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. Author manuscript; available in PMC: 2014 Apr 28.

Published in final edited form as: Soft Matter. 2013 Mar 13;9(16):10.1039/C3SM50176K. doi: 10.1039/C3SM50176K

Fig. 4 — [(a)–(c)] Normalized diffusion matrices ${\overset{⇀}{\overset{⇀}{D}}}_{{k k}^{'}}^{Φ Φ}, {\overset{⇀}{\overset{⇀}{D}}}_{i j}^{R R}$ and ${\overset{⇀}{\overset{⇀}{D}}}_{i k}^{Φ R}$ with k₁+ k₂+ k₃≤ 6 (implying 3³ OPs) and S=1,…,60 showing that they are diagonally dominant, and ${\overset{⇀}{\overset{⇀}{D}}}_{k k}^{Φ Φ} \geq {\overset{⇀}{\overset{⇀}{D}}}_{i i}^{R R} > {\overset{⇀}{\overset{⇀}{D}}}_{i k}^{Φ R}$ for the protein monomer RNA aggregation. (d) Diagonal diffusion terms of (a) and (b) clearly show the noted trend. Dominant diagonal terms of diffusion matrices. (e) ${\overset{⇀}{\overset{⇀}{D}}}_{{k k}^{'}}^{Φ Φ}$ and (g) ${\overset{⇀}{\overset{⇀}{D}}}_{i j}^{R R}$ , and the entire ${\overset{⇀}{\overset{⇀}{D}}}_{i k}^{Φ R}$ matrix. [(h)–(i)] computed after 1 and 10ns of MD simulation showing that all three types of correlations grow. This suggests large-scale motions of the system become more coordinated with time. The ${\overset{⇀}{\overset{⇀}{D}}}_{{k k}^{'}}^{Φ Φ}$ term increases most as it implies system-wide collective motion. (f) Normalized OP velocity autocorrelation functions (VACF) for OP Φ₁₀₀ _X, which captures overall extension-compression along the X-direction (refer to SI), at times 1 and 10ns. The relaxation time increases as the system shrinks, thereby suggesting an increase in coherence of collective modes accompanying growth in inter-monomer interaction during the assembly process.

Fig. 4 — [(a)–(c)] Normalized diffusion matrices ${\overset{⇀}{\overset{⇀}{D}}}_{{k k}^{'}}^{Φ Φ}, {\overset{⇀}{\overset{⇀}{D}}}_{i j}^{R R}$ and ${\overset{⇀}{\overset{⇀}{D}}}_{i k}^{Φ R}$ with k₁+ k₂+ k₃≤ 6 (implying 3³ OPs) and S=1,…,60 showing that they are diagonally dominant, and ${\overset{⇀}{\overset{⇀}{D}}}_{k k}^{Φ Φ} \geq {\overset{⇀}{\overset{⇀}{D}}}_{i i}^{R R} > {\overset{⇀}{\overset{⇀}{D}}}_{i k}^{Φ R}$ for the protein monomer RNA aggregation. (d) Diagonal diffusion terms of (a) and (b) clearly show the noted trend. Dominant diagonal terms of diffusion matrices. (e) ${\overset{⇀}{\overset{⇀}{D}}}_{{k k}^{'}}^{Φ Φ}$ and (g) ${\overset{⇀}{\overset{⇀}{D}}}_{i j}^{R R}$ , and the entire ${\overset{⇀}{\overset{⇀}{D}}}_{i k}^{Φ R}$ matrix. [(h)–(i)] computed after 1 and 10ns of MD simulation showing that all three types of correlations grow. This suggests large-scale motions of the system become more coordinated with time. The ${\overset{⇀}{\overset{⇀}{D}}}_{{k k}^{'}}^{Φ Φ}$ term increases most as it implies system-wide collective motion. (f) Normalized OP velocity autocorrelation functions (VACF) for OP Φ₁₀₀ _X, which captures overall extension-compression along the X-direction (refer to SI), at times 1 and 10ns. The relaxation time increases as the system shrinks, thereby suggesting an increase in coherence of collective modes accompanying growth in inter-monomer interaction during the assembly process.