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Archive for April, 2007

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

Sunday, April 22nd, 2007

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

Mrs. Joanne Constas Allis, December 19, 1923 – April 11, 2007

Sunday, April 22nd, 2007

Still a bit surreal, so am, for now, erring on the side of reference and organization. Safe to say that everyone that knows me knows my yia yia, family matriarch, always the classiest person in the room. Her published obituary is below, the hardest-fastest thing I’ve ever written. I’ve also pdf’ed the Syracuse.com guest book, which closes May 12th.


Before my thesis dinner, May 14, 2005

Razbari Sumthing gig, June 2, 2006

Joanne C. Allis, 83, of Syracuse, beloved sister, mother, and “yia yia” to her grandsons and many who knew her, passed away on Wednesday. A life-long resident of Syracuse, she retired after 30 years as an administrative assistant from the Department of Social Services, was a volunteer for Meals-On-Wheels, and worked at Taylor Copy Services up to the beginning of this month.

A life-long member of St. Sophia Greek Orthodox Church, she was a Sunday School Teacher, member and former president of The Philoptochos Society, a member of The Daughters of Penelope, and a member of the Board of Directors for the Syracuse Ahepa House.

She is survived by are her brothers and sisters-in-law Olympia (DeWitt), Robert (Syracuse), Gus and Claudia (Jamesville), and George and Elaine (North Syracuse) Constas and their families; her sons and daughters-in-law John and Maria of Jamesville and Christopher and Cynthia of Liverpool; four grandsons, Christopher of Los Angeles, Dr. Damian and Gregory of Syracuse, and Nicholas of Liverpool, and many, many cousins, godchildren, nieces and nephews. She was predeceased by her husband George Allis in 1970, sister-in-law Jean in 2003 and brother Nicholas Constas in 1991.

Funeral Services will be at 10 a.m. on Saturday, April 14, at St. Sophia Greek Orthodox Church. Burial will be at Oakwood Morningside Cemetery in Syracuse. Calling hours are Friday from 3 to 7 p.m. at Greenleaf Funeral Home Inc. 503 W. Onondaga St. Syracuse.

Contributions to be made to St. Sophia Greek Orthodox Church.

Syracuse obituary (pdf), Message Board 1 (pdf), Message Board 2 (pdf)

www.google.com/maps?num=100&hl=en&safe=off&client=firefox-a&rls=org.mozilla:en-US:unofficial&hs=em1&q=taylor+copy
www.google.com/maps?num=100&hl=en&safe=off&client=firefox-a&rls=org.mozilla:en-US:unofficial&hs=Qp1&q=greenleaf
www.google.com/maps?num=100&hl=en&safe=off&client=firefox-a&rls=org.mozilla:en-US:unofficial&q=ahepa
en.wikipedia.org/wiki/Faith,_Hope,_and_Charity
www.ongov.net/DSS/adult_services.html
www.myspace.com/djrazorsharp
www.shadesofoakwood.com
www.somewhereville.com
www.christopherallis.com
www.philoptochos.org
www.syracuse.ny.us
www.stsophias.org
www.mowaa.org
www.goarch.org
www.ahepa.org

Assignment Of The Lowest-Lying THz Absorption Signatures In Biotin And Lactose Monohydrate By Solid-State Density Functional Theory

Wednesday, April 18th, 2007

In press, available from Chemical Physics Letters. This is a first foray into the very-low frequency terahertz region (3 to 30 cm-1) for the study of hydrogen-bonded molecular solids in collaboration with J. Bjarnason and E. Brown in the Electrical and Computer Engineering Department of the University of California, Santa Barbara. The analysis of these systems is generally more complicated because the extensive hydrogen bonding networks strongly connect individual molecules, which leads to a blurring of the line between internal (intramolecular) and external (crystal cell, intermolecular) vibrational modes. It is clear from these studies that the crystal cell strongly influences the predicted positions of both the molecular vibrations and the molecular conformations. In the case of lactose, the molecule exists in a configuration that breaks an important intramolecular hydrogen bonding interaction (blue arrow in the figure) in the crystal cell of its monohydrate form. For biotin, the conformation of the molecule in its crystal is NOT the conformation of the solution-phase molecule, with the many neighboring hydrogen bonding interactions forcing the single molecule to conform to its elongated (extended) hydrocarbon tail structure. In both cases, isolated-molecule computational studies would lead to incorrect assignments for the simple reason that the molecules are conformationally different in their solid-state forms.

