Machine Phase

Been a while

2012-01-12T13:10:00.000-08:00

Quick MD simulation done in SIESTA and visualized in VMD. I have a back log of stuff to post, but I might move on to the new stuff.

pillared graphene

2010-09-09T06:41:00.000-07:00

Small molecular dynamics simulation carried out in GROMACS and visualized in Blender as part of a larger project I'm still working on.

Rolling my own part two

2010-05-29T22:27:00.001-07:00

The version numbers could be a little nuts here for a while. I probably won't post anything else until they get into double digits as I can't imagine this is interesting to anyone but me. The major improvement here is the ability to distinguish different atoms in the input file and draw them accordingly. The radii still need a little adjusting.

Rolling my own

2010-05-25T20:18:00.001-07:00

Reading in xyz coordinates and rendering them in PyOpenGl

I figure by the time I'm done it will be best-in-class, export controlled and retail for a couple hundred thousand dollars. You saw it here first.

Oh yeah, I can rotate and zoom the camera using the mouse. Jealous?

Scripting atom color changes as a function of velocity in Blender

2010-05-24T16:15:00.000-07:00

Atom colors change as a function of their velocity using the basic how-hard-is-it-raining convention, slower is blue, white is pouring. RGB values for individual atoms were calculated from molecular dynamics data and imported as object color IPO curves. For this I expanded Miron's import IPO script to include three more curves, one for each RGB.

I plan to develop this more to represent temperatures.

Diamond Bearing

2010-05-19T19:31:00.000-07:00

I obviously have a small glitch in importing these models from NE1 to Blender in that I lose a single atom. I bet it is either the first or last.

For a beautiful version of the same structure check out Euplotes'
He has lots of other good stuff too.

Atomistic Large Bearing: dynamics performed in NanoEngineer-1, vizualized in Blender

2010-05-09T18:15:00.000-07:00

The initial visualization of 550 frames, skipping two simulation steps at 50f/s, motion blur set 0.5 averaged over 5 frames. This took about 20 hours to render on a basic core 2 duo notebook.

9 frames, skipping 100 frames looped, motion blur set to 5 averaged over 16 frames. About 20 minutes per frame to render.

C60 fullerene melting

2010-05-03T15:31:00.000-07:00

Atomistic Small Bearing: dynamics performed in NanoEngineer-1, visualized in Blender

2010-04-28T16:33:00.000-07:00

The astute viewer will notice two things first:
1-I still can not frame a shot for shit.
2-The back side of the rotor is missing a hydrogen atom

Well, these are still more or less movies where I am more concerned with getting different things to work than I am with cinematography and such. Maybe next time I'll throw in some long parallel walls to frame the action. Also any long time readers of this site will know that I have had my problems with hydrogen in the past, but, all in all, things have come a long way from the last time I posted anything about the famous small bearing first proposed by K. Eric Drexler back in 94, I believe.

A little about how I did it:

NE1 will save simulations in two ways, either as a binary file (which I can't do much with right now expect turn into gibberish) and a series of POV-Ray files, one for each time step. So you are probably thinking "why not just stitch the povs together, adjust the lighting, camera, materials, whatever and call it a day?" I know POV-Ray is great, and I'm pretty sure it is all Pixar uses, but I'm just a gui type of guy I guess. So I have written a Frankenstein's Monster of a script that will read in a series of povs and create atom trajectory files, one for each atom. Normally it would then just be a matter of using Miron Cuperman's import_ipo_script to connect the atom trajectory files with a PDB model which NE1 exports and Miron has also provided a very fast importer for.

The only problem here is NE1 writes the atoms in a different order in povs and PDBs. It is very important that the right trajectory matches up with the right atom. So I added another section (subroutine?) to my script that will read in the first pov ray file and create a bona fide .xyz chemical format file. I went with the .xyz because it is the simplest format I know of. Then all you have to do is run it through Open Babel to convert it into a PDB file that has the same atom order as the pov files and can be imported into Blender. That's all there is to it.

I fully intend to clean it up, rewrite parts so they're not embarrassing (even for me) but if you can't wait, you can get a copy of my ne12blendXXX.py script. The XXX stands for a couple of things. Guess!

C60 and C240 collision at 300eV

2010-04-27T15:58:00.000-07:00

Related:

C60 and C240 collision at 10eV

C60 and C240 collision at 10eV

2010-04-23T13:31:00.000-07:00

Something a little more than just jiggling

This would not have been possible without the help of Miron Cuperman and his coding skills. Miron has written a nice python script to automate the process of importing csv data in Blender to animate objects. You can get a copy here

I will be the first to admit I am far from a Blender pro, but I hope to be able to show off some of the features that other visualizers don't have or do in a way I find cumbersome. This episode: Camera Tracking

More interesting stuff is on the way too.

MTF

fullerene capsule: molecular dynamics performed in GROMACS, visualized in Blender

2010-04-13T19:57:00.000-07:00

and one more, why not?

Can you put it in a wine glass?

2010-04-11T12:20:00.000-07:00

Sure

C60 fullerene- molecular dynamics performed in GROMACS, visualization done in Blender

2010-04-10T19:30:00.000-07:00

visualizing GROMACS simulations with Blender (teaser)

2010-04-08T18:16:00.001-07:00

This was a proof of concept test, so I'm not going into the details of how to do it right now. There are also a couple of steps I still need to automate to make this a practical solution; that's why there is only five atoms in this one. However I'm optimistic those can be worked out easy enough. After that I'll upload a turn-key script of sorts that will give you the features and flexibility of Blender to render GROMACS molecular dynamics simulations.

Related:
Atom Trajectories from GROMACS
Carbon Nanotube Animated in Blender
Molecular Rotor Animated in Blender

MTF

Carbon Nanotube Manipulator Concept

2010-03-13T17:16:00.000-08:00

Branched carbon nanotubes have been in the literature for a while now* and make up the business end of this manipulator concept. The idea was inspired by a wire grasper out in the garage. The macro-scale version looks something like this:

The way I picture the nanotube version working is a little different in that instead of the grasping fingers retracting in, the cnt version would use electrostatic forces to extend the outer carbon nanotubes over the branched tube. This lowers the chance that the fingers slip off whatever is being grasped. This would also require the inner-most tube to be anchored.

MTF

*Branched carbon nanotube junctions predicted by computational
nanotechnology and fabricated through nanowelding
,D. Srivastava, M. Menon and P.M. Ajayan,
Journal of Nanoparticle Research 5: 395–400, 2003.

getting trusted with ever more expensive equipment...

