打结高分子链穿孔行为的研究

以三叶草型结(即3₁结)为例,采用分子动力学(MD)方法,研究打结高分子链在外场力作用下穿越微孔的动力学过程.模拟发现,在拉动打结高分子链的过程中,结的大小呈涨落变化,直至最后散结.定性讨论了结的存在对高分子链穿孔速率的影响.在外场力作用下,打结高分子链平均穿孔时间(τ)与链长(N)满足标度关系τ～N ^α,其中标度系数α随外场力f增大而增大.对于短链,外场力越大,平均穿孔时间越短     

Two-dimensional diffusion model for the biopolymers dynamics at nanometer scale

In this paper the driven transport of linear polymers through a nanopore is presented. Biopolymer physical behavior in an external electric field is modeled and its motion is simulated using the Langevin impulse integrator method. Within fairly large limits, the polymer translocation time is inversely proportional with the electric field intensity and directly proportional with the polymer chain length.      

Single long-polymer translocation through a long pore

This paper theoretically studies the free energy and conformational entropy of a long polymer threading a long nanopore (n₀/N \ge 0.1) on external electric field. The polymer expanded model is built in this paper, that is, a single long polymer chain with N monomers (each of size a) threading a pore with n₀ monomers can be regarded as polymer with N+n_{0} monomers translocating a 2-dimension hole embedded in membrane. A theoretical approach is presented which explicitly takes into account the nucleation theory. Our calculations imply that, the structure of polymer changes more acutely than other situation, while its leading monomer reaches the second vacuum and its end monomer escapes the first vacuum. And it is also shown that the length scale of polymer and pore play a very important role for polymer translocation dynamics. The present model predicts that the translocation time depends on the chemical potential gradient and the property of the solvent on sides of pore to some extent.     

Noise effects in two different biological systems

We investigate the role of the colored noise in two biological systems: (i) adults of Nezara viridula (L.) (Heteroptera: Pentatomidae), and (ii) polymer translocation. In the first system we analyze, by directionality tests, the response of N. viridula individuals to subthreshold signals plus noise in their mating behaviour. The percentage of insects that react to the subthreshold signal shows a nonmonotonic behaviour, characterized by the presence of a maximum, as a function of the noise intensity. This is the signature of the non-dynamical stochastic resonance phenomenon. By using a “soft” threshold model we find that the maximum of the input-output cross correlation occurs in the same range of noise intensity values for which the behavioural activation of the insects has a maximum. Moreover this maximum value is lowered and shifted towards higher noise intensities, compared to the case of white noise. In the second biological system the noise driven translocation of short polymers in crowded solutions is analyzed. An improved version of the Rouse model for a flexible polymer is adopted to mimic the molecular dynamics by taking into account both the interactions between adjacent monomers and the effects of a Lennard-Jones potential between all beads. The polymer dynamics is simulated in a two-dimensional domain by numerically solving the Langevin equations of motion in the presence of thermal fluctuations and a colored noise source. At low temperatures or for strong colored noise intensities the translocation process of the polymer chain is delayed. At low noise intensity, as the polymer length increases, we find a nonmonotonic behaviour for the mean first translocation time of the polymer centre of inertia. We show how colored noise influences the motion of short polymers, by inducing two different regimes of translocation in the dynamics of molecule transport.     

Active polymer translocation through flickering pores

Single file translocation of a homopolymer through an active channel under the presence of a driving force is studied using Langevin dynamics simulation. It is shown that a channel with sticky walls and oscillating width could lead to significantly more efficient translocation as compared to a static channel that has a width equal to the mean width of the oscillating pore. The gain in translocation exhibits a strong dependence on the stickiness of the pore, which could allow the polymer translocation process to be highly selective.     

Polaron dynamics in a system of coupled conjugated polymer chains

The motion of excitations such as polarons is believed to be of fundamental importance for the transport properties of conjugated polymers for the use in, e.g., polymer based LED's. We have investigated polaron dynamics in a system of coupled polymer chains in the presence of an external electric field. In particular, we focus on how a polaron migrates through the polymer lattice, i.e., the situation in which a polaron reaches a chain end and is scattered to the surrounding chains. We show that the outcome of this event strongly depends on the strength of the electric field, and we identify three different cases for the polaron migration.     

