Ultrasonic in-situ determination of the regression rate of the melting interface in burning metal rods

Results of tests in which metallic rods are burned in oxygen enriched atmospheres often include the determination of the regression rate of the melting interface for the burning test specimen. This regression rate is used as an indication of a metallic material's relative flammability and its general ability to sustain burning under the test conditions. This paper reports on the development and first application of an ultrasonic measurement system that enables in situ measurement of the regression rate of the melting interface in burning metal rods. All other methods currently used for determining this parameter are based on posttest, visual interrogation, which is costly and often inaccurate. The transducer and associated equipment used to drive and record the transducer's output signal are described and typical results for iron rods burning in pure oxygen at different gauge pressures are given along with a comparison of these results with regression gates obtained from visual interrogation. The excellent sensitivity, accuracy and reliability of the new ultrasonic transducer are demonstrated, thus indicating the transducer's great potential. (C) 1999 Acoustical Society of America. [S0001-4966(99)00702-X]

The Thermonuclear Explosion Of Chandrasekhar Mass White Dwarfs

The flame born in the deep interior of a white dwarf that becomes a Type Ia supernova is subject to several instabilities. We briefly review these instabilities and the corresponding flame acceleration. We discuss the conditions necessary for each of the currently proposed explosion mechanisms and the attendant uncertainties. A grid of critical masses for detonation in the range $10^7$ - $2 \times 10^9$ g cm$^{-3}$ is calculated and its sensitivity to composition explored. Prompt detonations are physically improbable and appear unlikely on observational grounds. Simple deflagrations require some means of boosting the flame speed beyond what currently exists in the literature. ``Active turbulent combustion'' and multi-point ignition are presented as two plausible ways of doing this. A deflagration that moves at the ``Sharp-Wheeler'' speed, $0.1 g_{\rm eff} t$, is calculated in one dimension and shows that a healthy explosion is possible in a simple deflagration if the front moves with the speed of the fastest floating bubbles. The relevance of the transition to the ``distributed burning regime'' is discussed for delayed detonations. No model emerges without difficulties, but detonation in the distributed regime is plausible, will produce intermediate mass elements, and warrants further study.Comment: 28 pages, 4 figures included, uses aaspp4.sty. Submitted to Ap

Hydrodynamic Stability Analysis of Burning Bubbles in Electroweak Theory and in QCD

Assuming that the electroweak and QCD phase transitions are first order, upon supercooling, bubbles of the new phase appear. These bubbles grow to macroscopic sizes compared to the natural scales associated with the Compton wavelengths of particle excitations. They propagate by burning the old phase into the new phase at the surface of the bubble. We study the hydrodynamic stability of the burning and find that for the velocities of interest for cosmology in the electroweak phase transition, the shape of the bubble wall is stable under hydrodynamic perturbations. Bubbles formed in the cosmological QCD phase transition are found to be a borderline case between stability and instability.Comment: preprint # SLAC-PUB-5943, SCIPP 92/56 38 pages, 10 figures (submitted via `uufiles'), phyzzx format minor snafus repaire

Geometry-controlled kinetics

It has long been appreciated that transport properties can control reaction kinetics. This effect can be characterized by the time it takes a diffusing molecule to reach a target -- the first-passage time (FPT). Although essential to quantify the kinetics of reactions on all time scales, determining the FPT distribution was deemed so far intractable. Here, we calculate analytically this FPT distribution and show that transport processes as various as regular diffusion, anomalous diffusion, diffusion in disordered media and in fractals fall into the same universality classes. Beyond this theoretical aspect, this result changes the views on standard reaction kinetics. More precisely, we argue that geometry can become a key parameter so far ignored in this context, and introduce the concept of "geometry-controlled kinetics". These findings could help understand the crucial role of spatial organization of genes in transcription kinetics, and more generally the impact of geometry on diffusion-limited reactions.Comment: Submitted versio

Finite size effects near the onset of the oscillatory instability

A system of two complex Ginzburg - Landau equations is considered that applies at the onset of the oscillatory instability in spatial domains whose size is large (but finite) in one direction; the dependent variables are the slowly modulated complex amplitudes of two counterpropagating wavetrains. In order to obtain a well posed problem, four boundary conditions must be imposed at the boundaries. Two of them were already known, and the other two are first derived in this paper. In the generic case when the group velocity is of order unity, the resulting problem has terms that are not of the same order of magnitude. This fact allows us to consider two distinguished limits and to derive two associated (simpler) sub-models, that are briefly discussed. Our results predict quite a rich variety of complex dynamics that is due to both the modulational instability and finite size effects

Formation of regulatory modules by local sequence duplication

Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here, we show that a large fraction of neighboring transcription factor binding sites in the fly genome have formed from a common sequence origin by local duplications. This mode of evolution is found to produce regulatory information: duplications can seed new sites in the neighborhood of existing sites. Duplicate seeds evolve subsequently by point mutations, often towards binding a different factor than their ancestral neighbor sites. These results are based on a statistical analysis of 346 cis-regulatory modules in the Drosophila melanogaster genome, and a comparison set of intergenic regulatory sequence in Saccharomyces cerevisiae. In fly regulatory modules, pairs of binding sites show significantly enhanced sequence similarity up to distances of about 50 bp. We analyze these data in terms of an evolutionary model with two distinct modes of site formation: (i) evolution from independent sequence origin and (ii) divergent evolution following duplication of a common ancestor sequence. Our results suggest that pervasive formation of binding sites by local sequence duplications distinguishes the complex regulatory architecture of higher eukaryotes from the simpler architecture of unicellular organisms

