Figure 1.
Snap shots of the protein at the end of 107 time steps at temperature T = 0.020 for the solvent interaction strength fs = 1, 5, 14, 16, and 20 (from left to right) on a 643 lattice.
Colors pink (hydrophobic residues), golden (polar), and blue (electrostatic) represent residues in different groups without distinction within.
Figure 2.
Average energy of each residue (of H3.1 protein) immersed in solvent (with fs = 5) at temperatures T = 0.010–0.030.
The interaction energy of each residue with its surrounding solvent and other residues within the range (rc) of interaction is evaluated at each time step but only its asymptotic (i.e., equilibrium) values are used in averaging. Simulations are performed on a 643 lattice for 107 time steps with 100 independent samples at each temperature and solvent strength.
Figure 3.
Average mobility (fraction of successful moves per unit time step) of each residue (of H3.1 protein) immersed in a solvent with the interaction strength fs = 5 at temperatures T = 0.010–0.030 (corresponding to figure 2).
Simulations are performed on a 643 lattice for 107 time steps with 100 independent samples at each temperature and solvent strength.
Figure 4.
Variation of the root mean square displacement of the center of mass of the protein with the time step at a low (T = 0.010) and a high (T = 0.030) temperature in solvent with different interaction strengths (fs = 0–5).
Simulations are performed on a 643 lattice with 100 independent samples at each temperature and solvent strength.
Figure 5.
Variation of the radius of gyration of the protein with the magnitude of the solvent interaction at temperatures T = 0.010–0.040.
Simulations are performed on a 643 lattice with 100 independent samples at each temperature and solvent strength.
Figure 6.
Variation of the structure factor S(q) of the protein H3.1 with the wave vector q in solvent with interaction strength 0–20 at temperatures T = 0.010–0.025.
Slopes of the fitted data (covering the spread of the radius of gyration, see figure 5) are included with appropriate solvent interaction strength in parenthesis; the wave vector q = 1 corresponds to a linear distance of 6.28 in units of lattice constant and q = 0.1 to 62.8 (almost the entire lattice). Simulations are performed on a 643 lattice with 100 independent samples at each temperature and solvent strength.
Figure 7.
Variation of the radius of gyration of the protein with the magnitude of the solvent interaction at a temperature T = 0.025 for protein h3.1 with multi-grain representations, i.e., one node, two nodes, and three nodes to represent each residue.
Simulations are performed on a 643 lattice with one node residue and on 1003 and 2103 lattices with two-node and three-node residues representations respectively. 100 independent samples with one-node, 50 with two-node, and 25 with three-node representations are used at each solvent strength. The inset is the structure factor S(q) versus wave vector q on a log-log scale at a representative solvent interaction strength fs = 15.