2009-12-18T17:58:00.000-08:00

...this time a SEM. I finished up my qualifications for "limited supervision" use of a SEM at Michigan State Thursday. Basically I can use it as long as there is a guru at least in the building, so normal business hours. I had planned to wrap this up a couple of months ago, but right after my second training session the scope went down and then a slew of scheduling problems. The down time had nothing to do with me, despite the rumors, but something about turning off the air conditioning for season.

BSD mode

Now to sweet talk my way on to the TEM and AFMs

getting atom trajectory files from GROMACS

2009-12-18T09:27:00.000-08:00

What I mean by atom trajectories is the xyz coordinates of each atom at each time step. I could not find any program in the gmx package that did this, so I wrote my own. You can get it here.

From gromacs, use the trjconv program to create a series of pdb files for each time step of the simulation.

trjconv -s swnt -f traj.trr -o last.pdb -sep

swnt is the structure, traj is the trajectory file created from running a dynamics simulation and last.pdb is the name you give to the pdb series.

After running the script you get a text file for each atom the has the time and xyz coordinates:

Here is a sample output for atom 1

convert protein data bank files into Ansys nodes, key points and lines

2009-11-30T20:14:00.001-08:00

Here are two small python scripts I wrote that will read in a PDB file and output a text file to be used as input for Ansys finite element analysis. They're still kind of rough in that the input directory is hard coded, but they seem to work great at least for carbon nanotubes and other fullerenes.

convert PDB file to Ansys key points and lines

convert PDB file to Ansys nodes

To use these scripts:

1. create a protein data bank file of your structure
2. name it test.pdb and save it in a folder: C:\xyz
3. make sure you have python installed
4. and to make things easier for development and use, grab the free version of Wingware IDE 101
5. download the two scripts and open them in Wing
6. run the scripts

The output file will be in the xyz directory. To load them in Ansys: File > Read input from...

carbon nanotube NEM animated in Blender

2009-08-23T17:55:00.000-07:00

This is a version that won't be used, so I decided to post it here. I'll post a flow chart on how to visualize actual dynamics data in Blender when I get back. It has all the steps, but not all the steps are finished yet on my end. Maybe it will be a good stroy arc.

molecular rotor animation rendered in Blender

2009-08-22T23:53:00.000-07:00

I think blender can be a very useful tool for scientific visualizations, particularly with respect to visualizations of molecular dynamics simulations. There's a couple of missing steps as far as I can tell, but I'm working on them and will save that for the next post. However if you just want to make some eye candy, you can pretty much dive right in. This is a good example of something I've come to understand: modeling stuff is easy, the tricky part is making those models represent something relevant.

free stickers!

2009-08-16T19:25:00.000-07:00

I came up with this a while ago as a purposed emblem of a certain sub-culture that, if you're reading this, you may belong to. I don't want it to go to waste, and I'm not even a bumper sticker guy. Email me a mailing address, and when I get a good collection I will send them out. Or you could always make your own, but that's not really the same, is it?

molecular gear published in Nature Materials

2009-06-22T21:40:00.000-07:00

Step-by-step rotation of a molecule-gear mounted on an atomic-scale axis
C. Manzano1*,W.-H. Soe1*, H. S.Wong, F. Ample, A. Gourdon, N. Chandrasekhar and C. Joachim1,2

compared to the small bearing (disassembled) of old:

riding the rails

2009-06-13T22:05:00.000-07:00

MATLAB function to calculate the energy of double wall carbon nanotubes

2009-06-01T18:45:00.000-07:00

function [U dr dt]=DWNT(n1, m1, n2, m2)
% this function uses the chiral vectors of two carbon nanotubes as inputs
%(n1 m1)-inner & (n2 m2)-outer and returns the energy of the tube in kcal
%mol^-1 atom^-1 using an empirical equation found in
%"Double-Wall carbon nanotubes...",
%Bakalis & Zerbetto, Chemical Physics Letters 463 (2008) 139-140
%function written by Tom Moore

%define energy constants
a= 1665.51; %kcal A^6 mol^-1 atom^-1
b= -92.85; %kcal A^3 mol^-1 atom^-1
c= 2.50; %kcal A^1 mol^-1 atom^-1
d= 17.24 ; %kcal A^4 mol^-1 atom^-1
f= -58.56; %kcal A^5 mol^-1 atom^-1

%define graphene lattice constant in A
k= 2.49;

% calculate the chiral angles of both tubes in radians
t1_rad=acos((2*n1+m1)/(2*(n1^2+m1^2+n1*m1)^.5));
t2_rad=acos((2*n2+m2)/(2*(n2^2+m2^2+n2*m2)^.5));

dt=t1_rad-t2_rad %may need to do a <1 check here

% calculate the radius of both tubes
r1=(2.49*(n1^2+m1^2+n1*m1)^.5)/(2*pi);
r2=(2.49*(n2^2+m2^2+n2*m2)^.5)/(2*pi);
dr= r2-r1;

%find the energy of the tube
A= (a/dr^6)+(b/dr^3)+(c/dr);
B=sin(dt)*cos(dt);
C=(d/dr^4)+(f/dr^5);
U=A+B*C

multiwall carbon nanotube & GROMACS

2009-04-28T18:03:00.000-07:00

Force constants:

Bonds 47890 KJ/mol/nm^2
Angle 400 KJ/mol/rad^2
Dihedral 167.36 KJ/mol/rad^2

more swnts in GROMACS (back to large image files)

2009-04-28T12:18:00.001-07:00

The tubes look a lot better when simulated without the caps. There is none of that weird buckling as before. It is interesting to note that the buckling occurred along a line containing a pentagon defect in the lattice.

Single Wall Carbon Nanotubes in 4.0.3 GROMACS and Windows Vista Part 1

2009-04-21T12:25:00.000-07:00

Okay, I am starting to get results that are at least approximating what I would expect, by that I mean stays together and jiggles around. I'll get down to brass tacks and lay out how I did it and then later on talk about why I went about it this way, lessons learned, what's next, all that.

1. I used the oplsaa force field for this. This force field is not included in older versions of gmx. It already contains carbon in the atom types, so we don't have to add that. However we do have to add some cnt parameters to a couple of files. These files are all located in gromacs/top. The first file to change is ffoplsaa.n2t . We need to add a couple of carbon atoms bonded to two and three other carbon atoms. Open up the file in a text editor and add them to the bottom:

C opls_240 0 12.011 3 C 0.142 C 0.142 C 0.142

C opls_239 0 12.011 2 C 0.142 C 0.142

You can probably guess what's going on here: atom type, charge, mass, # of bonds, what they're bonded to and bond length in nm.

