CoNTub
Encyclopedia
CoNTub is software written in Java
which runs on Windows
, Mac OS X
, Linux
and Unix
Operating systems. It is the first implementation of an algorithm for generating the 3D structure of two arbitrary connected carbon nanotube
s by means of one defect or disclination (pentagonal or heptagonal).
The software is a set of tools dedicated to the construction of complex carbon nanotube
structures for use in computational chemistry
. CoNTub[1] is the first implementation of building these complex structures, including nanotube heterojunctions, for designing and investigating new nanotube-based devices. CoNTub is based on strip algebra
, and is able to find the unique structure for connecting two specific and arbitrary carbon nanotube
s.
CoNTub[1] allows the geometry
of some two-tube heterojunctions to be easily generated, including single-walled nanotubes (SWNTs) and multi-walled nanotubes (MWNTs). The program itself is organized in five Tabbed panelsCoNTub[1], the first three being dedicated to structure generation, the fourth to the output in PDB format
, and the fifth contains a short help section.
), and the type of atom for termination of dangling bonds. ConTub displays the resulting nanotube, as well as its electronic band structure
and density of states
(DOS), following a tight binding model.
MWNT - multiple tubes with the same axis and length - are created by providing 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 crystalline graphite
(3.4 Å). ConTub automatically selects 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.
was implemented, which allows two perfect carbon nanotube
s to be joined, independently of their geometry, radius or chirality
, with the simplest geometry possible, i.e. with the lowest number of non-hexagonal rings (a pentagon
and a heptagon), also called defects or disclination
s. There is always a possible connection between two tubes and strip algebra ensues that the solution is unique and depending only of the indices (i,j) of both tubes.
Java (programming language)
Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...
which runs on Windows
Microsoft Windows
Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...
, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...
, Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
and Unix
Unix
Unix is a multitasking, multi-user computer operating system originally developed in 1969 by a group of AT&T employees at Bell Labs, including Ken Thompson, Dennis Ritchie, Brian Kernighan, Douglas McIlroy, and Joe Ossanna...
Operating systems. It is the first implementation of an algorithm for generating the 3D structure of two arbitrary connected carbon nanotube
Carbon nanotube
Carbon nanotubes are allotropes of carbon with a cylindrical nanostructure. Nanotubes have been constructed with length-to-diameter ratio of up to 132,000,000:1, significantly larger than for any other material...
s by means of one defect or disclination (pentagonal or heptagonal).
The software is a set of tools dedicated to the construction of complex carbon nanotube
Carbon nanotube
Carbon nanotubes are allotropes of carbon with a cylindrical nanostructure. Nanotubes have been constructed with length-to-diameter ratio of up to 132,000,000:1, significantly larger than for any other material...
structures for use in computational chemistry
Computational chemistry
Computational chemistry is a branch of chemistry that uses principles of computer science to assist in solving chemical problems. It uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids...
. CoNTub[1] is the first implementation of building these complex structures, including nanotube heterojunctions, for designing and investigating new nanotube-based devices. CoNTub is based on strip algebra
Strip algebra
Strip Algebra is a set of elements and operators for the description of carbon nanotube structures, considered as a subgroup of polyhedra, and more precisely, of polyhedra with vertices formed by three edges...
, and is able to find the unique structure for connecting two specific and arbitrary carbon nanotube
Carbon nanotube
Carbon nanotubes are allotropes of carbon with a cylindrical nanostructure. Nanotubes have been constructed with length-to-diameter ratio of up to 132,000,000:1, significantly larger than for any other material...
s.
CoNTub[1] allows the geometry
Geometry
Geometry arose as the field of knowledge dealing with spatial relationships. Geometry was one of the two fields of pre-modern mathematics, the other being the study of numbers ....
of some two-tube heterojunctions to be easily generated, including single-walled nanotubes (SWNTs) and multi-walled nanotubes (MWNTs). The program itself is organized in five Tabbed panelsCoNTub[1], the first three being dedicated to structure generation, the fourth to the output in PDB format
Protein Data Bank (file format)
The Protein Data Bank file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, observed...
, and the fifth contains a short help section.
Features
- 3D molecular viewer
- Structure generation of carbon nanotube Heterojunctions from indices(i,j) and length (l) of the two nanotubes.
- Structure generation of single-walled nanotubes (SWNTs) from indices(i,j) and length (l)
- Plotting the electronic band structureElectronic band structureIn solid-state physics, the electronic band structure of a solid describes those ranges of energy an electron is "forbidden" or "allowed" to have. Band structure derives from the diffraction of the quantum mechanical electron waves in a periodic crystal lattice with a specific crystal system and...
and density of statesDensity of statesIn solid-state and condensed matter physics, the density of states of a system describes the number of states per interval of energy at each energy level that are available to be occupied by electrons. Unlike isolated systems, like atoms or molecules in gas phase, the density distributions are not...
