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A coarse-grained model for double-helix molecules in solution: Spontaneous helix formation and equilibrium properties
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10.1063/1.1869417
/content/aip/journal/jcp/122/12/10.1063/1.1869417
http://aip.metastore.ingenta.com/content/aip/journal/jcp/122/12/10.1063/1.1869417

Figures

Image of FIG. 1.
FIG. 1.

Schematic picture of the base pair (light-gray beads), with its connection to the backbone (dark gray). The numbers along the springs refer to the base-pair bond potentials of Table I, and the symbols above and below the base pair denote the angular potentials. The straight angle corresponds to in Table I and the oblique one to .

Image of FIG. 2.
FIG. 2.

Schematic picture of the backbone connectivity. The springs and the (straight) angle correspond to the parameter definitions in Table I.

Image of FIG. 3.
FIG. 3.

Representative snapshots of a spontaneous helix formation, starting from a straight ladder conformation (first frame). Only the solute molecule is shown, the surrounding solvent is removed. In each frame, the molecule is displayed with its long axis vertically aligned, although in the actual simulation the molecule is free to rotate. Note the appearance of a major (bottom half) and a minor groove (top half) in the final state.

Image of FIG. 4.
FIG. 4.

Coarse description of the helix with only the four sugar beads (grey spheres) at the ends of the chain. The white spheres denote the midpoints of two sugar beads. Shown are the twist angle and the end-to-end distance .

Image of FIG. 5.
FIG. 5.

Time evolution of the twist angle in five sample runs of Case 1.

Image of FIG. 6.
FIG. 6.

Time evolution of the twist angle between base pair 6 and base pair for 1 representative run of Case 1. Solid lines correspond to and dotted lines to .

Image of FIG. 7.
FIG. 7.

Time evolution of the distance between base pair 1 and base pair with increasing from top to bottom.

Image of FIG. 8.
FIG. 8.

Kinetically trapped conformation of the molecule with a chiral defect in the center. The bottom half of the molecule has a left-handed twist while the top half is right handed.

Image of FIG. 9.
FIG. 9.

Average decay of twist angle as a function of time for Case 1 (solid lines), Case 2 (dotted lines), and Case 3 (dashed lines). In each case, the upper line denotes the average over the whole ensemble of initial conditions, the lower line only over the subset of molecules that completed a full helical turn during the length of the run.

Image of FIG. 10.
FIG. 10.

Average decay of twist angle as a function of time for Case 1b (solid line), Case 1c (dotted line), and Case 1b with diminished strength of the backbone angular potential (dashed line).

Image of FIG. 11.
FIG. 11.

Average twist angle (circles, left scale) and average end-to-end distance (diamonds, right scale) as a function of the inter-base-pair Lennard-Jones energy parameter .

Image of FIG. 12.
FIG. 12.

Average twist angle (circles, left scale) and average end-to-end distance (diamonds, right scale) as a function of the strength of the angular potential along the backbone.

Image of FIG. 13.
FIG. 13.

Wall clock time for simulations of the generic model (circles, dashed line, left scale) and an atomistic model (diamonds, dotted line, right scale) as a function of box length in the direction. Reported clock times are for simulation time.

Tables

Generic image for table
Table I.

Bond and angle parameters for the coarse-grained model [Eqs. (1) and (2)]. The bond harmonic force constants are given in and equilibrium lengths in . The angular harmonic force constants are given in and their equilibrium angles in degrees.

Generic image for table
Table II.

Nonbonded interaction parameters for the different bead types of the model: (backbone beads), (base-pair beads), and (solvent beads).

Generic image for table
Table III.

Different variations of the models of Table II to study the effect of the ratio of attractive and repulsive interactions. ShLJ refers to the shifted Lennard-Jones potential [Eqs. (3) and (4)], -12 to the first (repulsive) term of the Lennard-Jones potential, and WCA to the Weeks–Chandler–Andersen potential [Eq. (5)].

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/content/aip/journal/jcp/122/12/10.1063/1.1869417
2005-03-30
2014-04-23
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: A coarse-grained model for double-helix molecules in solution: Spontaneous helix formation and equilibrium properties
http://aip.metastore.ingenta.com/content/aip/journal/jcp/122/12/10.1063/1.1869417
10.1063/1.1869417
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