Here is my copy of the file: ffoplsaa.n2t

2. Next we are going to add some bond parameters to ffoplsaabon.itp. I just dropped these in at the bottom of the file where I saw other people had made some prior modifications:

; Added by TEM for CNTs

[ bondtypes ]

C C 1 0.14210 478900

[ angletypes ]

C C C 1 120.000 397.480

[ dihedraltypes ]

C C 1 0.000 167.360 1

Note there is some weirdness happening on the one side of the above tube. I'm not quite sure the dihedraltypes are correct, may need to revise that. Again here is my file: ffoplsaabon.itp

Okay, those were the changes. If you had read my previous post, don't worry about messing with the .rtp file. That was a messy fix and not necessary.

Next fire up cygwin and cd your directory to where you have you cnt pdb file. If you want a copy of my nano-capsule, here it is: swnt_capped.pdb

in cygwin, type: editconf -f swnt_capped.pdb -o swnt_capped.gro -d 2.0

This will create your .gro file with a 2.0 nm box around the tube.

next type: x2top -f swnt_capped.gro -o swnt_capped.top

This will create the topology file. The documentation says you can use a pdb file as input however I never got it to work with anything but the .gro file.

Next you need a simulation parameter file, md.mdp. Here is the one I used to get you started:
md.mdp

Put this file in your directory with your pdb, .gro and .top files. If you copy the text into a text file and save it as a text file, it usually doesn't work; copy an actual .mdp file and change the contents. So far the only thing I feel comfortable messing around with in this file is the simulation length and time step, lot going on here.

Now type: grompp -f md.mdp -c swnt_capped.gro -p swnt_capped.top -maxwarn 3

The experienced user may be interested to know that I used to have to set the maximum number of warnings to 150 to get past this...

And now: mdrun -s topol.tpr

The sim takes a couple of minutes to run through. You can then load the .gro and . trr file into VMD to view the results, make movies, whatever.

There is still more to go, need to figure out what is causing that buckling, a very knowledgeable professor has told me the potentials look too soft, bunch of stuff. If you have something to add to this, let me know.

Special thanks to Brian and Damian for putting up with the play-by-play emails, hope I'm not on the spam list now guys.

step closer to GROMACS and Carbon nanotubes, or some ramblings

2009-04-20T17:53:00.000-07:00

Okay I figured out why I was getting all the short bond errors when I ran pdb2gmx (see previous post). I came across this paragraph in the gmx wiki:

"One point that is not made clearly in the manual is how to specify the connectivity between residues. This mechanism is protein-specific, and relies on the existence in each residue of atoms with the same names, i.e. the protein backbone atoms. The [ bonds ] section in the example in section 5.6.1 of the manual defines a bond between -C and N. This refers to the C atom in the previous residue. Similarly, one might use a +N prefix to refer to the N atom in the following residue."

http://wiki.gromacs.org/index.php/.rtp_file#.rtp_Residue_Topology

This meant I never defined how the residues were connected together in my .rtp file. This explains why I got a bunch of short bond warnings and my topology file never had pairs, angles or dihedrals.

I've changed the [bonds] section of the .rtp from the cnt carbons to:

NT1 ]
[atoms]
C C 0 0

C C 0 0

[ bonds ]
C +C 0.14210 478900

However I can't be certain that adding a +C to the second C in all the bonds makes sense for all of them. I guess I need to know how you put together a large protein and then figure out how you assemble a carbon nanotube using the same basic steps...

2009-04-15T15:50:00.000-07:00

I am trying to use GROMACS (gmx) to do some molecular dynamics simulations on carbon nanotubes. Since this is not what gmx is built for, I need to do a bunch of things to get it to simulate them. This is also, pretty much, my first time using gmx. Please note that there are a few missing pieces with the following, in that it WON'T allow you to simulate carbon nanotubes but instead create a pretty tube that dissociates/was never together in the first place/blows up. I will write a full, accurate, tutorial once all the kinks have been worked out. I am posting this here in the hope of finding some help working out those kinks, or maybe giving a couple of chuckles to those that have this down cold <-I don't think there are many though.

PART I

1. got a pdb file of a small carbon nanotube and made each atom a residue with a unique name, for example:
ATOM 4 C NT1 1 2.624 3.131 -6.155 1.00 0.00
ATOM 5 C NT2 1 2.043 3.538 -7.386 1.00 0.00
ATOM 6 C NT3 1 0.707 4.023 -7.386 1.00 0.00

Here is the pdb file of the test specimen. This is something I will automate if it turns out there's no better way. I'll post the script too.

2. added carbon to encadv's atom type file, ffencadv.ATP

C 12.011 ; cnt carbon

3. added the following to encadv's include topology file, ffencadvbon.ITP I got this information from Christopher Stiles' site. It is rare to find such good instructions for something like this. However these are for a previous version of gmx, and you quickly run into problems when trying to follow it for 4.0. This is what set me on my own course to trying to solve this problem; without Christopher's site though, I would not have even known where to begin with tubes.

[ bondtypes ]
; i j func b0 kb
C C 1 0.14210 478900

[ angletypes ]
; i j k func th0 cth
C C C 1 120.000 397.480

[dihedraltypes ]
; Encad proper dihedrals. Note that there is a difference pf
; sign in the cosine definition between Gromacs and Encad. All angle values
; here are thus offset 180 degrees.
; i l func q0 cq
C C C C 1 0.000 167.360 1

4. I added carbon to ffencadvnb.ITP. Right now I don't have a reason why I added it, and if these are non-bonded parameters, then I'm thinking it shouldn't be there?

name at.num mass charge ptype sigma epsilon
C 6 12.011 0.0 A 3.84423e-01 3.08863e-01

5. Created ffencadv.N2T using information from Christopher Stiles' site

6. Updated encadv's residue topology database by adding a residue for each atom in the tube. This will be a problem for large tubes, but I can automate the process too unless better ways are to be found. Here is an example for the first residue:

[ NT1 ]
[atoms]
C C 0 0

C C 0 0

[ bonds ]
C C 0.14210 478900

[angles]
C C C 120.000 397.480

Here is the file ffencadv.RTP

Ok I think that is all the changes to gmx files I made.

PART II

1. fired up gmx in cygwin and from the prompt:

pdb2gmx -f swnt.pdb -o swnt.gro -p swnt.top

The console print can be seen here. Notice all the warnings about the short bonds? I originally thought these were from shifting the columns in the pdb file when I renamed the residues, but I realigned them with a PDB spec and still get the warnings. I think whatever is causing this could be a major problem.

swnt.gro swnt.top posre.itp

It looks like whatever is wrong is most likely in the above. I'm going to leave it there for now until I know all that's correct.