(DOS) for single-walled nanotubes (SWNTs) - Structure generation of multi-walled nanotubes from indices(i,j) and length (l), number of shells(N) and spacing(S).
- Output the xyzCartesian coordinate systemA Cartesian coordinate system specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length...
coordinates of the structures in a (PDB) file format
Nanotube generation
To generate a SWNT, it is only necessary to introduce the indices of the tube, its desired length (AngstromÅngström
The angstrom or ångström, is a unit of length equal to 1/10,000,000,000 of a meter . Its symbol is the Swedish letter Å....
), and the type of atom for termination of dangling bonds. ConTub displays the resulting nanotube, as well as its electronic band structure
Electronic band structure
In solid-state physics, the electronic band structure of a solid describes those ranges of energy an electron is "forbidden" or "allowed" to have. Band structure derives from the diffraction of the quantum mechanical electron waves in a periodic crystal lattice with a specific crystal system and...
and density of states
Density of states
In solid-state and condensed matter physics, the density of states of a system describes the number of states per interval of energy at each energy level that are available to be occupied by electrons. Unlike isolated systems, like atoms or molecules in gas phase, the density distributions are not...
(DOS), following a tight binding model.
MWNT - multiple tubes with the same axis and length - are created by providing 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
Ångström
The angstrom or ångström, is a unit of length equal to 1/10,000,000,000 of a meter . Its symbol is the Swedish letter Å....
. The default value for spacing corresponds to the standard distance between layers in crystalline graphite
Graphite
The mineral graphite is one of the allotropes of carbon. It was named by Abraham Gottlob Werner in 1789 from the Ancient Greek γράφω , "to draw/write", for its use in pencils, where it is commonly called lead . Unlike diamond , graphite is an electrical conductor, a semimetal...
(3.4 Å). ConTub automatically selects the indices of the remaining tubes, trying to adjust the interlayer spacing, and tries to use tubes with the same chirality
Chirality (chemistry)
A chiral molecule is a type of molecule that lacks an internal plane of symmetry and thus has a non-superimposable mirror image. The feature that is most often the cause of chirality in molecules is the presence of an asymmetric carbon atom....
as that of the inner nanotube.
Heterojunction generation
This is the core of the CoNTub[1] program. Strip algebraStrip algebra
Strip Algebra is a set of elements and operators for the description of carbon nanotube structures, considered as a subgroup of polyhedra, and more precisely, of polyhedra with vertices formed by three edges...
was implemented, which allows two perfect carbon nanotube
Carbon nanotube
Carbon nanotubes are allotropes of carbon with a cylindrical nanostructure. Nanotubes have been constructed with length-to-diameter ratio of up to 132,000,000:1, significantly larger than for any other material...
s to be joined, independently of their geometry, radius or chirality
Chirality (chemistry)
A chiral molecule is a type of molecule that lacks an internal plane of symmetry and thus has a non-superimposable mirror image. The feature that is most often the cause of chirality in molecules is the presence of an asymmetric carbon atom....
, with the simplest geometry possible, i.e. with the lowest number of non-hexagonal rings (a pentagon
Pentagon
In geometry, a pentagon is any five-sided polygon. A pentagon may be simple or self-intersecting. The sum of the internal angles in a simple pentagon is 540°. A pentagram is an example of a self-intersecting pentagon.- Regular pentagons :In a regular pentagon, all sides are equal in length and...
and a heptagon), also called defects or disclination
Disclination
A disclination is a line defect in which rotational symmetry is violated. In analogy with dislocations in crystals, the term, disinclination, for liquid crystals first used by F. C. Frank and since then has been modified to its current usage, disclination.It is a defect in the orientation of...
s. There is always a possible connection between two tubes and strip algebra ensues that the solution is unique and depending only of the indices (i,j) of both tubes.
See also
- Boron nitride nanotube
- Silicon nanotubesSilicon nanotubesSilicon nanotubes are nanoparticles which create a tube-like structure from silicon atoms. The nanotubes' discovery has many significant implications for electronics development, as silicon is already a vastly important material in the semiconductor industry. Only recently has it been possible to...
- List of software for nanostructures modeling
- Potential applications of carbon nanotubesPotential applications of carbon nanotubesCarbon nanotubes, a type of fullerene, have potential in fields such as nanotechnology, electronics, optics, materials science, and architecture. Over the years new applications have taken advantage of their unique electrical properties, extraordinary strength, and efficiency in heat...