Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userUsing a Peclet Number for the Translocation of Polymer through a Nanopore to Tune Coarse-Grained Simulations to Experimental Conditions
79
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relatively generic sense and do not endeavour to match any particular set of experimental conditions. In this manuscript, we use the concept of a Peclet number for translocation, $P_t$, to compare the drift-diffusion balance in a typical experiment vs a typical simulation. We find that the standard coarse-grained approach over-estimates diffusion effects by anywhere from a factor of 5 to 50 compared to experimental conditions using dsDNA. By defining a coarse-graining parameter, $lambda$, we are able to correct this and tune the simulations to replicate the experimental $P_t$ (for dsDNA and other scenarios). To show the effect that a particular $P_t$ can have on the dynamics of translocation, we perform simulations across a wide range of $P_t$ values for two different types of driving forces: a force applied in the pore and a pulling force applied to the end of the polymer. As $P_t$ brings the system from a diffusion dominated to a drift dominated regime, a variety of effects are observed including a non-monotonic dependence of the translocation time $tau$ on $P_t$ and a steep rise in the probability of translocating. Comparing the two force cases illustrates the impact of the crowding effects that occur on the trans side: a non-monotonic dependence of the width of the $tau$ distributions is obtained for the in-pore force but not for the pulling force.
rate research
Read More
Using Langevin dynamics simulations, we investigate the dynamics of chaperone-assisted translocation of a flexible polymer through a nanopore. We find that increasing the binding energy $epsilon$ between the chaperone and the chain and the chaperone concentration $N_c$ can greatly improve the translocation probability. Particularly, with increasing the chaperone concentration a maximum translocation probability is observed for weak binding. For a fixed chaperone concentration, the histogram of translocation time $tau$ has a transition from long-tailed distribution to Gaussian distribution with increasing $epsilon$. $tau$ rapidly decreases and then almost saturates with increasing binding energy for short chain, however, it has a minimum for longer chains at lower chaperone concentration. We also show that $tau$ has a minimum as a function of the chaperone concentration. For different $epsilon$, a nonuniversal dependence of $tau$ on the chain length $N$ is also observed. These results can be interpreted by characteristic entropic effects for flexible polymers induced by either crowding effect from high chaperone concentration or the intersegmental binding for the high binding energy.
We determine the scaling exponents of polymer translocation (PT) through a nanopore by extensive computer simulations of various microscopic models for chain lengths extending up to N=800 in some cases. We focus on the scaling of the average PT time $tau sim N^{alpha}$ and the mean-square change of the PT coordinate $<s^2(t)> sim t^beta$. We find $alpha=1+2 u$ and $beta=2/alpha$ for unbiased PT in 2D and 3D. The relation $alpha beta=2$ holds for driven PT in 2D, with crossover from $alpha approx 2 u$ for short chains to $alpha approx 1+ u$ for long chains. This crossover is, however, absent in 3D where $alpha = 1.42 pm 0.01$ and $alpha beta approx 2.2$ for $N approx 40-800$.
Using two dimensional Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a fluidic channel with diameter $R$ through a nanopore under a driving force $F$. Due to the crowding effect induced by the partially translocated monomers, the translocation dynamics is significantly altered in comparison to an unconfined environment, namely, we observe a nonuniversal dependence of the translocation time $tau$ on the chain length $N$. $tau$ initially decreases rapidly and then saturates with increasing $R$, and a dependence of the scaling exponent $alpha$ of $tau$ with $N$ on the channel width $R$ is observed. The otherwise inverse linear scaling of $tau$ with $F$ breaks down and we observe a minimum of $alpha$ as a function of $F$. These behaviors are interpreted in terms of the waiting time of an individual segment passing through the pore during translocation.
We study the driven translocation of a semi-flexible polymer through a nanopore by means of a modified version of the iso-flux tension propagation theory (IFTP), and extensive molecular dynamics (MD) simulations. We show that in contrast to fully flexible chains, for semi-flexible polymers with a finite persistence length $tilde{ell}_p$ the {it trans} side friction must be explicitly taken into account to properly describe the translocation process. In addition, the scaling of the end-to-end distance $R_N$ as a function of the chain length $N$ must be known. To this end, we first derive a semi-analytic scaling form for $R_N$, which reproduces the limits of a rod, an ideal chain, and an excluded volume chain in the appropriate limits. We then quantitatively characterize the nature of the {it trans} side friction based on MD simulations of semi-flexible chains. Augmented with these two factors, the modified IFTP theory shows that there are three main regimes for the scaling of the average translocation time $tau propto N^{alpha}$. In the stiff chain (rod) limit $N/tilde{ell}_p ll 1$, {$alpha = 2$}, which continuously crosses over in the regime $ 1 < N/tilde{ell}_p < 4$ towards the ideal chain behavior with {$alpha = 3/2$}, which is reached in the regime $N/tilde{ell}_p sim 10^2$. Finally, in the limit $N/tilde{ell}_p gg 10^6$ the translocation exponent approaches its symptotic value $1+ u$, where $ u$ is the Flory exponent. Our results are in good agreement with available simulations and experimental data.
The translocation dynamics of a polymer chain through a nanopore in the absence of an external driving force is analyzed by means of scaling arguments, fractional calculus, and computer simulations. The problem at hand is mapped on a one dimensional {em anomalous} diffusion process in terms of reaction coordinate $s$ (i.e. the translocated number of segments at time $t$) and shown to be governed by an universal exponent $alpha = 2/(2 u+2-gamma_1)$ whose value is nearly the same in two- and three-dimensions. The process is described by a {em fractional} diffusion equation which is solved exactly in the interval $0 <s < N$ with appropriate boundary and initial conditions. The solution gives the probability distribution of translocation times as well as the variation with time of the statistical moments: $<s(t)>$, and $<s^2(t)> - < s(t)>^2$ which provide full description of the diffusion process. The comparison of the analytic results with data derived from extensive Monte Carlo (MC) simulations reveals very good agreement and proves that the diffusion dynamics of unbiased translocation through a nanopore is anomalous in its nature.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