GROMACS basics: running through the demo

2009-04-11T13:08:00.001-07:00

I need to update my previous post on how to install gromacs (gmx). There is one more package you need to install with cygwin: tcsh

Apparently this is required to run csh scripts, which you need to do. If you have already installed cygwin, you can add the package to it by running the setup again and selecting the package. If you want to know what packages you have installed, you can use: cygcheck -cd

Now, there is a built in demonstration script that comes with gmx. It is located in:

[your path]/gromacs/tutor/gmxdemo (as you are about to see my path is rather redicioulous)

1. fire up cygwin
2 change your directory to gmxdemo:
cd c:cygwin/usr/local/gromacs/share/gromacs/tutor/gmxdemo

3. after you have the tcsh package installed, all you have to do is type:

./demo

This should start the demo and you'll get:

-----------------------------------------------------------------

-----------------------------------------------------------------

Welcome to the GROMACS demo.

This is a script that takes about 10 min to run.

In this demo we will demonstrate how to simulate Molecular

Dynamics (MD) using the GROMACS software package.

The demo will perform a complete molecular dynamics (MD) simulation

of a small peptide in water. The only input file we need to do this

is a pdb file of a small peptide.

If you have any problems or remarks with respect to this demonstration,

please mail to: gromacs@gromacs.org , or check the resources on

our website http://www.gromacs.org .

-----------------------------------------------------------------

-----------------------------------------------------------------

Press

Then just follow the instructions, press enter when it says, pull on your beard every couple of seconds, hoping it doesn't choke again.

When the demo is finished, it'll ask you to start another program to view the results. I didn't. I used VMD to look at and make the above animation. And as you can tell there was a little help from videomach. There are lots of other programs to do this, just trying some thing new.

Once you have VMD installed:

1. From the main console: file>new molecule

2. load cpeptide_after_md.gro

3. in the main console, select cpeptide_after_md and file>load data into molecule

4. load cpeptide_md.trr this is the gmx trajectory file

5. use the play bar at the bottom of main to view the results.

MTF

How to install GROMACS on windows vista 64

2009-04-08T20:17:00.000-07:00

1. Download cygwin from http://www.cygwin.com/
a. click on the link to "install from internet" and run the installer
b. when you get the dialog that asks you what packages to install expand and select "gdn" "gdb" and "make"
c. follow the rest of the installation instructions

EDIT: this website has a pictorial guide to install the packages with cygwin. I forgot to mention they are all under Developer, so expand that first.

EDIT: also install the tcsh package

http://www.eecg.utoronto.ca/~aamodt/ece242/cygwin.html

2. Next you are going to need the GROMACS source code. You can get it here.
a. download and save the file someplace handy

3. Next you need FFTW. There are pre-compiled dlls for Windows, but I would recommend not using them unless you know how to set the path variables. The easiest way is to grab fftw-3.2.1.tar.gz . Again, save this someplace handy.

4. create a folder someplace (C:\FFTW) and extract FFTW to it.

5. start cygwin and change the directory to your FFTW folder: cd c:\fftw

6. type: ./configure --enable-threads --enable-sse --enable-float

7. then: make

8. then: make install

9. now create a folder for gromacs (C:\gromacs) and extract the distribution there. There should be a few folders like admin, src, etc.

10. in the cygwin console, change your directory to the gromacs folder: cd c:\gromacs

11. type: ./configure --enable-shared LDFLAGS='-L/usr/local/lib'

12. then: make (this took a couple of hours to run through)

13. then: make install

14. make links

15. make clean

when you get your prompt back in cygwin (or from a fresh session change your directory to c:\gromacs) type: luck

to test if you have access to gromacs. You should get something like:

gcq#93: "Pretend That You're Hercule Poirot" (TeX)

Also note I really haven't tested anything else yet, so this could all end up to be bogus. However if you're not really a computer guy, all bringing your ibook to dinner "in case you need to compile something" like me, then you may find this a good start. I'll update as necessary.

P.S. I like 7-zip for all my extracting needs. Let me know of any problems or mistakes with the above.

DFT optimization of adamantane minus bridgehead hydrogens

2009-03-14T16:30:00.000-07:00

! ================================================================
! Input file for PCGamess
! ================================================================
$CONTRL RUNTYP=Optimize $END
$CONTRL SCFTYP=RHF $END
$CONTRL ICHARG=-3 MULT=1 $END
$BASIS GBASIS=N31 NGAUSS=6 $END
$DATA
Molecule specification
C1
C 6.000000 -0.567000 2.956000 0.000000
H 1.000000 -0.679000 4.032000 0.001000
C 6.000000 0.897000 2.591000 -0.331000
H 1.000000 1.154000 2.981000 -1.307000
H 1.000000 1.553000 3.021000 0.414000
C 6.000000 -0.933000 2.399000 1.392000
H 1.000000 -0.277000 2.829000 2.137000
H 1.000000 -1.959000 2.654000 1.625000
C 6.000000 -1.503000 2.342000 -1.063000
H 1.000000 -2.529000 2.597000 -0.831000
H 1.000000 -1.246000 2.732000 -2.039000
C 6.000000 -0.773000 0.860000 1.391000
C 6.000000 1.057000 1.053000 -0.333000
C 6.000000 -1.343000 0.804000 -1.065000
C 6.000000 -1.711000 0.246000 0.328000
H 1.000000 -1.599000 -0.830000 0.326000
H 1.000000 -2.736000 0.501000 0.560000
C 6.000000 0.691000 0.495000 1.060000
H 1.000000 0.803000 -0.581000 1.060000
H 1.000000 1.347000 0.925000 1.806000
C 6.000000 0.121000 0.438000 -1.397000
H 1.000000 0.377000 0.829000 -2.373000
H 1.000000 0.232000 -0.638000 -1.398000
$END

Images created with Gabedit & POV-Ray
A.R. ALLOUCHE, Gabedit is a free Graphical User Interface for computational chemistry packages. It is available from http://gabedit.sourceforge.net/

http://www.povray.org/

Calculations with PCGAMESS, B3LYP/6-31G
Alex A. Granovsky, PC GAMESS/Firefly version 7.1.F, http://classic.chem.msu.su/gran/gamess/index.html

Carbon Nanotube Planetary Gear

2009-02-26T16:15:00.000-08:00

Might try for a simulation, see if the old gears still crank

modeling Pillared Graphene for hydrogen storage

2008-11-28T05:21:00.000-08:00

Pillared Graphene: A New 3-D Network Nanostructure for Enhanced Hydrogen Storage Georgios K. Dimitrakakis, Emmanuel Tylianakis and George E. Froudakis

This looked like something interesting to model:

again click the picture for a larger version

C240-nanobud size exclusion chromatography of diamondoids

2008-10-25T07:31:00.000-07:00

Sounds like a journal title; a chance candidate for some intensive molecular dynamics studies? The idea is these C240-nanobuds act as adamantane traps. The smaller molecules take a whole bunch of detours into these traps while the penta-adamantanes are too large to enter; they come out first on the other side.

