complex bio-systems to life's origins, brings up a paradox: how could simple organics--lacking the 'soft matter' response properties of today's bio-molecules--have dissipated energy from primordial reactions in a controlled manner for their 'ordering'? Nevertheless, a causal link of life's macroscopic irreversible dynamics to the microscopic reversible laws of statistical mechanics is indicated via the 'functional-takeover' of a soft magnetic scaffold by organics (c.f. Cairns-Smith's 'crystal-scaffold'). A field-controlled structure offers a mechanism for bootstrapping--bottom-up assembly with top-down control: its super-paramagnetic components obey reversible dynamics, but its dissipation of H-field energy for aggregation breaks time-reversal symmetry. The responsive adjustments of the controlled (host) mineral system to environmental changes would bring about mutual coupling between random organic sets supported by it; here the generation of long-range correlations within organic (guest) networks could include SOC-like mechanisms. And, such cooperative adjustments enable the selection of the functional configuration by altering the inorganic network's capacity to assist a spontaneous process. A non-equilibrium dynamics could now drive the kinetically-oriented system towards a series of phase-transitions with appropriate organic replacements 'taking-over' its functions.Comment: 54 pages, pdf fil

On the usefulness of finding charts Or the runaway carbon stars of the Blanco & McCarthy field 37

We have been recently faced with the problem of cross--identifying stars recorded in historical catalogues with those extracted from recent fully digitized surveys (such as DENIS and 2MASS). Positions mentioned in the old catalogues are frequently of poor precision, but are generally accompanied by finding charts where the interesting objects are flagged. Those finding charts are sometimes our only link with the accumulated knowledge of past literature. While checking the identification of some of these objects in several catalogues, we had the surprise to discover a number of discrepancies in recent works.The main reason for these discrepancies was generally the blind application of the smallest difference in position as the criterion to identify sources from one historical catalogue to those in more recent surveys. In this paper we give examples of such misidentifications, and show how we were able to find and correct them.We present modern procedures to discover and solve cross--identification problems, such as loading digitized images of the sky through the Aladin service at CDS, and overlaying entries from historical catalogues and modern surveys. We conclude that the use of good finding charts still remains the ultimate (though time--consuming) tool to ascertain cross--identifications in difficult cases.Comment: 4 pages, 1 figure, accepted by A&

Protein multi-scale organization through graph partitioning and robustness analysis: Application to the myosin-myosin light chain interaction

Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the intricate coupling between the different scales. Starting from a physico-chemical atomistic network of interactions that encodes the structure of the protein, we introduce a methodology based on multi-scale graph partitioning that can uncover partitions and levels of organization of proteins that span the whole range of scales, revealing biological features occurring at different levels of organization and tracking their effect across scales. Additionally, we introduce a measure of robustness to quantify the relevance of the partitions through the generation of biochemically-motivated surrogate random graph models. We apply the method to four distinct conformations of myosin tail interacting protein, a protein from the molecular motor of the malaria parasite, and study properties that have been experimentally addressed such as the closing mechanism, the presence of conserved clusters, and the identification through computational mutational analysis of key residues for binding.Comment: 13 pages, 7 Postscript figure

Trapping in the random conductance model

We consider random walks on $\Z^d$ among nearest-neighbor random conductances which are i.i.d., positive, bounded uniformly from above but whose support extends all the way to zero. Our focus is on the detailed properties of the paths of the random walk conditioned to return back to the starting point at time $2n$. We show that in the situations when the heat kernel exhibits subdiffusive decay --- which is known to occur in dimensions $d\ge4$ --- the walk gets trapped for a time of order $n$ in a small spatial region. This shows that the strategy used earlier to infer subdiffusive lower bounds on the heat kernel in specific examples is in fact dominant. In addition, we settle a conjecture concerning the worst possible subdiffusive decay in four dimensions.Comment: 21 pages, version to appear in J. Statist. Phy

Improved Procedures for Purification of the Bandeiraea simplicifolia I Isolectins and Bandeiraea simplicifolia II Lectin by Affinity Chromatography

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66350/1/j.1432-1033.1980.tb07197.x.pd