Category: various photos

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The Newer Nanorex, QuteMol Renderings, And A Summary Of Local, Ongoing Molecular Nanotechnology Projects

Greetings from Snowbird, Utah! At 7000 ft or so, I've been exhausted all week. They artillery the far side of the mountain at Cliff Lodge during major snow falls to get the avalanches out of the way before the tourists start their morning ski lift ascents.

And I thought I had a hip gig.

Click an image for a larger version.

Our first physical company meeting in 18 months, the Nanorex crew has used the ISNSCE FNANO conference (and, specifically, the non-random localization of many of the world's leading structural DNA nanotechnology (SDN) researchers) to introduce our new SDN focus and present the upcoming Alpha release (0.9) of NanoEngineer-1.

As with all significant updates, the Nanorex website received a major overhaul. Key points of interest include:

1. QuteMol: Mark Sims and I have taken a serious fancy to QuteMol. From the Nanorex site:

"Many of the images and animations in these galleries have been rendered with QuteMol, a new open-source, interactive, high quality molecular visualization system which exploits the latest GPU capabilities through OpenGL shaders to offers an array of innovative visual effects. QuteMol was developed by Marco Tarini and Paolo Cignoni of the Visual Computing Lab at ISTI – CNR. The Nanorex team is enthusiastic about their work and look forward to rendering even more awe-inspiring images for the NanoEngineer-1 gallery."

Only 0.4.0 and already among the best yet. Bravo Marco et Paolo! This also marks a site transition to png image format.

2. Molecular Manufacturing Gallery: The cientifica blog can once again wax unfoundedly antagonistic about Nanorex activities with the updated molecular manufacturing gallery. To all the moral transhumanists reading, rest assured that heavy-duty full-blown Drexlerian diamondoid mechanosynthesis studies will continue unabated by yours truly until such time that someone can hand me a SINGLE peer-reviewed paper that demonstrated that it will NOT work. I stopped caring about the academic debate (and engaging in online arguments) some time ago due to the preponderance of opinion and absence of hard experimental data in either direction. I'm 16 processors deep into tooltip calculations with the usual suspects (Drexler, Freitas, Merkle) and awaiting the printing of the Ge-Dimer Survey paper, the basis of the Q-SMAKAS defect study currently in its final WU phase at NanoHive@Home. The new gallery features tooltip structures related to the Nanofactory animation, the DC10c dimer tooltip (the article for which is freely available from the Journal of Computational and Theoretical Nanoscience), a monstrous tooltip assembly (whose green end is currently part of the tooltip queue. A few cutaway views that aren't in the Nanorex gallery are shown below), and an example of a potential defect structure for the C100GeATD tooltip analyzed in the Ge paper (see the NanoHive@Home results gallery for more info and a great pair of animations of the tooltip simulation by Andrew Haveland-Robinson of www.haveland.com).

tooltip
Click the image for a larger version.

3. Carbon Nanotube Gallery: more derivative than a molecular dynamics simulation, the new carbon nanotube gallery shows three carbon nanotube/diamondoid ring structures are in the gallery, as well as a dative carbon nanotube octahedron I generated nearly 5 years ago prior to my presentation at the 10th Foresight Conference. The first image is part of a tutorial on general nanoscale design considerations that will be posted soon for further reading on the Nanorex site. The second image is a carbon nanotube-based bearing assembly I rendered as part of a new line of study hybridizing self-assembly and molecular manufacturing approaches.

14x22
Click the image for a larger version.

Just about everything I mentioned above will be expanded upon either as blog content or for formal publications, so consider this post more FYI and my own formal marker of when the additional magic began to happen.

www.nanoengineer-1.com/content/index.php?option=com_content&task=view&id=34&Itemid=35
www.nanoengineer-1.com/content/index.php?option=com_content&task=view&id=36&Itemid=46
www.nanoengineer-1.com/content/index.php?option=com_content&task=view&id=39&Itemid=49
www.nanoengineer-1.com/content/index.php?option=com_content&task=view&id=38&Itemid=48
www.ingentaconnect.com/content/asp/jctn/2005/00000002/00000001/art00003
www.nanohive-1.org/atHome/view_profile.php?userid=3479
www.e-drexler.com/d/05/00/DC10C-mechanosynthesis.pdf
www.nanohive-1.org/atHome/Nanofactory_1_Damian.php
www.foresight.org/Conferences/MNT10/Abstracts/Allis
en.wikipedia.org/wiki/Molecular_nanotechnology
www.lizardfire.com/html_nano/themovies.html
en.wikipedia.org/wiki/Molecular_assembler
www.snowbird.com/lodging/clifflodge.html
en.wikipedia.org/wiki/Transhumanism
www.somewhereville.com/?p=63
www.cs.duke.edu/~reif/FNANO
www.nanohive-1.org/atHome
seemanlab4.chem.nyu.edu
cientifica.eu/blog/?p=240
www.libpng.org/pub/png
qutemol.sourceforge.net
www.cientifica.eu/blog
www.e-drexler.com
www.snowbird.com
www.haveland.com
www.nanorex.com
www.foresight.org
www.rfreitas.com
www.merkle.com
www.isnsce.org
www.aspbs.com