It just might look something like this:

carbon nanotube and diamondoid turbine

2008-10-17T15:58:00.001-07:00

What the hell, for old time sake I guess, want to see if I still have it.

I used to build Tesla-coils back in high school. It was while researching these I learned of Tesla's bladeless turbine. This is an extension of that to a degree. The two inner disks are based on Damian's low friction cnt bearing. In short, Telsa's turbine uses high pressure gas sprayed on the edge of the disks. Friction between the gas and the disks causes them to turn. I can't use that here because there would be no friction to speak of. Instead I was thinking of replacing the macro-scale friction with nano-scale electrostatic forces. Since the outside of the disks are hydrogenated, I'm assuming they have a large positive charge there. Perhaps spraying a stream of negativly charged particles between them would do much the same thing as viscosity in Tesla's.

possible reaction for attaching adamantane to 5 prime end of DNA

2008-10-01T14:10:00.000-07:00

So don't get me confused with ANY kind of chemist, but I've put together a nice little reaction here for attaching adamantane to a strand of DNA. And I apologize for not providing the usual sexy pictures (I wrote sexy pictures to try to increase my google rank. I totally got that idea from Damian who used "ecstasy" as a keyword in a post<- see what I did there?), but I understand that the above representation is closer to what shows up in journals, not that I'm too worried about that.

and thanks for the comments, Guy. Thoughts on this?

What's the next step? Do some ab initio calculations to try and determine positive reactivity?

MTF

more with HyperChem adamantane and nucleic acids

2008-09-20T15:11:00.000-07:00

I figured I better post more right away or else my signature MTF could suffer a credibility hit. Here is a POV-Ray trace of an adamantane molecule bonded to the 3' end of a short piece of ssDNA. I have been wondering about the wet chemistry necessary to pull something like this off, connecting to the oxygen (as shown) or to the phosphorous atom. I'm waiting to hear Guy's views on the subject, but if anyone else has some ideas, I would like to hear about them too.

(click for larger pic)

MTF

modeling adamantane in Hyperchem

2008-09-20T07:39:00.000-07:00

I actually meant to post this a while ago, but you know how things go...

Anyway, armed with my copy of Molecular Modeling for Beginners ( you probably think I should have bought that a long time ago, like before I started getting interested in molecular modeling, but I always jump first and ask questions later) I started getting into some programs used at my school, like HyperChem. The first thing I modeled was formaldehyde and then jumped to adamantane. Here's the short version:

Starting small by laying down six carbon atoms for what I like to call the bottom.

connecting them together...

working my way up...

almost there...

added the hydrogen atoms by selecting Add Hydrogens. Oh man. Did I do something wrong here? I once had the bottom of a box of spaghetti give out and the result looked a lot like this. I figured I had nothing to lose, so I optimized the geometry using RHF and the 6-31G* basis set.

Ta-Da! What were you worried about?

MTF

simulating a carbon nanotube memory element in NanoHive-1

2008-08-14T14:44:00.000-07:00

Link to original simulations done by Young-Kyun Kwon

POV-Ray video of mechanosynthesis with penta-adamantane

2008-08-02T16:22:00.000-07:00

I still might re-shoot this, but it is adequate for now-that's sort of my style. It is still only a partial movie as the tool-tip abstraction is not shown, mainly because it was never accomplished without destroying the tool-tip. I'm mostly posting this to give you an idea of what a pain in the ass this process appears to be. I'm definitely in the hunt for a hybrid system that combines the performance of the diamondoid materials with the determinability of biomaterials. It's back to the Big Ten for me at the end of this month. Maybe I'll find something there. I'll keep you posted on the chase.

mechanosynthesis with penta-adamantane

2008-07-25T18:35:00.000-07:00

On the left is adamantane with four hydrogen atoms abstracted. Previous simulations gave reason to suspect it would fail in mechanosynthesis due to internal cyclization. However I have misplaced those results. In order to overcome this problem a larger building block was chosen, penta-adamantane, rendered on the right also with four hydrogen atoms abstracted. I chose this because it has a similar shape as adamantane, and my collaborators decided we could run with it.

Here is a HD rendering of the system I built in the NanoHive-1 simulator:

The basic idea is a penta-adamantane block is attached to the tooltip by a single covalent bond. The tooltip drops the block into place where it forms three covalent bonds on the workspace. As the tooptip retracts, these bonds hold the block to the surface as the tooltip bond breaks.

Here is a close up of the system in the NanoHive-1 simulator with lines showing where the bonding is to take place:

I've worked out the bumps that were preventing me from making a full POV-Ray movie of this run. I intend to post one soon. The sim is pretty neat.

Working on this with Brian and Damian was one of coolest things I've been a part of to date.

hang on- I lost the results for the adamantane mechanosynthesis run

2008-07-22T10:36:00.000-07:00

I guess I didn't back up that run. I (with lots of help from Damian and Brian) did the simulation for the setup in the previous post months ago with NanoHive-1 using the AIREBO forcefield. I thought I would post that picture and then the simulation results the next day, but I don't have the results anymore and obviously didn't check before posting that. If you are dying to know, the adamantane molecules are too small: two of the open carbon atoms bond to each other before they reach the workspace. I understand this is referred to as internal cyclization.

I might try to redo this simulation to show what happens, but I'm still holding out hope that we may get the band back together on this project, so don't want to post too much just yet.

Also I'm having some trouble making POV-Ray movies with NanoHive which are what I will want to post and not just screen captures.

Please stand by.

what's wrong with this picture?

2008-07-20T18:22:00.001-07:00

designing an original DNA Cuboctahedron

2008-05-22T11:21:00.001-07:00

I'm using the same basic techniques as the DNA dodecahedron, tetrahedron and the DNA bucky ball, but instead of starting with the three-point motif, I used the four-point. However I didn't bother making the carbon-cage template for this. I increased the number of unpaired bases in the purple loop to make the tiles more flexible. You can see there is still some final refinement necessary (like in the lower left corner there), but I'm going to let the energy minimizer do that.