Contribution of Distinct Homeodomain DNA Binding Specificities to Drosophila Embryonic Mesodermal Cell-Specific Gene Expression Programs

Homeodomain (HD) proteins are a large family of evolutionarily conserved transcription factors (TFs) having diverse developmental functions, often acting within the same cell types, yet many members of this family paradoxically recognize similar DNA sequences. Thus, with multiple family members having the potential to recognize the same DNA sequences in cis-regulatory elements, it is difficult to ascertain the role of an individual HD or a subclass of HDs in mediating a particular developmental function. To investigate this problem, we focused our studies on the Drosophila embryonic mesoderm where HD TFs are required to establish not only segmental identities (such as the Hox TFs), but also tissue and cell fate specification and differentiation (such as the NK-2 HDs, Six HDs and identity HDs (I-HDs)). Here we utilized the complete spectrum of DNA binding specificities determined by protein binding microarrays (PBMs) for a diverse collection of HDs to modify the nucleotide sequences of numerous mesodermal enhancers to be recognized by either no or a single subclass of HDs, and subsequently assayed the consequences of these changes on enhancer function in transgenic reporter assays. These studies show that individual mesodermal enhancers receive separate transcriptional input from both I–HD and Hox subclasses of HDs. In addition, we demonstrate that enhancers regulating upstream components of the mesodermal regulatory network are targeted by the Six class of HDs. Finally, we establish the necessity of NK-2 HD binding sequences to activate gene expression in multiple mesodermal tissues, supporting a potential role for the NK-2 HD TF Tinman (Tin) as a pioneer factor that cooperates with other factors to regulate cell-specific gene expression programs. Collectively, these results underscore the critical role played by HDs of multiple subclasses in inducing the unique genetic programs of individual mesodermal cells, and in coordinating the gene regulatory networks directing mesoderm development.National Institutes of Health (U.S.) (Grant R01 HG005287

The Role of Glypicans in Wnt Inhibitory Factor-1 Activity and the Structural Basis of Wif1's Effects on Wnt and Hedgehog Signaling

Proper assignment of cellular fates relies on correct interpretation of Wnt and Hedgehog (Hh) signals. Members of the Wnt Inhibitory Factor-1 (WIF1) family are secreted modulators of these extracellular signaling pathways. Vertebrate WIF1 binds Wnts and inhibits their signaling, but its Drosophila melanogaster ortholog Shifted (Shf) binds Hh and extends the range of Hh activity in the developing D. melanogaster wing. Shf activity is thought to depend on reinforcing interactions between Hh and glypican HSPGs. Using zebrafish embryos and the heterologous system provided by D. melanogaster wing, we report on the contribution of glypican HSPGs to the Wnt-inhibiting activity of zebrafish Wif1 and on the protein domains responsible for the differences in Wif1 and Shf specificity. We show that Wif1 strengthens interactions between Wnt and glypicans, modulating the biphasic action of glypicans towards Wnt inhibition; conversely, glypicans and the glypican-binding “EGF-like” domains of Wif1 are required for Wif1's full Wnt-inhibiting activity. Chimeric constructs between Wif1 and Shf were used to investigate their specificities for Wnt and Hh signaling. Full Wnt inhibition required the “WIF” domain of Wif1, and the HSPG-binding EGF-like domains of either Wif1 or Shf. Full promotion of Hh signaling requires both the EGF-like domains of Shf and the WIF domains of either Wif1 or Shf. That the Wif1 WIF domain can increase the Hh promoting activity of Shf's EGF domains suggests it is capable of interacting with Hh. In fact, full-length Wif1 affected distribution and signaling of Hh in D. melanogaster, albeit weakly, suggesting a possible role for Wif1 as a modulator of vertebrate Hh signaling

c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression

<p>Abstract</p> <p>Background</p> <p>Computational methods for characterizing novel transcription factor binding sites search for sequence patterns or "motifs" that appear repeatedly in genomic regions of interest. Correlation-based motif finding strategies are used to identify motifs that correlate with expression data and do not rely on promoter sequences from a pre-determined set of genes.</p> <p>Results</p> <p>In this work, we describe a method for predicting motifs that combines the correlation-based strategy with phylogenetic footprinting, where motifs are identified by evaluating orthologous sequence regions from multiple species. Our method, c-REDUCE, can account for variability at a motif position inferred from evolutionary information. c-REDUCE has been tested on ChIP-chip data for yeast transcription factors and on gene expression data in <it>Drosophila</it>.</p> <p>Conclusion</p> <p>Our results indicate that utilizing sequence conservation information in addition to correlation-based methods improves the identification of known motifs.</p