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<!-- Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details. -->
<div align="center"><h1>CoNTub 1.0:<br>
Software for connecting two arbitrary carbon nanotubes</h1>
Cite this work as: "CoNTub: an algorithm for connecting two arbitrary carbon nanotubes." S. Melchor; J.A. Dobado.
Journal of Chemical Information and Computer Sciences, 44, 1639-1646 (2004)S. Melchor; J.A. Dobado.</div><hr>
<h2>Introduction</h2>
This software is a set of tools dedicated to the construction of complex carbon nanotube structures for their use in computational chemistry.
CoNTub is organized in five Tabbed panels, the first three being dedicated to structure generation, the fourth to the output in the Protein Data Bank
(PDB) file format, and the fifth is the short help section you are reading right now.
<br><br>
Carbon Nanotubes are a new material discovered in 1991 by Sumio Iijima [1], consisting in nanoscopic graphitic fibers, where the carbon atoms
are arranged forming tubes. These fibers are hollow, and can be composed by more than one layer. Their tubular form gives them an extraordinary
mechanical ellasticity and strength, with lightweight characteristics.[2] Additionally, they show different conductivity
depending on their specific geometry [3]. In the recent years, it has been shown that bent nanotubes present asymmetric resistance,[4][5] similar
to that of diodes, that has opened the field of nanoelectronics. These bent nanotubes present a special geometry that causes this behavior, because it is not a
single nanotube, but rather the fusion of two perfect nanotubes, that is called a nanotube heterojunction, or more generally, carbon heterostructures
<br><br>
Therefore, it was needed a computer application to build these complex structures, and specially, nanotube heterojunctions, for designing and investigate
new nanotube-based devices, and this is what CoNTub was made for.
CoNTub allows you to generate easily the geometry of some of these molecules, and more specifically, two-tube heterojunctions, single walled
nanotubes (SWNT) and multi-walled nanotubes (MWNT).
<br><br>
Here follows a brief description of the components of CoNTub and their use.
<h2>3D Viewer</h2>
All panels that construct nanotube structures use the same 3D viewer, that allows an easy inspection of the molecule. You may rotate
the molecule by simply dragging the mouse over the viewer, as well as modify the molecule position with the arrow keys. The zoom scale
can be modified with <em><PgUp></em> and <em><PgDown></em> keys, and the original orientation and scale
is restored by pressing <em><Space></em> <br> at any time. The display incorporates several additional features:
<ul>
Display atoms in Ball&Stick Model: The default representation uses the simple Stick representation, but Ball&Stick can be used for special rendering (Text Shortcut - b)
</ul>
<ol>
Display atom labels: For Atom identification (Text Shortcut - l)
</ol>
<ol>
Cut back: Often, the structure is not clear if back part of the molecule is displayed.
Cutting the back makes a much nicer picture (Text Shortcut - c)
</ol>
<br>
Hint: the text shortcuts work only if the mouse is over the display.
<h2>Heterojunction Generation</h2>
This is the core of CoNTub program. Here we have implemented the algebra developed previously [6]. In this work we asked ourselves the question of wether it was or not possible
to join two perfect carbon nanotubes, independently of their geometry, radius or chirality. The answer was affirmative: the simplest heterojuction possible is
made with the insertion of non-hexagonal rings, called generally defects, or disclinations, and more precisely two, a pentagon and a heptagon. Within these
considerations, there is always a possible connection between them. provided by an specific mathematical formula. Even more, the solution is unique, depending only
of the indices (i,j) of both tubes.
<br><br>
If there is only one solution to the connection between two tubes, that means that there are a lot of "false" answers. Imagine two different nanotube
fragments, with their open ends located one next to the other. With luck, you can start connecting carbon atoms, introducing bonds bridging both
structures, until a stable structure is formed. But this would be highly unusual. More probably, after the construction, you may obtain dangling bonds, or
octagons, squares, or various pentagons and heptagons, leading to structures highly unstable, not resembling to the structures that appear in the real nanotubes.
<br><br>
CoNTub does all this connections for you. Translates the mathematical formula into real geometry that can be inmediately visualized and manipulated, providing a
ready-to-go PDB structure with the adequate connectivity. You have to merely introduce the indices of both tubes, and their length, and after pressing the CREATE button,
the structure is displayed. You may select also which atoms you prefer to be placed in the open parts of the nanotube. For structure stability, hydrogens and
nitrogens are offered for that purpose in the apropriate combo-box
<br><br>
Under the display is placed a log that keeps you informed about the generation process, that details which process has been employed, the number of atoms composing
each part, and so on.
