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Hybrid molecular dynamics simulations of living filaments
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Image of FIG. 1.
FIG. 1.

A schematic showing the model filament with beads of size σ and bond length l 0. The angle between successive bonds are denoted by θ.

Image of FIG. 2.
FIG. 2.

State I: The polymerized state where the reacting monomer shown in dark blue is connected to the filament through intramolecular interactions and is, necessarily, located in a low intramolecular energy volume resulting from the intersection of a conic volume (in green) and the spherical layer (red) which, respectively, limit the bending and the stretching energies (see main text). The dashed blue circles represent the volume V s and the light green particles represent free monomers.

Image of FIG. 3.
FIG. 3.

State J: The depolymerized state where the reacting monomer shown in blue is free but is necessarily located within the spherical layer shown with dashed blue lines whose minimum radius limits the excluded volume pair interaction energy with the last monomer of the target filament end (see main text).

Image of FIG. 4.
FIG. 4.

is plotted vs with (fixed) after numerical evaluation and inversion of Eq. (18). The solid line is for z = 18, the dashed line for z = 40 and the dashed-dotted line for z = 72. It is seen that when z → ∞, as becomes large. The green (light) line at is a guide for the eye. Such curves have only a universal character for ideal solution conditions as the reduction factor 1/K 0 is only a function of temperature (see text).

Image of FIG. 5.
FIG. 5.

Theoretical bounded filament distributions for subcritical () and supercritical () monomer densities shown as P eq(i) = ρ i f vs i. The solid, dotted, dashed, and dashed-dotted lines are for and 1.67, respectively, in the conditions of the plot for z = 18 in Fig. 4. The solid horizontal line corresponds to the case.

Image of FIG. 6.
FIG. 6.

Plot of P eq(i) = ρ i f vs i for two different values, namely subcritical experiment G2 (black circles) and supercritical experiment G4 (black squares). The solid black lines are the corresponding fits. The two dashed straight lines indicate the expected distributions in ideal solution conditions for the same state point (N t , N f , V, T).

Image of FIG. 7.
FIG. 7.

The equilibrium constant calculated from the simulations. The open black circles are calculated from the free monomer density and the exponential filaments densities while the red stars are estimated from the ratio of the rates (1/ρ1)U/W. Within the error bars, the agreement between the two estimates is excellent. The solid red line is the ratio (1/ρ1)f1)/g1) estimated from the fits. The dotted line represents the equilibrium constant for the ideal case.

Image of FIG. 8.
FIG. 8.

Polymerization rate U (circles) and depolymerization rate W (squares) vs ρ1 for all experiments. The solid lines are linear (W) and quadratic (U) fitting curves discussed in the text. In the inset, the global growth rate J = UW is indicated (diamonds). The solid line showing J = 0 is only for reference.

Image of FIG. 9.
FIG. 9.

C(t) vs t for experiments G1 (squares), G3 (circles), and G5 (diamonds). The solid curves represent the theoretical expressions of C(t) based on Eqs. (51) and (52) where the conditional probabilities are computed by solving according to standard methods, the mean field population dynamics given by Eqs. (50), using the U and W actual tabulated values of the same state point.

Image of FIG. 10.
FIG. 10.

〈ΔN(t)〉 N(0) = i vs t at short times for different values of . The lines refer (from bottom) to an average over filaments i = 8, 9, and 10 in experiment G1, an average over filaments i = 9, 10, and 11 in experiment G3 and an average over filaments i = 11, 12, and 13 in experiment G5.


Generic image for table
Table I.

Table with simulation results for different values of N t . The particle packing fraction is represented by η. We fix N f = 80 in all the experiments with their size limited between 3 and z = 18. Here is the reduced monomer density obtained from the slope of the logarithm of the equilibrium filament length distribution, and is the measured single monomer density. For comparison, we also tabulate ρ1 numerically calculated from Eq. (18). The polymerization (U) and depolymerization (W) rates are calculated directly by counting.


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Hybrid molecular dynamics simulations of living filaments