AFM images of NE1 designed origami

2008-04-24T16:51:00.000-07:00

Since this was just announced at FNANO, I can drop it here. I built this DNA origami structure partially in bed using NanoEngineer-1 which also exported all the strand sequences. Those strands were sent off to IDT and Paul Rothemund was kind enough to mix them up and image them. This is the first time anything designed with NE1 was actually built.

MTF

nine hours and it doesn't even turn

2008-04-23T20:52:00.000-07:00

I guess I need to up the torque, nice diffusion though...

everyone knows that NE1 is being released on (or about) the 24th, so that wouldn't really be anything to tune in for here, huh? I agree, so it has to be something better then, right?

catching up on the pump

2008-04-23T08:32:00.000-07:00

I have a little down time here at FNANO, so I am working on the Ne pump. I finally have an optimal amount of Ne in the bottom chamber so the pump doesn't just blow up.

here it is with the pump casing hidden.

Be sure you tune in Thursday night (or Friday morning) for some major stuff.

intermission

2008-04-17T19:43:00.000-07:00

Looks like I am out of town for the next few days or so. We'll get back to this then. Thanks for the comments though.

Perry! Where have you been?

well, maybe I need a tighter tube

2008-04-16T17:19:00.000-07:00

If the sleeve is propelled by phonons from the narrow tube, I need to come up with something else. You can see the seem where I split and anchored the tube (a potential problem). Everything to the left is at 200 K and everything to the right, including the sleeve, (maybe another problem) is at 500 K. Plus since this sim is in a vacuum, I would need to ensure there is some physical contact between the two tubes. It doesn't look like there is, and maybe my temp gradient is too steep. I need a nice scale from crazy vibrations pushing to moderate vibrations pushing to minimal vibrations?

A lot of stuff to consider.

right, Jim...no cheating

2008-04-16T16:54:00.000-07:00

Jim: "....maybe you can simulate the movement using the temp setting instead of having the "computer" push it."

And thanks! (see comments last post)

I'm working on it. I am using some thermostats to create a temperature differential. From the Nanorex wiki:

"Attaches a Langevin Thermostat to a single selected atom, thereby associating the thermostat to the entire molecule of which the selected atom is a member. The user specifies the temperature (in Kelvin). The Langevin Thermostat is used to set and hold the temperature of a molecule during a simulation run..."

I have to split up the tube into two separate ones. The sim is currently running, I'll post more details later.

still got it...

2008-04-16T09:08:00.000-07:00

too much throttle before

carbon nanotube thermo motor-first try

2008-04-16T07:40:00.000-07:00

This showed up in one of my aggregators this morning. Looks like temperature changes are being used to move a cnt concentric to another one. In the linked article there is a claim of "... movements along the longer tube can be controlled with a precision of less than the diameter of an atom." Well, just sitting here reading that, I'm a little skeptical, but since I don't have the original paper I can't really be sure* However I can be 100% sure if that claim is true, it would not look anything like this:

I guess I'm a little rusty

*I really need to call the library and find out what's the deal with my online access to the journals; I haven't been able to get to them in a while.

exploring that old neon pump

2008-04-15T15:59:00.000-07:00

Remember this old gem? As far as I know there are not any simulations of it actually pumping, a sound challenge. I wrote a full tutorial on how to build it last fall, but stop short of a sim. However I feel I am particularly qualified to get this to work because I have built pumps that almost pumped, and cnts filled with gas that eventually held together.

Here's a pick with the Ne pool. We'll see how it goes, as always, but the last few months have been crazy, and the next couple of weeks are downright bonkers, so stay tuned.

MTF

planetary gear simulation

2008-04-15T08:10:00.000-07:00

It has been a while since I uploaded a huge gif file to slow everything down, so here is an oldy but goody:

dna and carbon buckyball for comparison

2008-04-01T16:21:00.000-07:00

There you go, Guy. There is a pretty substantial size difference.

planning the basement lab

2008-03-29T11:32:00.000-07:00

Here is an old, but interesting, article from Scientific American about "how you can carry out the polymerase chain reaction in your kitchen"

and for the hell of it "print your atomic force microscope"

rough DNA buckyball

2008-03-28T16:43:00.001-07:00

Not much to say, same overall techniques, but of course there's still a lot to do.

MTF

small pic of the DNA dodecahedron and what's next

2008-03-28T07:29:00.001-07:00

You know what's left, right? Yep, the DNA buckyball.

Some regular visitors to this site may be asking, "I wonder whatever happened to that big ol' super-fullerene thing he was working on..."

most of the DNA dodecahedron

2008-03-26T09:04:00.000-07:00

Here's some on the DNA dodecahedron (Mao et al. 2008):

Really, the carbon atoms with stretched bonds is definitely the way to go on these geometric projects. They make great templates. Be sure you write that down in your Tips Journal and don't say I never gave you anything.

Yeah, so I back tracked on this too and decided to pre-bend my tiles to the correct angles. I figure the energy minimization process doesn't need any unnecessary problems, except the one other one I'm going to give it...

Yep, just work my way around here...

...and here we are. Don't worry, it should shrink up in minimization...and this allows me to easily scrutinize and adjust the final tile connects.

MTF

decided to start smaller with Chengde Mao's dna polyhedra

2008-03-25T09:52:00.000-07:00

Yeah, decided to back up a little on the ambition scale, about a third of the way to be exact. This isn't finished all the way either, but enough for you to get the idea.

MTF

DNA Dodecahedron

2008-03-23T14:56:00.000-07:00

Here's the start of this. I built a wire frame out of carbon atoms first to use as a template to hang the 3-star DNA tiles on. Now I am working on a rough placement of tiles. Each of these tiles has nine unpaired bases (three on each arm) in the center to give it flexibility. The amount of flexibility can determine the type of structure that gets created.

Originally my 3-star tiles were designed to make flat 2-d arrays, so the pitch of the arms is not correct to make a dodecahedron. This will be an interesting test of NE1's energy minimization abilities.

hang on, DNA buckyballs

2008-03-14T07:39:00.000-07:00

This could potentially interfere with the nano brain project.

when it rains and all...

duroquinone nano brain system model - the start

2008-03-13T07:09:00.001-07:00

I'm sure anyone familiar with the site and access to technology news in the last few days would have probably been expecting this. I'm getting a late start on this though. I wanted to start yesterday, but wasn't feeling too hot.

Well, let's see where this goes. So far I am up to my usual MO: read through the article as fast as possible trying to contain the excitement, build something, post something, go back and worry about the details.

thanks for the initial tip, Guy.

