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Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices
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10.1063/1.2751169
/content/aip/journal/jcp/127/4/10.1063/1.2751169
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/4/10.1063/1.2751169

Figures

Image of FIG. 1.
FIG. 1.

The 2D triangular lattice (a) and a unit cell in the face centered cubic lattice (b).

Image of FIG. 2.
FIG. 2.

Examples of a Hamiltonian circuit (a) and a Hamiltonian path (b) within a parallelogram of size on the 2D triangular lattice.

Image of FIG. 3.
FIG. 3.

Examples of protein shapes on the triangular and the fcc lattices studied in the present work. (a) a parallelogram, (b) a regular (equilateral) hexagon having side lengths of 1 (in lattice units), (c) a regular (equilateral) triangle with sides of length 3, and (d) a skewed parallelepiped on the fcc lattice.

Image of FIG. 4.
FIG. 4.

Shapes embedded in the 3D fcc lattice. (a) , (b) , (c) , (d) , (e) , and (f) . The symmetries of each are referred to in the preceding table. Cross sections are shown on the right side.

Image of FIG. 5.
FIG. 5.

Dealing with symmetric conformations. (a) An example of two conformations exhibiting head-tail symmetry. The two structures are equivalent upon rotation by 180° in the plane. Shown in (b) is the method we use to eliminate symmetries. If we start our path from the central node then only one of the six equivalent nodes is chosen as the first step and only one of the two equivalent nodes as the second step (the first two steps are shown as dark lines). The other step, shown as a broken line, would produce conformations symmetrical to the first one.

Image of FIG. 6.
FIG. 6.

All possible connectivity states (only physically acceptable states are labeled from 1 to 6) (a) and bond distributions (b) for generation of Hamiltonian circuits within rectangles of size .

Image of FIG. 7.
FIG. 7.

The extension of the transfer matrix method to the triangular lattice must take into account nodes (such as the central one in the figure) that are already occupied during the process of piecewise building of the chain. The consideration of such nodes on the triangular lattice leads to an extension of the definition of connectivity states compared to the square lattice.

Image of FIG. 8.
FIG. 8.

All possible connectivity states for Hamiltonian circuits on parallelograms on the triangular lattice. The cross symbol denotes connectivity states containing excluded nodes, such as the central node in Fig. 7.

Image of FIG. 9.
FIG. 9.

Bond distributions (a) for each of the five connectivity states. All other distributions will not lead to valid conformations. (b) shows an example of a valid transfer from one state to another while (c) shows an invalid transfer from state 5 to state 4 because of a triple-bonded node.

Image of FIG. 10.
FIG. 10.

All possible transitions between various connectivity states for Hamiltonian circuits on parallelograms on the triangular lattice. The notation means the transition from connectivity state 1 (in Fig. 8) to connectivity state 3.

Image of FIG. 11.
FIG. 11.

Connectivity states that are the starting states (a) or the ending states (b) for Hamiltonian circuits on the parallelograms on the triangular lattice.

Image of FIG. 12.
FIG. 12.

All possible connectivity states for Hamiltonian circuits on parallelograms on the triangular lattice.

Image of FIG. 13.
FIG. 13.

Connectivity states that are starting states for Hamiltonian circuits on the parallelograms on the triangular lattice.

Image of FIG. 14.
FIG. 14.

Connectivity states that are ending states for Hamiltonian circuits on the parallelograms on the triangular lattice.

Image of FIG. 15.
FIG. 15.

The plot of the number of possible Hamiltonian chains vs the length for varying widths of the parallelogram.

Image of FIG. 16.
FIG. 16.

The volume/area ratio comparison of 3D cubic lattice conformations and real proteins as a function of protein length (length meaning number of residues).

Tables

Generic image for table
Table I.

Symmetries for several classes of shapes on the 2D triangular (top) and 3D face centered cubic (fcc) (bottom) lattices.

Generic image for table
Table II.

Numbers of Hamiltonian circuits within parallelograms of size on the triangular lattice and the ratio .

Generic image for table
Table III.

Enumerations of all paths and circuits for various geometries for the 2D triangular lattice and the 3D fcc lattice.

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/content/aip/journal/jcp/127/4/10.1063/1.2751169
2007-07-23
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/4/10.1063/1.2751169
10.1063/1.2751169
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