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Open source nanotechnology CAD with distributed computing

News from Howard Lovy, now working with Nanorex:

I wanted to make sure you saw this news item about molecular simulation
software maker Nanorex acquiring Nano-Hive, developer of a powerful open
source tool that speeds up nanoscale simulation through distributed
computing. Together, Nanorex’s NanoEngineer-1 and the renamed NanoHive-1 are
going to produce faster, better-quality animations.

Researchers and instructors working with current simulation technologies can
tell you how frustrating it is to wait hours or days for a nanoscale
simulation program to perform all the necessary calculations. Nanorex’s
acquisition of NanoHive promises to turbo-charge that process.

The news release…can be found at this URL:
http://www.nanoengineer-1.com/mambo/index.php?option=com_content&task=view&id=122&Itemid=1

If you want some illustrations you won’t find in the press release, take a look at this link
http://www.nanoengineer-1.com/mambo/index.php?option=com_content&task=view&id=101&Itemid=69

This is the result of work done by Nanorex CEO Mark Sims earlier this year.
Sims used NanoHive-1 to give NanoEngineer-1 the ability to visualize the
electrostatic potential (ESP) of molecular devices, and then calculated the
ESP of a small nanomechanical bearing. To understand a molecular device’s
ESP is to know its potential to “push” or “pull” other charged objects. But
to model ESP on such a tiny scale takes quantum mechanical calculations that
NanoEngineer-1 could not perform without the help of NanoHive-1.

Another example of the kind of power unleashed by NanoHive-1 can be found in
this video:
http://www.nanoengineer-1.com/nh1/videos/dc-cnt1.mpg

This one was produced by Nano-Hive founder Brian Helfrich last year as a
demonstration of distributed computing mechanisms. It simulates three carbon
nanotubes being pushed on by a diamondoid carbon “knife.” Did the knife cut
through the tough tubes? Watch the simulation and find out.

This combined software will be open source, although I don’t think it has been
released yet. —Christine
UPDATE: bad URLs have been fixed, sorry. –C

9 Responses to “Open source nanotechnology CAD with distributed computing”

  1. NanoEnthusiast Says:

    Wow, this is all very exciting news. I wonder if any parts already simulated via NanoEngineer-1 will prove to be unstable in NanoHive-1. Also, it was my understanding that NanoEngineer-1 was so be released as open-source, but being a new company I always thought they could reserve the right to change their minds if need be to raise money. NanoHive-1 to the best of my knowledge is already open-source, I don’t know if the license is the GPL or some other “viral” license. If so, I wonder what potential issues might arise for Nanorex by mixing their codebases.

    I would also like to know if anybody has a link to a definitive list of all the force field approximations available, with their respective strengths and weaknesses. Particularly I am curious as to how NanoHive’s approach stacks up to say, DFT. Is it DFT or something else? I think in this case the source code absolutely needs to be open to convince skeptics of any findings that arise via these packages.

    p.s. Christine the links do not work for me; I either get a 404, or the message “You are not authorized to view this resource.
    You need to login.”

  2. Tim McDonald Says:

    Neither of the links with illustrations seems to be working.

  3. Christine Peterson Says:

    I have sent an inquiry to Howard Lovy regarding the graphics URLs not working. –Christine

  4. Brian Helfrich Says:

    Here is a link to the Physical Interactions implemented so far in NanoHive-1 (as definitive a list of its MD and QM approximations as any): http://www.nanoengineer-1.com/nh1/index.php?option=com_staticxt&staticfile=bodyframe/PluginReference.html#PluginReference.PIPs

    Sorry for the crazy-long URL. BTW, the links in the article above have extraneous characters in the URLs (extra “”s), that’s why they don’t work.

    Basically, NanoHive-1 (NH1) is not limited to any particular simulation methodology. It is capable of assimilating methodologies by wrapping them as plugins. We’ve focused on open source methodologies so that we can easily redistribute them with NH1.

  5. Christine Peterson Says:

    Bad URLs have been fixed, sorry. –C

  6. John Novak Says:

    Maybe you could ask them when the software is going to be released to the public.
    One hates to sound like a whiny brat, but I’ve been looking forward to toying with the software for a good long while, now.

  7. Novak Says:

    (Hah. Christiine, the point of my earlier private e-mail was to not have the previous note go through moderation and be made public. Oh well.)

    I should note that the software has been open sourced and released for public use. I myself never saw a notice of its release. Moreover, the news page indicates it was released late last year, and I would have sworn that when I looked, that release was for select individuals and institutions only.

    However, I was able to download the software to my laptop last night, and make it function at least enough to run through the example simulations. I haven’t even begun to dig down into the software far enough to make my own simulations of anything, either useful or meaningless.

    I also suspect that this is not going to be laptop-friendly software, simply in terms of sheer processing requirements. A short simulation of a nanotube doing nothing but undergoing thermal vibration took about a minute on a fairly high-end laptop. One idly wonders, if the Sony PS3 is going to have a Folding@home application, how hard it would be to run nanohive simulations on it….

  8. Brian Helfrich Says:

    Running NanoHive-1 simulations on a Sony PS3 via an @home-style mechanism is on our list. In fact we’ve already got the NanoHive@Home project running (www.nanohive-1.com/atHome) in beta with open enrollment beginning this month. The Sony PS3 client will come after the usual Windows, Mac OS X, Linux, and Solaris clients.

    So stay tuned,
    –Brian.

  9. Kuber Says:

    Hi guys, I need to download nanoengineer-1 maybe you know where can i find this? I’ve checked main nanorex site, all torrents and so on.. nothing in the web:/
    Please help …

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