MTF

much more from Lee Nelson

2008-03-11T17:53:00.000-07:00

http://leenelsonengineer.spaces.live.com/default.aspx

I'm bringing this out of the comments and into a post, what could be considered the first NE1 developer's site.

Thanks Lee!

still here and some original DNA stuff

2008-03-10T17:07:00.000-07:00

This evening I got an email from a gentleman that pointed out I haven't posted in a while. I haven't, but that doesn't mean I'm not working on stuff. I have an agreement not post some stuff I'm working on, for a little while anyway. However I believe this is okay, because it falls under original research, might be cutting edge or pure moonshine stuff. I don't know yet. I am taking Paul Rothemund's origami techniques and extending them to 3 dimensions, in a way I don't think anyone else is or planning. Here is a small example:

I know a guy that knows a guy that has an AFM, and the DNA for this would be in my budget. Still a few (tons of) details to work out though.

MTF

and if anyone needs a C540, let me know

2008-02-20T16:40:00.001-08:00

cnt extension optional

breaking 200,000 atoms with pieces of a shaft

2008-02-06T15:49:00.000-08:00

I went on something of a quest a few days ago to break one million atoms, that is to model a single structure made of at least 1,000,000 atoms. I started with a shaft section, a little over 50,000 atoms (the above picture is four of these sections), and then just kept extruding and fusing, but ultimately I (or NE1 failed). I did get two long shafts that together were over a half million atoms, but things started to get a little buggy when I tried to fuse them together.

I don't think NE1 has ever been tested out on this side of the envelope, so it's not that much of a surprise this started to get weird. I have a screen shot of the 500,000 atom shafts not quite drawn all the way. I intend to send it to the guy working on improving how NE1 handles those things.

I find this scale interesting, maybe because it is approaching that point were materials can start to be seen at continuous. I can easily transition from my macro-scale machining experience.

and an hour later -or- rough model inspired by Guy's post

2008-02-06T10:23:00.000-08:00

Guy just posted a link to an enzyme powered MWNT. I called dibs and produced this from the short article he linked to. I didn't have time to get the full article; that is why I am calling it a rough model.

The upper enzyme is catalase and the lower one is glucose oxidase. Both enzymes are from the PDB.

Atomistic Holliday Junction and RuvA (2)

2008-02-06T08:10:00.001-08:00

This atomistic Holliday Junction was created in alpha 9.1 of NE1. The RuvA protein was downloaded from the protein databank and rendered in VMD because QuteMol currently doesn't support the ribbon and tube displays that work so well for proteins. The two images were then combined in PaintShop, but I have an mmp file (NE1's native file format) somewhere with the two structures positioned together.

Sometime this week I intend to bring home Big Red (the tricked out Dell XPS notebook I use at work) to finish the linkages on the Superfullerene.

why artists have apprentices -or- more on the super fullerene

2008-02-01T16:59:00.000-08:00

I have been putting this off. It is tedious going, but it's going. There are more finished linkages on the other side. I estimate I'm about 20% done.

a confirmed triad

2008-01-27T18:20:00.000-08:00

Guy is posting on some great stuff he is doing with NE1 at his blog NanoGuy

The regulars here will be familiar with the insightful comments Guy has been kind enough to leave on some of my projects. I can't wait to see all the stuff he comes up with.

Anyone else doing anything with NE1?

welcome Lee Nelson

2008-01-26T09:53:00.000-08:00

This is a draft tutorial put together by Lee Nelson showing how to construct ethylene in NE1. Lee has stated there are more to follow too. I believe we have the makings of a community here.

MMTF* (I hope)

*Much More To Follow

molecular bearing, inner shaft teaser

2008-01-24T09:35:00.000-08:00

The raw footage before all the FXs are added.

adding the linkages, not pretty, but I have a system

2008-01-23T15:14:00.000-08:00

My dreams of dropping in the linkages on the super fullerene like an easy game of Tetris is coming up short. However it is working, and only ugly for a minute. I am pretty much just dropping them in and bonding accordingly. Then I have NE1 adjust the atoms to a energy minimum position, and eventually they get orientated the right way.

Now I am reaping the fruits of not organizing my model tree better; meaning that I have to randomly unhide the various parts until I find a grouping to link up. Also in the previous QuteMol pictures it looks like the ends that make up the inner shell are a little smashed. This doesn't come through as bad in NE1, nothing a day of energy minimization won't fix; that's what I'm counting on anyway, but either way, I'm in this one to win.

MTF

Video of building a DAE-junction crossover

2008-01-21T10:46:00.000-08:00

Please feel free to leave any feedback you have on how effective these videos would be at teaching you to use NE1, but keep in mind I am still learning the video editing software, and plan to add a narration at some point. I think I would prefer watching them to reading tutorials, and I know I prefer making them to writing tutorials.

Is that another sign of the times; print is dead and all?

building the linakges for the super fullerene

2008-01-20T07:22:00.000-08:00

Here I have hid everything at a junction except the 12 nitrogen atoms I'm using for a linkage. This is a must otherwise you quickly lose the ability to see what you are doing. Here is a first attempt at a linkage design that was inspired by "what's the quickest way to connect everything".

The yellow atoms are sulfur. Any feed back on this?

back early, even more on the super fullerene

2008-01-19T17:57:00.000-08:00

I had expected to be out of town until tomorrow, but ended up coming home early. It was a good little trip though; I learned a few things:

1. I prefer my own bed.

2. It doesn't matter; wine will always taste like vinegar to me.

3. Seeing a new baby kicks off some paternal instinct that gets me jazzed up to build my own stuff out of DNA, with NE1 acting as a mediator for now.

I am knees deep into the super fullerene, which I plan to pack with genetic material and rechristen a synthetic virus, good enough for now.

Here is the latest, all the 5ers in place. They have not been hydrogenated yet. That is why their ends are gray.

Now the tricky part.

MTF

more on the super fullerene

2008-01-15T16:02:00.001-08:00

picking this up again...

First I had to turn some of the 6ers around so the nitrogen (blue) were facing out. First I was just really really focused on getting them positioned around the ball; I didn't care which way they faced. Next I had to try and build something similar with five fold symmetry (5er). I carved down a 6er to what I thought would be a good moiety and went from there. It wasn't the toughest I've built, but it still took a lot a spacial perception.

I will now work on positioning the rest of the 5ers. The nitrogen atoms will form the basis of the linkages. That will be tricky, but if I can build one that works, I should be able to just drop them in.

Still a metric crap load of twisting and adjusting...

MTF

small video of me building a cnt

2008-01-14T09:30:00.000-08:00

welcome back...

2008-01-11T11:50:00.000-08:00

A little preview before I get back to what we are affectionately calling the super fullerene and all the other things I left hanging over the holidays...