biotin lactose

D.G. Allis, A.M. Fedor, T.M. Korter, J.E. Bjarnason,* and E.R. Brown*

Abstract: The narrow terahertz (THz) features in crystalline biotin and lactose monohydrate observed in recent experimental studies are considered by solid-state density functional theory (DFT) calculations. The lowest-frequency THz features in both solid-state biotin and lactose monohydrate are assigned to external hindered rotational modes and not to the lowest-frequency internal modes predicted from isolated molecule calculations. The motions of the molecules associated with these narrow THz features and the interactions between molecules in the hydrogen-bonded networks of these molecular crystals are discussed, and comparisons are made to similar studies on molecular crystals not exhibiting strong intermolecular interactions.

Keywords: Biotin, lactose monohydrate, terahertz spectroscopy, solid-state density functional theory

www.elsevier.com/…/505707/description?navopenmenu=-2
www.ece.ucsb.edu/Faculty/Brown/default.html
en.wikipedia.org/wiki/Terahertz_radiation
en.wikipedia.org/wiki/Lactose
en.wikipedia.org/wiki/Biotin
www.ece.ucsb.edu
www.ucsb.edu

Syracuse Astronomical Society President’s Message for April, 2007

Wednesday, April 18th, 2007

A repost of the original at the Syracuse Astronomical Society website.

Observatory Opening And Messier Mini-thon

It is that time of year again! When the snow is melted enough that the Darling Hill grounds become a soup of mud and leaves just thick enough for a vehicle to make it up the driveway and into a parking spot (angled down back towards the driveway, of course). The opening, slated for this Friday (20) or Saturday (21, weather date) will also be the official make-up for the Messier Marathon in mid-March that was snowed-out. Regretfully, I post this from Utah, where steep mountains obstruct everything but the zenith, and will have to review the Observatory log at our next meeting to see what I missed.

MOST Space Science Series Recap

“Politics politics politics politics politics!” – Mel Brooks

The final MOST Space Science Series lecture provided a very insightful look into the differences between science, scientists, and truth in general (an appropriately broad range given the lecture content). After a brief history of our Solar System and how we have classified it since Galileo, the discussion turned to the recent demotion of Pluto and the original attempt to either classify 12 objects in the solar system as planets or, at the very least, grandfather Pluto into the classification scheme to keep our current 9 planet count.

The foundation of Prof. Margot’s lecture can be found at the “What Is A Planet?” page at his own website.

His discussion eventually settled into the very non-scientific aspects of the debate concerning the classification of Pluto and how the opinions of people added to the tension of the final decision. Do we hold on to the standard model we’ve all grown up with because it makes people feel good? Well, we’ve certainly not fallen into that rut in the “hard sciences,” with Galileo, Kepler, Newton, Darwin, and Einstein certainly shaking the foundations of science, leaving others to come to terms with the “new math.” Ultimately, Pluto is just a solid object orbiting a star and, pending further investigation, could not care less what it is called. It is very likely that there are so many objects in orbit around the Sun that we will never have an official number. Despite blatantly political maneuvers among members of the IAU (and, to a far, far lesser extent, the efforts of save-pluto.org and its many, many ilk), the final decision was made to remove Pluto from the formal “planet” list, classifying it instead as a “dwarf planet.”

After the events of late 2006, how quickly does the scientific consensus enter the mainstream? Just to check, I asked my 11-year-old cousin Nicholas “How many planets are there.” “8,” he said, with some small fraction of a look that said “isn’t it obvious?” “Pluto’s just a secondary planet.” No surprise, it has been a whole 6 months, of course. I think all civilized people would agree. Someone will have to explain to children in a generation what that last white dot on many of our best solar system images is…


from sse.jpl.nasa.gov
Click for a larger version

ET On Meteors

The following came to us from Ed Tarney of Baldwinsville, NY regarding a March 11th light show between 8 and 8:30 pm. When we hear about meteors in the news, it is usually in the context of meteor shower announcements that happen predictably all year. We are, of course, constantly bombarded by debris from space. Any amateur astronomer or night observer with any number of days under their belt will know that a streak could appear at any moment. I suspect at least 3 or 4 trails are seen a night during SAS observing activities, with one person seeing and several others trying to spin their heads in time. One can only imagine what our ancestors must have thought was happening to the falling sky before we became aware of meteor origins.

