Translocation Of Polymer Chain Research Articles

Mean velocity and effective diffusion constant for translocation of biopolymer chains across membrane

Chaperone-assisted translocation through a nanopore embedded in membrane holds a prominent role in the transport of biopolymers. Inspired by classical Brownian ratchet, we develop a theoretical framework characterizing such a translocation process through a master equation approach. In this framework, the polymer chain, provided with reversible binding of chaperones, undergoes forward/backward diffusion, which is rectified by chaperones. We drop the assumption of timescale separation and keep the length of a polymer chain finite, both of which happen to be key points in most of the previous studies. Our framework makes it accessible to derive analytical expressions for mean translocation velocity and an effective diffusion constant in a stationary state, which is the basis of a comprehensive understanding of the dynamics of such a process. Generally, the translocation of polymer chains across a membrane consist of three subprocesses: initiation, termination, and translocation of the main body part of a polymer chain, where the translocation of the main body part depends on both the binding/unbinding kinetics of chaperones and the diffusion of the biopolymer chain. This is the main concern of this study. Our results show that the increase of the forward/backward diffusion rate of a polymer chain and the binding/unbinding ratio of chaperones both raise the mean translocation velocity of a polymer chain, and the mean velocity finally reaches a saturation amount with an extremely rapid diffusion or extremely high binding/unbinding ratio. Roughly speaking, the dependence of effective diffusion constant on these two major processes achieves similar behavior. Besides, longer polymer chains employ higher velocity when the diffusion rate and binding/unbinding ratio are both large and similar results hold for polymer chains that are not too long in terms of the effects on the effective diffusion constant.

Translocation of polymer chain in post array induced by arrangement differ

We demonstrate that the arrangement differs of posts have significant effect on the translocation of polymer chains which are embedded in the post arrays by using Monte Carlo algorithm. Due to the equivalent entropic force, polymers have a tendency to translocate to the disordered-arranged post array side other than the ordered-arranged side even though the post densities are equal on both sides. By changing the diameter of the posts, we find that the associated translocation times are strongly affected by the structure of the post array. Since the entropic force is almost identical for each monomer of the polymer chain and the free energy difference between two differently-arranged sides increases linearly with the polymer chain length, the directional preference strongly depends on the polymer chain length, and the ratio between the probabilities for a polymer to move either side obeys the Boltzmann distribution. Hence, a new microfabricated device which is used to separate deoxyribonucleic acid (DNA) by molecular weight can be designed using this idea. Moreover, this study can help us to develop a better understanding on the passages of polymers across membranes in nature.

How Do Polymer Chains with Different Topologies Pass Through a Cylindrical Pore under an Elongational Flow Field

Translocation of polymer chains through nanopores( ultrafiltration behavior) is not only a basic problem in polymer physics and biophysics,but also related to many physical and chemical processes,such as gene transfection,protein transportation,and separation of polymer chains by size exclusion chromatography.However,due to the lack of appropriate polymer model samples as well as ideal elongational flow fields,the ultrafiltration behavior of polymer chains has not been systematically explored experimentally for a long time.To deeply understand the ultrafiltration behavior of polymer chains and verify relevant theory,we have made much effort on this subject in the past decade. In this article,we'll first review the classic theory of polymer chains passing through nanopores,and then provide an overview of our recent theoretical and experimental research achievements in this field,more specifically,we have( 1) successfully observed the"coil-to-stretch"first-order transition of polymer linear chain passing through nanopores,and found that the critical flow rate( q c) is indeed independent on the chain length,but dependent on the pore size,inconsistent with de Gennes' prediction;( 2) developed a unified theoretical description of polymer chains with different topologies passing through a nanopore;( 3) systematically studied the effects of polymer chain topology and pore structure on the ultrafiltration behavior of polymer chains; and( 4) successfully applied the ultrafiltration method into the separation of polymer chain mixtures and the rapid transition between various polymeric aggregated structures.

DYNAMICAL MODES OF POLYMER TRANSLOCATING THROUGH INTERACTING PORE UNDER CHEMICAL POTENTIAL DIFFERENCE

The translocation of polymer chain through an interacting pore under chemical potential difference Δμ is simulated using Monte Carlo technique. Three translocation modes, dependent on the polymer–pore interaction ε and Δμ, are discovered. The translocation process is found to be an nonequilibrium process, which influences the dependence of translocation time τ on ε and Δμ. It is found that τ decreases in a power law relation with the increase of Δμ, and the exponent is dependent on the interaction.

Polymer Translocation Through a Nanopore in an Interacting Membrane

The translocation of polymers through nanopores in membranes occurs in many biological processes, such as proteins transporting through membrane channels, DNA and RNA translocating across nuclear pores, and drug delivery. The mechanism of the translocations has attracted a lot of attention from experiments, analytical theories and computer simulations. In a recent simulation study, the influence of pore-polymer interaction on the polymer translocations was discussed. Some experiments implied that the interaction between polymers and membranes might play an important role in the polymer translocation through membranes. In the present work, we use dynamic Monte Carlo simulations to study the effects of interaction between polymer segments and the membrane on the translocation of polymer chains through an interacting membrane from cis side ( high concentration of chains ) to trans side (zero concentration ). Results show that there is a critical adsorption point ec of the interaction strength e. We find the translocation timeτ is almost independent from e fore ec, where n is the length of polymer chains. We estimate the value of the critical adsorption point ec is about −0.3, which is in good agreement with previous results in many literatures studying the adsorptions of polymers on surfaces.

