arXiv subjects

Kaifu Luo

Publications and source records attributed to Kaifu Luo.

At least 19 recordsLinked to original sources

arXiv2012

Dynamics of polymer translocation into an anisotropic confinement

Using Langevin dynamics simulations, we investigate the dynamics of a flexible polymer translocation into a confined area under a driving force through a nanopore. We choose an ellipsoidal shape for the confinement and consider the dependence of the asymmetry of the ellipsoid measured by the aspect ratio on the translocation time. Compared with an isotropic confinement (sphere), an anisotropic confinement (ellipsoid) with the same volume slows down the translocation, and the translocation time increases with increasing the aspect ratio of the ellipsoid. We further find that it takes different time for polymer translocation into the same ellipsoid through major-axis and minor-axis directions, depending on the average density of the whole chain in the ellipsoid, $ϕ$. For $ϕ$ lower than a critical value $ϕ_c$, the translocation through minor axis is faster, and vice versa. These complicated behaviors are interpreted by the degree of the confinement and anisotropic confinement induced folding of the translocated chain.

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arXiv2012

Dynamics of polymer translocation into a circular nanocontainer through a nanopore

Using Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a circular nanocontainer through a nanopore under a driving force $F$. We observe that the translocation probability initially increases and then saturates with increasing $F$, independent of $ϕ$, which is the average density of the whole chain in the nanocontainer. The translocation time distribution undergoes a transition from a Gaussian distribution to an asymmetric distribution with increasing $ϕ$. Moreover, we find a nonuniversal scaling exponent of the translocation time as chain length, depending on $ϕ$ and $F$. These results are interpreted by the conformation of the translocated chain in the nanocontainer and the time of an individual segment passing through the pore during translocation.

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arXiv2012

Translocation of stiff polymers through a nanopore driven by binding particles

We investigate the translocation of stiff polymers in the presence of binding particles through a nanopore by two-dimensional Langevin dynamics simulations. We find that the mean translocation time shows a minimum as a function of the binding energy $ε$ and the particle concentration $ϕ$, due to the interplay of the force from binding and the frictional force. Particularly, for the strong binding the translocation proceeds with a decreasing translocation velocity induced by a significant increase of the frictional force. In addition, both $ε$ and $ϕ$ have an notable impact on the distribution of the translocation time. With increasing $ε$ and $ϕ$, it undergoes a transition from an asymmetric and broad distribution under the weak binding to a nearly Gaussian one under the strong binding, and its width becomes gradually narrower.

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arXiv2012

Chain conformation of ring polymers under a cylindrical nanochannel confinement

We investigate the chain conformation of ring polymers confined to a cylindrical nanochannel using both theoretical analysis and three dimensional Langevin dynamics simulations. We predict that the longitudinal size of a ring polymer scales with the chain length and the diameter of the channel in the same manner as that for linear chains based on scaling analysis and Flory-type theory. Moreover, Flory-type theory also gives the ratio of the longitudinal sizes for a ring polymer and a linear chain with identical chain length. These theoretical predictions are confirmed by numerical simulations. Finally, our simulation results show that this ratio first decreases and then saturates with increasing the chain stiffness, which has interpreted the discrepancy in experiments. Our results have biological significance.

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arXiv2012

Driven polymer translocation through a cylindrical nanochannel: Interplay between the channel length and the chain length

Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation through a nanochannel embedded in two dimensions under an applied external field. We examine the translocation time for various ratio of the channel length $L$ to the polymer length $N$. For short channels $L\ll N$, the translocation time $τ\sim N^{1+ν}$ under weak driving force $F$, while $τ\sim F^{-1}L$ for long channels $L\gg N$, independent of the chain length $N$. Moreover, we observe a minimum of translocation time as a function of $L/N$ for different driving forces and channel widths. These results are interpreted by the waiting time of a single segment.

