Detection of a Cool, Accretion-Shock-Generated X-Ray Plasma in EX Lupi During the 2008 Optical Eruption

EX Lupi is the prototype for a class of young, pre-main-sequence stars which are observed to undergo irregular, presumably accretion-generated, optical outbursts that result in a several magnitude rise of the optical flux. EX Lupi was observed to optically erupt in 2008 January, triggering Chandra ACIS Target of Opportunity observations shortly thereafter. We find very strong evidence that most of the X-ray emission in the first few months after the optical outburst is generated by accretion of circumstellar material onto the stellar photosphere. Specifically, we find a strong correlation between the decreasing optical and X-ray fluxes following the peak of the outburst in the optical, which suggests that these observed declines in both the optical and X-ray fluxes are the result of declining accretion rate. In addition, in our models of the X-ray spectrum, we find strong evidence for an approx 0.4 keV plasma component, as expected for accretion shocks on low-mass, pre-main-sequence stars. From 2008 March through October, this cool plasma component appeared to fade as EX Lupi returned to its quiescent level in the optical, consistent with a decrease in the overall emission measure of accretion-shock-generated plasma. The overall small increase of the X-ray flux during the optical outburst of EX Lupi is similar to what was observed in previous X-ray observations of the 2005 optical outburst of the EX Lupi-type star V1118 Ori but contrasts with the large increase of the X-ray flux from the erupting young star V1647 Ori during its 2003 and 2008 optical outbursts

X-raying the Beating Heart of a Newborn Star: Rotational Modulation of High-energy Radiation from V1647 Ori

We report a periodicity of ~1 day in the highly elevated X-ray emission from the protostar V1647 Ori during its two recent multiple-year outbursts of mass accretion. This periodicity is indicative of protostellar rotation at near-breakup speed. Modeling of the phased X-ray light curve indicates the high-temperature (~50 MK), X-ray-emitting plasma, which is most likely heated by accretion-induced magnetic reconnection, resides in dense (>~5e10 cm-3), pancake-shaped magnetic footprints where the accretion stream feeds the newborn star. The sustained X-ray periodicity of V1647 Ori demonstrates that such protostellar magnetospheric accretion configurations can be stable over timescales of years.Comment: 26 pages, 10 figure

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework, and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours

Discovery of MK-8718, an HIV Protease Inhibitor Containing a Novel Morpholine Aspartate Binding Group

A novel HIV protease inhibitor was designed using a morpholine core as the aspartate binding group. Analysis of the crystal structure of the initial lead bound to HIV protease enabled optimization of enzyme potency and antiviral activity. This afforded a series of potent orally bioavailable inhibitors of which MK-8718 was identified as a compound with a favorable overall profile