I missed you.

elbows deep into some geometry

2007-12-20T16:29:00.000-08:00

I am developing some techniques to make big old structures out of individual tiles/structures. It's going ok. I started trying for a diamond sphere, and then Damian suggested using rods with six and five fold symmetry. I still need to make the fives.

MTF

holiday wishes

2007-12-19T14:42:00.000-08:00

Twas the night before christmas and all through the house
I was busy building with a three button mouse

The stockings had been extruded and hung out to dry
Made by machines invisible to the eye

The gears were spinning, wrapping diamondiod thread,
While cams spun, positioning tool tip heads

As the feed stock flowed and the cooling plate chilled
Dreams of super toys would soon be fulfilled

When deep inside the fabber there arose such a hiss
Another toy done, to be crossed off the list

I set it aside to cool, its atoms precise
Another wonderful gift at a very low price.

The sides pearlescent, in quantum dot light
But still I wondered, did I infringe on copy right

No matter, the factory untraceable
The data file small and easily erasable

No doubt a great holiday is at foot
Brought by machine phase and not a man covered in soot.

Happy Holidays from Me and all of us at Machine Phase (Me)

new large diamond cam

2007-12-12T11:10:00.000-08:00

It's getting easier and easier to carve these parts.

and after all that an inconclusive end

2007-12-11T14:45:00.000-08:00

The CNT has been hidden for clarity, and I did a bad job of framing too. There is not a clear stratification of the different molecules (acetylene and N2).

I am not sure if the centrifugal force* can overcome the electrostatic repulsion of all those hydrogens on the acetylenes. Perhaps this is making for a more viscous fluid and harder to stratify? I can up the RPMs, try for a longer sim and see if things sort out, but I'll want to run this on one of my back up sim computers to leave the others free.

*My apologies to Dr. G

selling out on intermittent motion

2007-12-05T18:01:00.000-08:00

I still think I'll need to come up with something to stop the Maltese cross from continuing to rotate, but I have some ideas. As always I am open to suggestions too.

Yes, my pin is made out of c60s:

I built a smaller test case of this last night. When the energy is minimized, the slots on the cross had a tendency to close. However the diamond slab is a lot like Jell-O at this scale, so maybe the pin will still slide in.

I am going to have all my pots cooking, simulation wise, over the next couple of weeks, plus finals, just saying.

MTF

intermittent motion back on deck

2007-12-03T17:28:00.001-08:00

I have been researching other movements for intermittent motion. I don't think this one is the most practical, or what I'll end up using for a moderately complex system, but it looks pretty sweet.

MTF

if it's not the ice it's the wind

2007-12-03T04:38:00.001-08:00

the wind knock out the power last night, centrifuge simulation has to be restarted

and another

2007-12-02T15:07:00.000-08:00

I was trying to recreate motion blur.

Centrifuge sim is 60% done.

MTF

added to post at 10:18

artistic rendition of a Respirocyte

2007-12-02T08:13:00.000-08:00

Still playing around with Paint Shop. This was heavily inspired by Robert A. Freitas Jr's Respirocyte

It took about a half hour to put together. I know; I'm sure a pro would spend at least twice that long preparing an image for display in a public forum, but I am still learning the software.

The centrifuge is still crunching away; the power stayed on last night.

MTF

some artistic interpretations while we wait -or THE INVASION

2007-12-01T21:24:00.001-08:00

There is something of a winter storm taking place here, and while I am waiting for the power to go out again, and updating my Christmas list to include a back up power supply, I thought I would mess around with some image editing software. I am a little hard up for processor cycles right now, so molecular dynamics will have to wait.

I threw the above picture together pretty quick out of stuff I had laying around. If any professional graphic artists see it, be kind. It was really fun to make though.

The restart of the centrifuge is crunching away. I opted for a slightly shorter simulation, but we are still days away from the result.

MTF

another power outage

2007-11-29T15:17:00.000-08:00

about 200 hours down the drain

I haven't been thinking of any other things to do while we wait, but now I guess my hand is forced.

MTF

green light on the centrifuge

2007-11-21T17:08:00.001-08:00

I ran a short simulation to see if everything stayed together. For the most part it did. There were about a dozen molecules that few apart; I assume from being in a too energetic position. I played around with moving them around, but it was just a lot easier to delete them, so we are playing with 12-14 less specimens. The above arrangement is what I am going with for the long sort sim. It is going to take a while, but I'll try to come up with some stuff to entertain you while we are waiting.

MTF

the nitrogen and the acetylene

2007-11-20T17:10:00.001-08:00

Think this is asking too much? I better run a quick test.

after one revolution of the carbon nanotube centrifuge

2007-11-20T15:09:00.000-08:00

Red is Helium and green is Krypton. Next up N2 and Acetylene with a few more rotations.

MTF

I think we are ready for some RPMs

2007-11-17T21:52:00.000-08:00

I was having trouble building a stable funnel with such a small diameter but moving to a wider tube solves that problem. It also apparently makes the check valve unnecessary in the first place.

There must be some electrostatic interaction between the atoms in the tube and tube walls that increasing this distance lowers significantly-as it would. In fact if you look real close in the simulation, the He atoms never touch the wall and are repelled by it.

I think for now I will leave the funnel on for looks but remove the C60, fill the tube with some different things and spin it.

MTF

adding a back flow preventer -or- atoms enter but they can't leave

2007-11-16T17:54:00.000-08:00

First, I want to make sure everyone knows my last post meant to be humorous, and I am sure our core group does, but for any interlopers-there is no crying in molecular dynamics.

Now, back to the task at hand. This makes the pressure of the escaping gas work, work to seal its doom! It could push the C60 into the funnel, sealing the tube, or blow up into dozens of pieces. Either way it should be fun to watch.

MTF

sort of a disapointing start to the weekend

2007-11-16T16:27:00.000-08:00

And I went and left the power supply to Big Red at work
:(
.
.
. <--blog tears

first try cheating then use a more realistic tube

2007-11-15T16:33:00.000-08:00

Capping the tube works, but complicates build anything approaching a practical sorter. Also with using helium it still leaks a little, but through the walls.

Next I figured using a tube 32 Angstroms long would make for a pretty short tube. I tripled the length . The contents stay in. It is my hope they stay in long enough for things to get up to speed.

Other things I tried before these two:

deleting half the atoms
plugging it with a fullerene- it made a cannon
decreasing the rotation

I hope to spend some time on the diamondiod systems this weekend on a high-end gaming rig.

Longish sim on the longish tube overnight.

MTF