<h2>Single-walled Nanotube Generation</h2>
Although the geometry of a single walled carbon nanotube can be calculated by any undergraduate student with programming skills,
it can be useful for those people with no time for programming and debugging. It use is even simpler than in the previous section:
It is only necessary to introduce the indices of the tube,
its desired length, and the type of atom for termination of dangling bonds. After pressing the CREATE button or <em><Enter></em> key, the Nanotube is
displayed, as well as its electronic band structure and density of states (DOS), following a simple tight-binding model.[7]
<h2>Multi-walled Nanotube Generation</h2>
This section corresponds to the building of multiple tubes with the same axis and length. You have to introduce the indices of the most inner tube (i,j),
the desired length (l), the number of shells (N), and the approximate distance between shells or spacing (S) in Angstrom. The default value for spacing
corresponds to the standard distance between layers in cristalline graphite (3.4 Å). The program selects automatically the indices of the remaining tubes,
trying to adjust the interlayer spacing, and tries to use tubes with the same chirality as that of the inner nanotube.
<h2>Output</h2>
Here, the structures generated in the first three panels are prepared for their storage in the Protein Data Bank (PDB) File format. Pressing one of the
three buttons that appear below, the PDB file for heterojunctions, SWNT or MWNT is displayed.
<br><br>
This is an application that is downloaded to your computer and executed there, so there are security restrictions inherent to JAVA applications.
The most confortable option for the user is to allow writing the structure directly in the hard disk, but this requires what is called <em>Signed Applets</em>,
what means that the user trusts the software. Unfortunately, the increasing number of viruses and malicious code has reduced the confidence in software
applications, so we have decided to provide the safest option: The structure is displayed and the user can copy the file to his favourite Text editor with
the traditional <em>Copy & Paste</em> technique.
<br><br>
<font size="-1">Hint: If the file is large, selecting the whole text could be tedious. We reccomend the following: Mouse-clicking at the end of the document;
Press (and keep pressed) the <em><UpCase></em> key; With the mouse, move the vertical displacement bar to the beginning of the document, where you may click now
at the first character. The whole file should be now selected, and now you may release the <em><UpCase> </em>key and copy the text with <em><CTRL></em>-C
</font>
<h2>Limits and Requirements</h2>
The structures that can be generated with CoNTub can be really huge, if certain values are introduced in the input. Therefore, in order to prevent
overflowing your computer, we have limited the use of CoNTub to molecules with less than 6000 atoms. For large molecules (4000-6000 atoms),
a low-end display is used, and you are prompted for confirmation.
<br>
Generally speaking, any 1Ghz computer should handle any structure. With a Pentium 200Mhz, it is not recomended to generate strutures with more than 1000 atoms.
<h2>Short Bibliographic Reference</h2>
<font size="-1">
[1] Iijima, S. Helical Microtubules of Graphitic Carbon. <em>Nature</em> <strong>1991</strong>, <em>354</em>, 56-58.<br>
[2] Dresselhaus, M.S.; Dresselhaus, G.; Eklund, P.C. Science of Fullerenes and Carbon Nanotubes; <em>Academic Press: San Diego</em>, <strong>1995</strong>.<br>
[3] Hamada, N.; Sawada. S.; Oshiyama, A. New One-Dimensional Conductors - Graphitic Microtubules. Phys. Rev. Lett. <strong>1992</strong>, <em>68</em>, 1597-1581.<br>
[4] Collins, P.G.; Zettl, A.; Bando, H.; Thess, A.; Smalley,R.E. Nanotube Nanodevice. <em>Science</em> <strong>1997</strong>, <em>278</em>, 100-103.<br>
[5] Yao, Z.; Postma, H.W.C.; Balents, L.; Dekker, C. Carbon Nanotube Intramolecular Junctions. <em>Nature</em> <strong>1999</strong>, <em>402</em>, 273-276.<br>
[6] Melchor, S.; Khokhriakov, N.V.; Savinskii, S.S. Geometry of Multi-Tube Carbon Clusters and Electronic Transmission in Nanotube Contacts. <em>Mol. Eng.</em> <strong>1999</strong>, <em>8</em>, 315-344.<br>
[7] Savinskii, S.S.; Khokhriakov, N.V. Characteristic Features of the Pi-Electron States of Carbon Nanotubes. <em> J. Exp. Theor. Phys.</em> <strong>1997</strong>, <em>84</em>, 1131-1137.<br>
</font>
<img src="tubo.png" width="800" height="126" align="middle" border="0">
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