Effect of attractive polymer-pore interactions on translocation dynamics

The effect of attractive polymer-pore interaction on the translocation of polymer chain through a nanopore under electric field is studied by using dynamical Monte Carlo method. The translocation dynamics is remarkably influenced by the interaction. The translocation time for chain moving through nanopore is strongly dependent on the interaction. It reaches minimum at a moderate interaction which is found to be roughly independent of electric field as well as chain length. At weak interaction region, chain spends long time to overcome the barrier of the pore entrance, i.e., the chain is trapped at the entrance. While at strong interaction region, chain is difficult to leave the nanopore, that is, the chain is trapped at the exit of nanopore. The phenomenon is discussed from the view of free energy landscape.

Translocation of Polymer Chains Through a Channel with Complex Geometries

The elastic behavior of a single chain transporting through complex channel which can be seen as the combination of three different channels (left channel, middle channel, and right channel, respectively) is investigated using the new pruned-enriched Rosenbluth method with importance sampling. The elastic force during the translocation process is calculated. At the entrance into the middle channel, there is the first plateau in the curve of the elastic force f (f > 0) versus x, here x represents the position of the first monomer along the x-axis direction. When the first monomer moves to a certain position, a second plateau is observed with the elastic force f 0, which represents spontaneous translocation. The free energy difference between the subchain in the right channel and the subchain in the left channel may drive the translocation. The influence of chain length and width of the left and right channels on the translocation process are also investigated. From the simulation results, more detailed explanations for the reason why the component translocation time is not the same for different channels can be presented.

Hard Sphere Diffusion Behaviour of Polymer Translocating through Interacting Pores

The translocation of polymer chain through a small pore from a high concentration side (cis side) to a low concentration side (trans side) is simulated by using Monte Carlo technique. The effect of the polymer-pore interaction on the translocation is studied. We find a special interaction at which the decay of the number of polymer chain, N, at the cis side obeys Fick's law, i.e. N decreases exponentially with time. The behaviour is analogous to the diffusion of hard sphere.

Translocation of polymer chains through interacting nanopores

The effect of the interaction between nanopore and chain segment on the translocation of polymer chains through an interacting nanopore from a confined environment (cis side, high concentration of chain) to a spacious environment (trans side, zero concentration) was studied by using dynamic Monte Carlo simulations. Results showed that a moderate attractive pore–polymer interaction accelerates the translocation of chain. The optimal interaction at which translocation is the fastest increases with the concentration of chain on the cis side. The dependence of microscopic behaviors of chain translocation on the interaction was investigated.

Simulation study on the translocation of polymer chains through nanopores

The translocation of polymer chains through nanopores is simulated by dynamical Monte Carlo method. The free energy landscape for the translocation of polymer is calculated by scanning method. The dependence of the free energy barrier Fb and the chemical difference Deltamu on the concentration of chains can explain the behavior of polymer translocation at low and high concentration limits. The relationship between Deltamu and the escaping time tau(2) is in good agreement with the theoretical conclusions obtained by Muthukumar [J. Chem. Phys. 111, 10371 (1999)]. Our simulation results show that the relaxation time is mainly dominated by Fb, while the escaping time is mainly dominated by Deltamu.

Effect of interchain interactions on the translocation of polymer chains through small holes

AbstractThe translocation of polymer chains through a small hole was simulated with the dynamic Monte Carlo method. The dependence of the relaxation time (τ1) and escaping time (τ2) on the chain concentration (C) was studied. The interchain interaction played an important role in the translocation process. Different behaviors were discovered at low and high C regions. τ1 presented a power law behavior with C at low and high C values with exponents of −1 and −3, respectively. τ2 was roughly independent of C at low C values but decreased with power law exponent −1.3 at high C values. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 103: 1200–1205, 2007

Translocation of a polymer chain across a nanopore: A Brownian dynamics simulation study

We carried out Brownian dynamics simulation studies of the translocation of single polymer chains across a nanosized pore under the driving of an applied field (chemical potential gradient). The translocation process can be either dominated by the entropic barrier resulted from restricted motion of flexible polymer chains or by applied forces (or chemical gradient across the wall), we focused on the latter case in our studies. Calculation of radius of gyrations at the two opposite sides of the wall shows that the polymer chains are not in equilibrium during the translocation process. Despite this fact, our results show that the one-dimensional diffusion and the nucleation model provide an excellent description of the dependence of average translocation time on the chemical potential gradients, the polymer chain length and the solvent viscosity. In good agreement with experimental results and theoretical predictions, the translocation time distribution of our simple model shows strong non-Gaussian characteristics. It is observed that even for this simple tubelike pore geometry, more than one peak of translocation time distribution can be generated for proper pore diameter and applied field strengths. Both repulsive Weeks–Chandler–Anderson and attractive Lennard-Jones polymer–nanopore interaction were studied, attraction facilitates the translocation process by shortening the total translocation time and dramatically improve the capturing of polymer chain. The width of the translocation time distribution was found to decrease with increasing temperature, increasing field strength, and decreasing pore diameter.