Finally! A Good Use For The Nano Gallery (Kudos To

An unlabeled version of the fused-diamondoid-carbon-nanotube-van-der-waals-crimp-junction found a home in the NanoSonic Nanotechnology Coloring Book, page 8 (I show it below (with mine shown a little more nano-sized)). I think that’s pretty hip.

Kudos to Tom Moore for pointing it out.

Cover Art For The 7 May 2010 Issue Of The Journal Of Organic Chemistry – Notes On Presentation

The cover art for the 7 May 2010 issue of the Journal of Organic Chemistry accompanies the article by (2nd semester organic chemistry professor, co-author, and 2010 American Chemical Society James Flack Norris Award in Physical Organic Chemistry recipient) John E. Baldwin and Alexey P. Kostikov entitled “On the Stereochemical Characteristic of the Thermal Reactions of Vinylcyclobutane.”

This Perspective outlines the stereochemical and mechanistic complexities inherent in the thermal reactions converting vinylcyclobutane to cyclohexene, butadiene, and ethylene. The structural isomerization and the fragmentation processes seem, at first sight, to be obvious and simple. When considered more carefully and investigated with the aid of deuterium-labeled stereochemically well-defined vinylcyclobutane derivatives there emerges a complex kinetic situation traced by 56 structure-to-structure transformations and 12 independent kinetic parameters. Experimental determinations of stereochemical details of stereomutations and [1,3] carbon sigmatropic shifts are now being pursued and will in time contribute to gaining relevant evidence casting light on the reaction dynamics involved as flexible short-lived diradical intermediates trace the paths leading from one d2-labeled vinylcyclobutane starting material to a mixture of 16 structures.

Continue reading “Cover Art For The 7 May 2010 Issue Of The Journal Of Organic Chemistry – Notes On Presentation”

POV-Ray The Error Number Is -199 Potential Remedy For OSX

This post provides a possible fix for an OSX POV-Ray error with precious little information available about it anywhere online. The error,

The Error number is -199. (For internal reference only!)

appears upon startup and exits from the program proper, such that POV-Ray becomes useless (not pleasant when you need that last minute image 30 seconds before lecturing).


The only mention online (if you search by the message text) can be found at

The error itself is not diagnosed, only noting that a corrupted file is not being accessed upon startup and that running a Disk Utility verification/fixing and reinstalling POV-Ray solves the problem. If this has happened to you, you may have noted that verification/fixing and re-installation does not do the trick.

The origin of the problem on my machine could be traced to a crashed POV-Ray rendering run of a number of images and the retention of the file POV-Ray Mac 3.6.plist in my /[USER]/Library/Preferences/ directory, which typically only contains the file POV-Ray Preferences 3.5 (why an installation of POV-Ray 3.6 would still leave a 3.5 Preference file is beyond the scope of this post).

Deleting the POV-Ray Mac 3.6.plist file fixes the problem.

Recent Appearances, Hessen-Nanotech and Institute of Physics

Not since Arthur Eddington‘s confirmation (from luck, skill, expectation, selective bias, or other) of space curvature by the Sun as predicted by Einstein‘s General Relativity have English and German scientists agreed so closely on a matter of scientific importance. Yes, the NanoEngineer-1 energy-minimized, POVRay-rendered fused diamondoid carbon nanotube van dew Waals crimp junction wins the eye candy prize yet again out of all the molecular mechanics-based structures in the gallery. Now that I’m trying more with Qutemol, we’ll see how subsequent selections go. Links and pdfs are provided below for bookkeeping purposes, as they’re already google-able.

Continue reading “Recent Appearances, Hessen-Nanotech and Institute of Physics”

NanoEngineer-1 + QuteMol Local Gallery Addition

Simply posting the addition of new gallery contents rendered with QuteMol. A number of these are included in the Nanorex Carbon Nanotube and Molecular Manufacturing Galleries, now provided here in significantly larger versions for your viewing pleasure. The carbon nanotube gallery contents have also been featured at Tom Moore‘s site and the previously posted A Low-Friction Molecular Bearing Assembly Tutorial, v1.

qutemol gallery

A Low-Friction Molecular Bearing Assembly Tutorial, v1

The largely nonspecific tutorial below was put together as part of design work currently featured in the Nanorex carbon nanotube gallery. This tutorial is/was meant to be introductory material for either engineers unfamiliar with chemistry or chemists unfamiliar with engineering, in either case not covering much material but providing some visuals and descriptions that highlight the complexities of designing simple nanosystems, avoiding any significant chemical or engineering jargon (and no equations). This is all related to the class project I developed as part of my travels to Clarkson University this past semester. Any more I would include here would likely overlap with the introductory material, so I will save additional explanations.

