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A NanoEngineer-1 Note (DNA Conversion Site, Recent Article, Related Links)

Above: A six-stranded triple-crossover (TX) DNA Junction. See Ned Seeman's ACS interview for more background.

Having just mentioned it in the context of making publication-quality pretty pictures, another brief note thanks to a citation request on the NanoEngineer Development/User Group (groups.google.com/group/nanoengineer-dev).

There's a website hosted at bionano.physics.illinois.edu for the conversion of NE-1 DNA mmp files to all-atom pdb ("Molecular Dynamics Simulation of Custom DNA Nanostructures Created by NanoEngineer-1") and NE-1's FNANO08 proceedings article ("NanoEngineer-1 – A CAD-based molecular modeling program for structural DNA nanotechnology") was included (with thanks to its use by German Barcenas) in the recent International Journal Of Molecular Sciences article "Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions."

The bionano site is a dramatic improvement from the NAMOT + sed'ing I worked up many years ago while getting something DNA-related stood up.

As a still-not-irregular user myself, I can appreciate the small hurdles needed to keep the program upright in modern OSs (or the need to just run VirtualBox and be done with it) – therefore noting both Bryan Bishop's dev page (worth the visit to github for the preserved gallery alone!) and Bruce Allen's Molecular Dynamics Studio effort and sourceforge-available download.

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Free Astronomy Magazine – March-April 2023 Issue Available For Reading And Download

Above: Technically, it could be worse. Just give it some time. From the World Atlas of the Artificial Night Sky Brightness. Image generated by David Lorenz, djlorenz.github.io/astronomy/lp2020/

The most recent issue of Free Astronomy Magazine (March-April 2023) is available for your reading and downloading pleasure at www.astropublishing.com (and facebook).

On the cover: View of Hollywood and Los Angeles from Mulholland Drive, slightly overexposed to show the orange haze that envelops the city at night. Photo by Mike Knell

The highlight of the issue is Michele's article "The Fermi paradox – many solutions, no certainty." This discussion extends his lengthy streak of articles on the topics of exobiology, technosignatures, SETI focus, and simple statistics by including a recent reading list of books published on the topics from which we might all glean insights into what the current state of the fields are as of the early 2020's (historians, or those aliens themselves, can someday revisit our thoughts on the topic and wonder how we managed to be so prescient/way-the-frack-off at this moment in time).

The lowlight of the issue concerns the state of light pollution and the "we can't seem to get there from here" state of our transition to LEDs. "Stars are disappearing faster and faster" is not only technically true due to the observed acceleration of the expansion of the universe, but also true down here on Earth with the continued proliferation of nighttime illumination (I assume this is correct, as we don't get out much at night given the ages of the kids in the house). Not enough of us are fortunate to have a John McMahon in our midst promoting proper lighting and pushing for lighting ordinances. I lament the apparent demise of selene-ny.org (now defunct, but the group and site left its mark as a source of information online – wikipedia, slideshare, sky&tel, The Astronomical League) and can only hope you consider visiting the International Dark-Sky Association website and giving the astronomically-more-friendly lighting fixtures list a once-over before renovating.

Browser-readable version (and PDF download): www.astropublishing.com/2FAM2023/