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arXiv2011

Ejection dynamics of a ring polymer out of a nanochannel

We investigate the ejection dynamics of a ring polymer out of a cylindrical nanochannel using both theoretical analysis and three dimensional Langevin dynamics simulations. The ejection dynamics for ring polymers shows two regimes like for linear polymers, depending on the relative length of the chain compared with the channel. For long chains with length $N$ larger than the critical chain length $N_{c}$, at which the chain just fully occupies the nanochannel, the ejection for ring polymers is faster compared with linear chains of identical length due to a larger entropic pulling force; while for short chains ($N<N_c$), it takes longer time for ring polymers to eject out of the channel due to a longer distance to be diffused to reach the exit of the channel before experiencing the entropic pulling force. These results can help understand many biological processes, such as bacterial chromosome segregation.

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arXiv2011

Chaperone-assisted translocation of a polymer through a nanopore

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 $ε$ 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 $τ$ has a transition from long-tailed distribution to Gaussian distribution with increasing $ε$. $τ$ 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 $τ$ has a minimum as a function of the chaperone concentration. For different $ε$, a nonuniversal dependence of $τ$ 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.

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arXiv2011

The chain sucker: translocation dynamics of a polymer chain into a long narrow channel driven by longitudinal flow

Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width $R$ embedded in two dimensions, driven by a force proportional to the number of monomers in the channel. Such a setup mimics typical experimental situations in nano/micro-fluidics. During the the translocation process if the monomers in the channel can sufficiently quickly assume steady state motion, we observe the scaling $τ\sim N/F$ of the translocation time $τ$ with the driving force $F$ per bead and the number $N$ of monomers per chain. With smaller channel width $R$, steady state motion cannot be achieved, effecting a non-universal dependence of $τ$ on $N$ and $F$. From the simulations we also deduce the waiting time distributions under various conditions for the single segment passage through the channel entrance. For different chain lengths but the same driving force, the curves of the waiting time as a function of the translocation coordinate $s$ feature a maximum located at identical $s_{\mathrm{max}}$, while with increasing the driving force or the channel width the value of $s_{\mathrm{max}}$ decreases.

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arXiv2010

Polymer translocation into a fluidic channel through a nanopore

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 $τ$ on the chain length $N$. $τ$ initially decreases rapidly and then saturates with increasing $R$, and a dependence of the scaling exponent $α$ of $τ$ with $N$ on the channel width $R$ is observed. The otherwise inverse linear scaling of $τ$ with $F$ breaks down and we observe a minimum of $α$ 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.

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arXiv2010

Polymer translocation into laterally unbounded confined environments

Using Langevin dynamics simulations in three dimensions (3D), we investigate the dynamics of polymer translocation into the regions between two parallel plane walls with separation $R$ under a driving force $F$, respectively. Compared with an unconfined environment, the translocation dynamics is greatly changed due to the crowding effect of the partially translocated monomers. Translocation time $τ$ initially decreases rapidly with increasing $R$ and then saturates for larger $R$, and the confined environment leads to a nonuniversal dependence of $τ$ on $F$.

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arXiv2009

Driven polymer translocation through nanopores: slow versus fast dynamics

We investigate the dynamics of polymer translocation through nanopores under external driving by 3D Langevin Dynamics simulations, focusing on the scaling of the average translocation time $τ$ versus the length of the polymer, $τ\sim N^α$. For slow translocation, i.e., under low driving force and/or high friction, we find $α\approx 1+ν\approx 1.588$ where $ν$ denotes the Flory exponent. In contrast, $α\approx 1.37$ is observed for fast translocation due to the highly deformed chain conformation on the trans side, reflecting a pronounced non-equilibrium situation. The dependence of the translocation time on the driving force is given by $τ\sim F^{-1}$ and $τ\sim F^{-0.80}$ for slow and fast translocation, respectively. These results clarify the controversy on the magnitude of the scaling exponent $α$ for driven translocation.

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arXiv2009

Polymer translocation out of confined environments

We consider the dynamics of polymer translocation out of confined environments. Analytic scaling arguments lead to the prediction that the translocation time scales like $τ\sim N^{β+ν_{2D}}R^{1+(1-ν_{2D})/ν}$ for translocation out of a planar confinement between two walls with separation $R$ into a 3D environment, and $τ\sim N^{β+1}R$ for translocation out of two strips with separation $R$ into a 2D environment. Here, $N$ is the chain length, $ν$ and $ν_{2D}$ are the Flory exponents in 3D and 2D, and $β$ is the scaling exponent of translocation velocity with $N$, whose value for the present choice of parameters is $β\approx 0.8$ based on Langevin dynamics simulations. These scaling exponents improve on earlier predictions.

