Model reduction by extended quasi-steady-state approximation

We extend the quasi-steady state approximation (QSSA) as well with respect to the class of differential systems as with respect to the order of approximation. As an application we prove that the trimolecular autocatalator can be approximated by a fast bimolecular reaction system. Finally we describe a class of singularly perturbed systems for which the first order QSSA can easily be obtained

Calibrant Delivery for Mass Spectrometry

This article describes a means of sampling ions that are created at a location remote from the primary ion source used for mass spectral analysis. Such a source can be used for delivery of calibrant ions on demand. Calibrant ions are sprayed into an atmospheric pressure chamber, at a position substantially removed from the sampling inlet. A gas flow sweeps the calibrants towards the sampling inlet, and a new means for toggling the second ion beam into the instrument can be achieved with the use of a repelling field established by an electrode in front of the sampling inlet. The physical separation of two or more sources of ions eliminates detrimental interactions due to gas flows or fields. When using a nanoflow electrospray tip as the primary ion source, the potential applied to the tip completely repels calibrant ions and there is no compromise in terms of electrospray performance. When calibrant ions are desired, the potential applied to the nanoflow electrospray tip is lowered for a short period of time to allow calibrant ions to be sampled into the instrument, thus providing a means for external calibration that avoids the typical complications and compromises associated with dual spray sources. It is also possible to simultaneously sample ions from multiple ion beams if necessary for internal mass calibration purposes. This method of transporting additional ion beams to a sampling inlet can also be used with different types of atmospheric pressure sources such as AP MALDI, as well as sources configured to deliver ions of different polarity

Magnetic Fields in Dark Cloud Cores: Arecibo OH Zeeman Observations

We have carried out an extensive survey of magnetic field strengths toward dark cloud cores in order to test models of star formation: ambipolar-diffusion driven or turbulence driven. The survey involved $\sim500$ hours of observing with the Arecibo telescope in order to make sensitive OH Zeeman observations toward 34 dark cloud cores. Nine new probable detections were achieved at the 2.5-sigma level; the certainty of the detections varies from solid to marginal, so we discuss each probable detection separately. However, our analysis includes all the measurements and does not depend on whether each position has a detection or just a sensitive measurement. Rather, the analysis establishes mean (or median) values over the set of observed cores for relevant astrophysical quantities. The results are that the mass-to-flux ratio is supercritical by $\sim 2$, and that the ratio of turbulent to magnetic energies is also $\sim 2$. These results are compatible with both models of star formation. However, these OH Zeeman observations do establish for the first time on a statistically sound basis the energetic importance of magnetic fields in dark cloud cores at densities of order $10^{3-4}$ cm$^{-3}$, and they lay the foundation for further observations that could provide a more definitive test.Comment: 22 pages, 2 figures, 2 table

Layered Social Network Analysis Reveals Complex Relationships in Kindergarteners.

The interplay between individuals forms building blocks for social structure. Here, we examine the structure of behavioral interactions among kindergarten classroom with a hierarchy-neutral approach to examine all possible underlying patterns in the formation of layered networks of "reciprocal" interactions. To understand how these layers are coordinated, we used a layered motif approach. Our dual layered motif analysis can therefore be thought of as the dynamics of smaller groups that tile to create the group structure, or alternatively they provide information on what the average child would do in a given local social environment. When we examine the regulated motifs in layered networks, we find that transitivity is at least partially involved in the formation of these layered network structures. We also found complex combinations of the expected reciprocal interactions. The mechanisms used to understand social networks of kindergarten children here are also applicable on a more general scale to any group of individuals where interactions and identities can be readily observed and scored

Alignment of protein structures in the presence of domain motions

Abstract Background Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies. However, proteins are flexible entities often undergoing movements that alter the positions of domains or subdomains with respect to each other. Such movements can impede the identification of structural equivalences when rigid aligners are used. Results We introduce a new method called RAPIDO (Rapid Alignment of Proteins in terms of Domains) for the three-dimensional alignment of protein structures in the presence of conformational changes. The flexible aligner is coupled to a genetic algorithm for the identification of structurally conserved regions. RAPIDO is capable of aligning protein structures in the presence of large conformational changes. Structurally conserved regions are reliably detected even if they are discontinuous in sequence but continuous in space and can be used for superpositions revealing subtle differences. Conclusion RAPIDO is more sensitive than other flexible aligners when applied to cases of closely homologues proteins undergoing large conformational changes. When applied to a set of kinase structures it is able to detect similarities that are missed by other alignment algorithms. The algorithm is sufficiently fast to be applied to the comparison of large sets of protein structures.</p