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"We have no idea what's going on up there."

Oswego

It's a fun story, certainly a prime example of my occasional lack of common sense, and more first-hand eyewitness reporting of the state of Oswego county and points nearby. So, because I'm here to blog it, I provide below my attempted travel to Clarkson for a department colloquium and nanoworkshop.

6:00 am – begin drive to Potsdam. Cold wind, blue skies.

6:20 am – approaching Mexico, NY. Few flakes, but nothing to stop a (er, my) VW Beetle.

6:25 am – within five minutes, blue skies had turned into white skies. The abruptness of the change from non-lake effect to lake effect should have been warning enough.

7:00 am – somewhere between 6:25 and 7:00 am, when it hadn't been snowing THAT BAD yet, I decided it was time to do something stupid, so I pulled out the digital Elph, set it to movie mode, and recorded the little snippet above.

7:25 am – the turning point. After 1 hr, the 4-car caravan I found myself (thankfully) at the back of had made it nearly 5 miles towards the Mexico exit (34 on 81 N). By this time, the red glow of the taillights two cars in front of me were intermittently viewable due to snow obstruction. The exit itself was marked with a tractor trailer pulled to the side of the road, lights flashing. The three cars ahead of me begin the slow rightward veer to the exit. I trudge ahead beyond the exit…

7:26 am – … 13 feet. I wish now that I had had the better mind to take a picture of the view in front of me. My wagon train had been the ONLY thing on the road in at least… 20 minutes. In that 20 minutes, any pair of tire tracks were filled in, leaving nothing to follow. For all intensive purposes, 81 North WAS GONE. Literally disappeared. It looked like I had taken a hard right turn off the road and were facing the woods, the woods as they would have appeared after any other snow storm. The snow was at 7 inches where the tracks would have been, making the actual level of the snow all of 13 inches, making the path in front of me at least 3 inches higher than the clearance of the Beetle.

7:27 am – for the first time in my otherwise spotless driving career, I threw the car into reverse (which has to be some kind of no-no on a state highway) and drove back towards exit 34. Just barely making it to Route 104, I wait with the accumulated cars in the accumulation.

7:45 am – some small group of drivers begin the trip along 104 Wes, theoretically back onto 81 S. The on-ramp, invisible and sign-less, is overshot by all involved, leaving us to slip+slide along 104 W towards… nowhere in particular. With nowhere to turn around due to the height of the snow drifts, we trudge along for several miles. I knew there were houses there, as I could see the orange glow of room lights cutting through thinned snow drifts building up at house walls.

8:05 am – some spot in the road was wide enough to turn around, which we all did.

8:25 am – We reached the 81 South on-ramp just in time for the National Weather Service to declare a state of emergency in Oswego. "Far out," I said. I hadn't gotten near Oswego yet.

After 9:30 am – now comfortably out of the worst of the weather, I make the first calls to Cetin Cetinkaya at Clarkson and let him know I'm going to be late. About a week and a half late.

3 hr 3 min or so to get all of 35 miles. I've mentioned this to every Syracusan I've told the story to. No matter what you've seen on the TV, heard on the radio, or read about in the paper, we have no idea what's going on up there.

www.usa.canon.com/consumer/controller?act=ModelDetailAct&fcategoryid=145&modelid=12466
www.google.com/maps?q=Mexico,+NY&sa=X&oi=map&ct=title
www.clarkson.edu/mae/faculty/cetinkaya.html
en.wikipedia.org/wiki/Lake_effect_snow
www.vw.com/newbeetle
www.co.oswego.ny.us
www.potsdam.ny.us
www.nws.noaa.gov
www.oswegony.org
www.clarkson.edu