While a final version will eventually make its way to the Nanorex website, I’m providing a first-pass (of the final draft) of the text and figures, having already sent out a copy to Tom Moore at, who’s doing an excellent job of putting the NE-1 simulator (and his own computers, given the number of machine problems he reports on!) through the ringer using carbon nanotube and diamondoid nanostructures. The two machine-phase posts to date related to the bearing assemblies on the Nanorex site are available at “simulation-update” and “revisiting-damians-bearing,” and I can’t wait to see what Tom winds up doing with them.

Continue reading “A Low-Friction Molecular Bearing Assembly Tutorial, v1”

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.

Continue reading “The Newer Nanorex, QuteMol Renderings, And A Summary Of Local, Ongoing Molecular Nanotechnology Projects”

The Ted Turner-ization of Drexlerian (and other) Nanotechnology

In the physical sciences, as is reportedly the case in other fields, a picture is worth 1000 words (within error bars). The goal of any good science image is to have the first 5 of those words not be “What the hell is that?” The description of a protein binding pocket without visual aids is about as painful to listen to as the description of a car engine without diagrams. These discussions are taxing even to people IN the field encompassing the details of the thing being described. In the case of science fields that receive lots of public attention (and nanotechnology is most definitely one of those), the need for visuals unencumbered by the assumptions of one’s barricaded discourse community are all the more important.

Continue reading “The Ted Turner-ization of Drexlerian (and other) Nanotechnology”

“In the future, it will be the little things that really matter.”

The latest publication (Vol. 15 No.3 2006) from the Business and Economic Research Center (BERC) at the Middle Tennessee State University features an excellent article by Dr. Richard W. Oliver and Ed Sperling on the growing influence of nanotechnology and some updated graphics that wouldn’t have come out as well as they did without NanoEngineer-1. Click on the pdf, which’ll open a linked Table of Contents to the whole article.

I’m not much for presenting critical discussions of content (that whole “spare time” thing), so will keep it brief. It is a very good, non-technical (well, non-technical to ME anyway) discussion of how our continued understanding of the nanoscale is shaping developments in all industries. While some general science is intermixed throughout, the focus of the article is on the shaping of economies, or how the current nanotech weather will eventually become the eye of the storm of the global manufacturing climate. I tend to not look far beyond my own computer screen as I push ahead in the field, so I very much enjoy reading coherent presentations of nanotech aspects I wouldn’t otherwise spend much time thinking about (yes, there are many in nanotechnology wondering IF we should, HOW we should, WHEN we should, WHAT we should and WHY we should, and many of those in the field have orthogonal interests that could all benefit from larger coefficients in their off-diagonal elements). That’s what makes David Berube’s Nano-Hype so interesting to read and Rob Tow so interesting to listen to.

Continue reading ““In the future, it will be the little things that really matter.””

American Pi + Old Ideas Revisited = A Few Thousand New Words For The Gallery

[Slipping into terminal blog mode for a moment] This past week saw (1) the second Technology Roadmap for Productive Nanosystems meeting at Brookhaven National Labs and the press release for (2) Nanorex’s first major educational outreach project as part of (3) the COSMOS (California State Summer School for Mathematics and Science) summer program. The purpose of (1) is to develop science and technology pathways with the intent of realizing the full potential of molecular nanotechnology, the purpose of (2) is to enable researchers, like myself, to have the best possible tools for designing molecules and nanosystems in order to go into experimental work with the most complete understanding of their properties, and the purpose of (3) is to make sure that we (that’s the world) will have researchers in the future capable of making it all happen (and, in case you’ve not been following the news, we need all the help we can get in the sciences).

The next major update to NanoEngineer-1 includes all of the force field parameters required to simulate carbon nanotubes and other structures with extended pi-systems. In anticipation, I began sorting through some very old designs of mine that I promised to revisit once computers and software became useful enough to allow for their simulation. Fortunately, the state of technology has moved faster than Barnard’s Star, so the old designs are rapidly being overwritten with new ideas. As for the gallery timing, I just completed some rerendering of gallery images for an upcoming article I’ll link to when it’s available, part of my work on the roadmap involves addressing steps to go from current technologies to motifs described in the new images, and, of course, Christine Peterson was kind enough to link to me in a recent nanodot post and I abhor the idea of having all the same old images up in the event anyone ever links to me again.

Continue reading “American Pi + Old Ideas Revisited = A Few Thousand New Words For The Gallery”