The meteor reported by Ed must have been a real winner, as his original email included a news clip about police calls stemming from the meteor in the March 11th Edition of the Toronto Star. It’s also worth being reminded that a meteor is a meteroid entering the atmosphere and burning up. A meteroid is, according to the American Heritage Dictionary, “A solid body, moving in space, that is smaller than an asteroid and at least as large as a speck of dust.”

From Ed:

The only other meteorites I have seen have been the “meteor shower” types, and they are nowhere near the brightness or color or apparent size of this one. This one was sparkling, almost iridescent green & white, with the “head” showing some substantial width (as opposed to the showers, which are mere streaks, only linear, hardly 2 dimensional at all), a bright but quickly diminishing whitish yellow tail, a solid streak of color against the sky, and a hearty “Hi Ho Silver” – oh no, not that last part! From where I was, in Radisson in Baldwinsville, it was streaking from just above Baker High School into the Seneca River at the lock. I would guess I saw it appear about 15 degrees above the horizon, just a little south of due west from my vantage point, and pass from N to S (right to left) at about a 10 degree angle. If I close my eyes & try to reconstruct it, it seems like it passed through about 30-40 degrees of the horizon, in perhaps a second, before it passed out of view. (I was just looking at a protractor & trying to recreate the scene!) I am trying to recall how the size compared to Halley’s comet from a few years ago, but unfortunately I cannot seem to construct a good comparison. I want to say this meteor was noticeably larger in apparent size, but I don’t recall many clear & studied looks at Halley’s.

I hope this is useful,

Ed Tarney
B’ville

And On A Far Heavier Note…

We mention the passing of 2006 VV2, a 2 kilometer wide asteroid that came within 2.1 million miles of hitting us (or 15 billion light years of not hitting us) on April 6th. News otherwise unnoticed, even though the asteroid was naked-eye visible. Provided no other surprises, our next great asteroid viewing is slated for 2029, when Apophis makes its first close-pass to Earth. It’s return pass, in 2036, has had the mathematicians at NASA number crunching for quite some time, as the odds of it impacting the planet have ranged from one in several hundred thousand to a mere 1 in 300. I, for one, will be making nothing larger than minimum payments starting in 2032.

Big Sky Astro Correction And Links

And now, a correction. In the “Pale Blue Dot” section of February President’s Message, I noted that the image Carl Sagan used as a base for his discussion of our place in the universe was being hosted by the Big Sky Astronomical Society in Montana (the site was dugg at digg, where I first found the Big Sky site). Lo and beholde, this organization is, in fact, the Big Sky Astronomy Club. As it happens, just North in Alberta, CA lies the REAL Big Sky Astronomical Society. Both are relatively new to the scene, with the Club forming in August 2000 and the Society forming in October 1998. My thanks for James Durbano of the Big Sky Astronomical Society for looking this far East.

Amassed Astronomy Media Part 2: Websites

Having covered a small number of astronomy podcasts in the March Message, we turn now to a list of websites.

hubblesite.org – The official website of the Hubble telescope. More likely than not, your favorite desktop background lies somewhere in the Hubble gallery. On this site you’ll also find Hubble history, technical information about the Telescope, a link to the SkyWatch podcast, and much more.

heavens-above.com – This site keeps track of the ISS, space shuttle, major satellites, and the ever-impressive Iridium satellites. The predictive power of physics never ceases to amaze. As if the website weren’t enough, they also provide a mobile service through AvantGo so you can identify what’s above anytime, anywhere (handy at Darling Hill when one can get reception).

www.spaceweather.com – My primary bookmark for checking the weather online is the ClearSkyClock (which will receive its own post at some point), which I only check to see if there’s hope for observing that night. The thorough climatologist or meteorologist knows that all weather events begin at the Sun, without which the Earth (if it were still here) would be a frozen rock with weather conditions (frozen) more predictable than those of San Diego (nice). Spaceweather.com is the site for keeping track of the Sun’s conditions, including Solar winds, sun spots, solar flares.

antwrp.gsfc.nasa.gov/apod/astropix.html – Astronomy Picture of the Day. Robert Nemiroff and Jerry Bonnell have done the work for you! The pictures are as beautiful as the descriptions and exhaustive web links are informative.

www.spaceref.com – A pro-space science news service that manages to collect just about every space news story that hits any internet wire. Topics range from NASA policy to major astronomical events to Space Science Research, all in an easily scannable interface.

Amateur Observers Society of New York AOS Starfest 2007

Our own Mike Brady forwarded us the following:

The Amateur Observers Society of New York is proud to announce the AOS Starfest 2007.