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arXiv2008

Scaling exponents of Forced Polymer Translocation through a nano-pore

We investigate several scaling properties of a translocating homopolymer through a thin pore driven by an external field present inside the pore only using Langevin Dynamics (LD) simulation in three dimension (3D). Specifically motivated by several recent theoretical and numerical studies that are apparently at odds with each other, we determine the chain length dependence of the scaling exponents of the average translocation time, the average velocity of the center of mass, $ $, the effective radius of gyration during the translocation process, and the scaling exponent of the translocation coordinate ($s$-coordinate) as a function of the translocation time. We further discuss the possibility that in the case of driven translocation the finite pore size and its geometry could be responsible that the veclocity scaling exponent is less than unity and discuss the dependence of the scaling exponents on the pore geometry for the range of $N$ studied here.

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arXiv2008

Dynamics of DNA translocation through an attractive nanopore

We investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences. We consider a coarse-grained model of DNA built from two bases $A$ and $C$, having different base-pore interactions, {\textit e.g.}, a strong (weak) attractive force between the pore and the base $A$ ($C$) inside the pore. From a series of studies on hetero-DNAs with repeat units $A_mC_n$, we find that the translocation time decreases exponentially as a function of the volume fraction $f_C$ of the base $C$. %($ε_{pC} < ε_{pA}$). For longer $A$ sequences with $f_C \le 0.5$, the translocation time strongly depends on the orientation of DNA, namely which base enters the pore first. Our studies clearly demonstrate that for a DNA of certain length $N$ with repeat units $A_mC_n$, the pattern exhibited by the waiting times of the individual bases and their periodicity can unambiguously determine the values of $m$, $n$ and $N$ respectively. Therefore, a prospective experimental realization of this phenomenon may lead to fast and efficient sequence detection technic.

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arXiv2008

Translocation Dynamics with Attractive Nanopore-Polymer Interactions

Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics. This can be understood by examining the three components of the total translocation time $τ\approx τ_1+τ_2+τ_3$ corresponding to the initial filling of the pore, transfer of polymer from the \textit{cis} side to the \textit{trans} side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from non-activated to activated in nature as the strength of the attractive interaction increases, and $τ_3$ becomes the dominant contribution to the total translocation time for strong attraction. This leads to a new dependence of $τ$ as a function of driving force and chain length. Our results are in good agreement with recent experimental findings, and provide a possible explanation for the different scaling behavior observed in solid state nanopores {\it vs.} that for the natural $α$-hemolysin channel.

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arXiv2007

Sequence dependence of DNA translocation through a nanopore

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases $A$ and $C$, which has been shown previously to have different interactions with the pore. We study DNA with repeating blocks $A_nC_n$ for various values of $n$, and find that the translocation time depends strongly on the {\em block length} $2n$ as well as on the {\em orientation} of which base entering the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences are contained in the periodicity of the residence time of the individual nucleotides inside the pore.

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arXiv2007

Comment on ``Passage Times for Unbiased Polymer Translocation through a Narrow Pore''

One of the most fundamental quantities associated with polymer translocation through a nanopore is the translocation time $τ$ and its dependence on the chain length $N$. Our simulation results based on both the bond fluctuation Monte Carlo and Molecular Dynamics methods confirm the original prediction $τ\sim N^{2ν+1}$, which scales in the same manner as the Rouse relaxation time of the chain except for a larger prefactor, and invalidates other scaling claims.

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arXiv2007

Influence of polymer-pore interactions on translocation

We investigate the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. An attractive interaction can greatly improve translocation probability. At the same time, it also increases translocation time slowly for weak attraction while exponential dependence is observed for strong attraction. For fixed driving force and chain length the histogram of translocation time has a transition from Gaussian distribution to long-tailed distribution with increasing attraction. Under a weak driving force and a strong attractive force, both the translocation time and the residence time in the pore show a non-monotonic behavior as a function of the chain length. Our simulations results are in good agreement with recent experimental data.

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