A grammatical specification of human-computer dialogue

The Seeheim Model of human-computer interaction partitions an interactive application into a user-interface, a dialogue controller and the application itself. One of the formal techniques of implementing the dialogue controller is based on context-free grammars and automata. In this work, we modify an off-the-shelf compiler generator (YACC) to generate the dialogue controller. The dialogue controller is then integrated into the popular X-window system, to create an interactive-application generator. The actions of the user drive the automaton, which in turn controls the application

Code Generation = A* + BURS

A system called BURS that is based on term rewrite systems and a search algorithm A* are combined to produce a code generator that generates optimal code. The theory underlying BURS is re-developed, formalised and explained in this work. The search algorithm uses a cost heuristic that is derived from the termrewrite system to direct the search. The advantage of using a search algorithm is that we need to compute only those costs that may be part of an optimal rewrite sequence

Confinement Effects on the Kinetics and Thermodynamics of Protein Dimerization

In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the interplay of these effects in the crowded cellular environment? We study dimerization of a model homodimer both when the mondimers are free or tethered to each other. We consider a structured environment: Two monomers first diffuse into a cavity of size $L$ and then fold and bind within the cavity. The folding and binding are simulated using molecular dynamics based on a simplified topology based model. The {\it confinement} in the cell is described by an effective molecular concentration $C \sim L^{-3}$. A two-state coupled folding and binding behavior is found. We show the maximal rate of dimerization occurred at an effective molecular concentration $C^{op}\simeq 1m$M which is a relevant cellular concentration. In contrast, for tethered chains the rate keeps at a plateau when $CC^{op}$. For both the free and tethered cases, the simulated variation of the rate of dimerization and thermodynamic stability with effective molecular concentration agrees well with experimental observations. In addition, a theoretical argument for the effects of confinement on dimerization is also made

Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occurs after the structure collapse

The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is achieved before water is expelled from the hydrophobic core. This view integrates water expulsion effects into the funnel energy landscape theory of protein folding. Comparisons to experimental results are shown for the SH3 protein. After the folding transition, a near-native intermediate with partially solvated hydrophobic core is found. This transition is followed by a final step that cooperatively squeezes out water molecules from the partially hydrated protein core.Comment: Proceedings of the National Academy of Science, 2002, Vol.99. 685-69

How native state topology affects the folding of Dihydrofolate Reductase and Interleukin-1beta

The overall structure of the transition state and intermediate ensembles experimentally observed for Dihydrofolate Reductase and Interleukin-1beta can be obtained utilizing simplified models which have almost no energetic frustration. The predictive power of these models suggest that, even for these very large proteins with completely different folding mechanisms and functions, real protein sequences are sufficiently well designed and much of the structural heterogeneity observed in the intermediates and the transition state ensembles is determined by topological effects.Comment: Proc. Natl. Acad. Sci. USA, in press (11 pages, 4 color PS figures) Higher resolution PS files can be found at http://www-physics.ucsd.edu/~cecilia/pub_list.htm

Three-helix-bundle Protein in a Ramachandran Model

We study the thermodynamic behavior of a model protein with 54 amino acids that forms a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid and has the Ramachandran torsional angles $\phi_i$, $\psi_i$ as its degrees of freedom. The force field is based on hydrogen bonds and effective hydrophobicity forces. For a suitable choice of the relative strength of these interactions, we find that the three-helix-bundle protein undergoes an abrupt folding transition from an expanded state to the native state. Also shown is that the corresponding one- and two-helix segments are less stable than the three-helix sequence.Comment: 15 pages, 7 figure

On the detectability of star-planet interaction

Magnetic (or tidal) interactions between "hot Jupiters" and their host stars can potentially enhance chromospheric and coronal activity. An ideal testbed for investigating this effect is provided by the extreme WASP-18 system, which features a massive (~10 times Jupiter) close-in (~1 day period) transiting planet orbiting a young F6 star. Optical and X-ray observations of WASP-18 were conducted in November 2011. The high-resolution echelle spectrograph MIKE was used on the 6.5m Magellan Clay telescope to obtain 13 spectra spanning planetary orbital phases of 0.7-1.4, while the X-ray Telescope on Swift provided contemporaneous monitoring with a stacked exposure of ~50 ks. The cores of the Ca II H and K lines do not show significant variability over multiple orbits spanning ~8 d, in contrast to the expectation of phase-dependent chromospheric activity enhancements for efficient star-planet interaction. The star is also X-ray faint, with log Lx < 27.6 erg/s (0.3-2 keV), indicating that coronal activity is likewise low. The lack of detectable star-planet interaction in this extreme system requires that any such effect must here be transient, if indeed present. We demonstrate that searches for Ca II H and K variability can potentially mistake a stellar hotspot, if observed over a short segment of the rotation period, for planet-induced activity. Taken together, these results suggest that the utility of star-planet interaction as a robust method of estimating exoplanet magnetic field strengths may be limited.Comment: Accepted to ApJ; 9 pages emulateapj, 5 figures, 1 table (v2: corrected fn15, typos, refs

Thermal Emission of WASP-14b Revealed with Three Spitzer Eclipses

Exoplanet WASP-14b is a highly irradiated, transiting hot Jupiter. Joshi et al. calculate an equilibrium temperature Teq of 1866 K for zero albedo and reemission from the entire planet, a mass of 7.3 +/- 0.5 Jupiter masses and a radius of 1.28 +/- 0.08 Jupiter radii. Its mean density of 4.6 g/cm3 is one of the highest known for planets with periods less than 3 days. We obtained three secondary eclipse light curves with the Spitzer Space Telescope. The eclipse depths from the best jointly fit model are $0.224\%$ +/- $0.018\%$ at 4.5 {\mu}m and $0.181\%$ +/- $0.022\%$ at 8.0 {\mu}m. The corresponding brightness temperatures are 2212 +/- 94 K and 1590 +/- 116 K. A slight ambiguity between systematic models suggests a conservative 3.6 {\mu}m eclipse depth of $0.19\%$ +/- $0.01\%$ and brightness temperature of 2242 +/- 55 K. Although extremely irradiated, WASP-14b does not show any distinct evidence of a thermal inversion. In addition, the present data nominally favor models with day night energy redistribution less than $~30\%$. The current data are generally consistent with oxygen-rich as well as carbon-rich compositions, although an oxygen-rich composition provides a marginally better fit. We confirm a significant eccentricity of e = 0.087 +/- 0.002 and refine other orbital parameters.Comment: 16 pages, 16 figure