Multi-Step Processing of Spatial Joins

Spatial joins are one of the most important operations for combining spatial objects of several relations. In this paper, spatial join processing is studied in detail for extended spatial objects in twodimensional data space. We present an approach for spatial join processing that is based on three steps. First, a spatial join is performed on the minimum bounding rectangles of the objects returning a set of candidates. Various approaches for accelerating this step of join processing have been examined at the last year’s conference [BKS 93a]. In this paper, we focus on the problem how to compute the answers from the set of candidates which is handled by the following two steps. First of all, sophisticated approximations are used to identify answers as well as to filter out false hits from the set of candidates. For this purpose, we investigate various types of conservative and progressive approximations. In the last step, the exact geometry of the remaining candidates has to be tested against the join predicate. The time required for computing spatial join predicates can essentially be reduced when objects are adequately organized in main memory. In our approach, objects are first decomposed into simple components which are exclusively organized by a main-memory resident spatial data structure. Overall, we present a complete approach of spatial join processing on complex spatial objects. The performance of the individual steps of our approach is evaluated with data sets from real cartographic applications. The results show that our approach reduces the total execution time of the spatial join by factors

Domain identification by iterative analysis of error-scaled difference distance matrices.

Iterative interpretation of error-scaled difference distance matrices is suggested as a means of dividing a protein into structural domains on the basis of conformational differences between different models. Two conformers of Src kinase {PDB codes 1fmk [Xu et al. (1997). Nature (London), 385, 595–602] and 2src [Xu et al. (1999). Mol. Cell, 3, 629–638]} in the inactive state with and without a substrate analogue bound are analysed in order to demonstrate the approach. SH3, SH2 and the N- and C-terminal lobes of the kinase domain are detected as structural modules that move with respect to each other. Notably, a relative movement between the SH3 and SH2 domains is detected although both structures of Src kinase are in the `assembled' state. Detailed analysis shows that Arg318, a residue topologically located in the N-terminal lobe of the kinase domain, structurally belongs to the C-­terminal lobe. The movement of this residue together with the C-terminal lobe upon substrate binding leads to the loss of a salt bridge between Arg318 and Asp117, a residue in the SH3 domain, providing an explanation for the increased mobility of the SH3 domain

On the role of shake-off in single-photon double ionization

The role of shake-off for double ionization of atoms by a single photon with finite energy has become the subject of debate. In this letter, we attempt to clarify the meaning of shake-off at low photon energies by comparing different formulations appearing in the literature and by suggesting a working definition. Moreover, we elaborate on the foundation and justification of a mixed quantum-classical ansatz for the calculation of single-photon double ionization

Exploiting the Temporal Logic Hierarchy and the Non-Confluence Property for Efficient LTL Synthesis

The classic approaches to synthesize a reactive system from a linear temporal logic (LTL) specification first translate the given LTL formula to an equivalent omega-automaton and then compute a winning strategy for the corresponding omega-regular game. To this end, the obtained omega-automata have to be (pseudo)-determinized where typically a variant of Safra's determinization procedure is used. In this paper, we show that this determinization step can be significantly improved for tool implementations by replacing Safra's determinization by simpler determinization procedures. In particular, we exploit (1) the temporal logic hierarchy that corresponds to the well-known automata hierarchy consisting of safety, liveness, Buechi, and co-Buechi automata as well as their boolean closures, (2) the non-confluence property of omega-automata that result from certain translations of LTL formulas, and (3) symbolic implementations of determinization procedures for the Rabin-Scott and the Miyano-Hayashi breakpoint construction. In particular, we present convincing experimental results that demonstrate the practical applicability of our new synthesis procedure