Date; June 15-17, 2007

This event will be hosted at the Stone Tavern Farm, under the exceptionally dark skies of Delaware Co. NY. The Stone Tavern Farm is a 400 acre working farm located near the Catskill town of Roxbury, NY This site is within a 3 to 4 hour drive of most of our members located on Long Island. Click HERE for directions.

Facilities on the farm include a Bunk House and a wood floored “MASH” style tent with bunks, a large Pavilion with enough seating for all the attendees, comfortable and private bath & showers, and a large grassy field that we can use to set our telescopes on. In addition there is a 12000 sq. ft indoor arena that can be used in the event of inclement weather. The farm also has enough space for camping, which is included free with your registration.

This is a family friendly Starparty with activities for both kids and adults planned throughout the day.

“Barlow Bob” will be bringing his incomparable H-Alpha telescope and “Tri-Spectra” Solar telescope, and along with others, be providing solar observing for attendees.

We have two of the top speakers in the astronomical community coming to give presentations at the AOS STARFEST; Bob Berman, writer for Astronomy Magazine, and author of several books, most recently “Cosmic Adventure: A Renegade Astronomer’s Guide To Our World And Beyond”, and Long Island’s own Phil Harrington, Astronomy professor, contributing editor for Astronomy magazine, and author of many books like “StarWare”, “StarWatch,” and his latest book, “The Illustrated Timeline of the Universe”. Phil will be also be staying with us Saturday night to observe, and help us celebrate our very first Starparty!

Friday night there is a free “Pizza Party” to welcome attendees, and meals will be available to purchase Saturday, including breakfast, lunch and dinner. Saturday Dinner we’re having a special “Star-B-Que” featuring the best of the Stone Tavern Farms “farm fresh” food.

You get camping, the outstanding speakers, activities, solar observing, and free HOT refreshments all night Friday & Saturday night with your $45 registration fee. Also for families, all children 14 and under are free!

As you can see we’ve tried to think of everything we can to make this the best Starparty you’ve ever been to. Attendence is limited to the first 100 adults, so please register soon before all the spaces are taken.

Whether this is your first Starparty or 50th, it’s going to be an event that is not to be missed!

Our website is; www.aosny.org

For more info email Geoff Cintron; Geoffcin@aol.com

Space is the place,
Damian Allis, Ph.D.
sas@somewhereville.com

Links Used Above (Subject To Web Changes)

www.syracuse-astro.org/observatory.html
www.seds.org/messier/xtra/marathon/marathon.html
www.syracuse-astro.org/index_march2007.html
en.wikipedia.org/wiki/Zenith
www.imdb.com/name/nm0000316
www.most.org
en.wikipedia.org/wiki/Solar_system
en.wikipedia.org/wiki/Galileo
en.wikipedia.org/wiki/Pluto
www.astro.cornell.edu/~jlm
www.astro.cornell.edu/~jlm/planet.html
en.wikipedia.org/wiki/Kepler
en.wikipedia.org/wiki/Isaac_newton
en.wikipedia.org/wiki/Charles_Darwin
en.wikipedia.org/wiki/Albert_einstein
www.iau.org
www.save-pluto.org
en.wikipedia.org/wiki/Planet
en.wikipedia.org/wiki/Dwarf_planet
en.wikipedia.org/wiki/Baldwinsville,_New_York
en.wikipedia.org/wiki/Meteor_shower
www.thestar.com/default
en.wikipedia.org/wiki/Meteor#Meteor
en.wikipedia.org/wiki/Meteor#Meteoroid
dictionary.reference.com/search?q=meteoroid&x=0&y=0
dictionary.reference.com/search?q=meteor&x=0&y=0
news.softpedia.com/news/Huge-Asteroid-Missed-Earth…shtml
neo.jpl.nasa.gov/cgi-bin/db?name=2006%20VV2
en.wikipedia.org/wiki/99942_Apophis
www.nasa.gov
www.syracuse-astro.org/index_february2007.html
www.carlsagan.com
www.digg.com
www.bigskyastroclub.org
www.alberta-canada.com
www.bigsky.ab.ca
hubblesite.org
hubblesite.org/explore_astronomy/skywatch
heavens-above.com
www.iridium.com
www.avantgo.com
www.spaceweather.com
www.clearskyclock.com
antwrp.gsfc.nasa.gov/apod/astropix.htm
www.spaceref.com
www.aosny.org

Obligatory


T R P Nanosys


Syracuse Astro


Ubuntu 4 Nano


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