Translocation of polymers in a lattice model

Voltage-driven polymer translocation is studied by means of a stochastic lattice model. The model incorporates voltage drop over the membrane as a bias in the hopping rate through the pore and exhibits the two main ingredients of the translocation process: driven motion through the pore and diffusive supply of chain length towards the pore on the cis-side and the drift away from the pore on the trans-side. The translocation time is either bias limited or diffusion limited. In the bias-limited regime the translocation time is inversely proportional to the voltage drop over the membrane. In the diffusion-limited regime the translocation time is independent of the applied voltage, but it is rather sensitive to the motion rules of the model. We find that the whole regime is well described by a single curve determined by the initial slope and the saturation value. The dependence of these parameters on the length of the chain, the motion rules and the repton statistics are established. Repulsion of reptons as well as the increase of chain length decrease the throughput of the polymer through the pore. As for free polymers, the inclusion of a mechanism for hernia creations/annihilations leads to the cross-over from Rouse-like behaviour to reptation. For the experimentally most relevant case (Rouse dynamics) the bimodal power law dependence of the translocation time on the chain length is found.     

Molecular Dynamics simulation of a polymer chain translocating through a nanoscopic pore

The detection of linear polymers translocating through a nanoscopic pore is a promising idea for the development of new DNA analysis techniques. However, the physics of constrained macromolecules and the fluid that surrounds them at the nanoscopic scale is still not well understood. In fact, many theoretical models of polymer translocation neglect both excluded-volume and hydrodynamic effects. We use Molecular Dynamics simulations with explicit solvent to study the impact of hydrodynamic interactions on the translocation time of a polymer. The translocation time τ that we examine is the unbiased (no charge on the chain and no driving force) escape time of a polymer that is initially placed halfway through a pore perforated in a monolayer wall. In particular, we look at the effect of increasing the pore radius when only a small number of fluid particles can be located in the pore as the polymer undergoes translocation, and we compare our results to the theoretical predictions of Chuang et al. (Phys. Rev. E 65, 011802 (2001)). We observe that the scaling of the translocation time varies from τ ∼ N ^11/5 to τ ∼ N ^9/5 as the pore size increases (N is the number of monomers that goes up to 31 monomers). However, the scaling of the polymer relaxation time remains consistent with the 9/5 power law for all pore radii.     

Formation dynamics of bipolaron in a metal/polymer/metal structure

Charge injection process from metal electrode to a nondegenerate polymer in a metal/ polymer/ metal structure has been investigated by using a nonadiabatic dynamic method. We demonstrate that the dynamical formation of a bipolaron sensitively depends on the strength of applied electric field, the work function of metal electrode, and the contact between the polymer and the electrode. For a given bias applied to one of the electrode (V₀) and coupling between the electrode and the polymer (t^′), such as V₀=0.79 eV and t^′=1 eV, the charge injection process depending on the electric field can be divided into the following three cases: (1) in the absence of the electric field, only one electron tunnels into the polymer to form a polaron near the middle of the polymer chain; (2) at low electric fields, two electrons transfer into the polymer chain to form a bipolaron; (3) at higher electric fields, bipolaron can not be formed in the polymer chain, electrons are transferred from the left electrode to right electrode through the polymer one by one accompanying with small irregular lattice deformations.     

Photorefractive effect of a novel conjugate polymer containing transition metal complex

The photorefractive effect (PR) of a novels σ-π alternating polymer having 2,2'-bipyridyl in the polymer backbone and their ruthenium complexes has been investigated. The ruthenium complex was used as the charge generator, the σ-π alternating polymer backbone as the charge transporting channel and second-order nonlinear (NLO) optical chromophore. The photorefractive properties were demonstrated by two-beam coupling (2BC), degenerated four-wave mixing (DFWM) and field-induced orientation birefringence at wavelength of 532 nm. This polymer shows a enhanced photorefractive effect due to the efficient photoinduced metal-to-ligand charge transfer (MLCT) inside the ruthenium complex. A net optical gain of about 22 cm^-1 and the diffraction efficiency about 10% were obtained at the external electric field of 30 V/μm. Received 21 December 1999 and Received in final form 7 July 2001     

有机高分子链内的场致激子解离

基于SSH(Su-Schrieffer-Heeger)模型,采用静态及动力学自洽算法模拟了有机高分子链内激子在光激发及外电场作用下的形成与解离过程。结果表明,受光激发后,有机高分子链内激子的生成与解离密切依赖于施加外电场的时机,当外电场与光激发同时发生时,激子能否生成完全取决于电场强度的大小;而当外电场在光激发后的一段时间(通常为皮秒量级)之后被引入,则在有机高分子链内能够形成稳定的激子,且该激子只有在强外电场(超过1MV/cm)的作用下,才会发生解离,临界场强量级与实验结果相符合。     

Free energy and scalings for polymer translocation through a nanopore: A molecular dynamics simulation study combined with milestoning

Coarse-grained molecular dynamics simulations combined with milestoning method are used to study the stochastic process of polymer chain translocation though a nanopore. We find that the scalings for polymer translocation process (the chain is initialized with the first monomer in the nanopore) and for polymer escape process (the chain is initialized with the middle monomer in the nanopore) are different. The translocation process is mainly controlled by the entropic barrier, while the polymer escape process is driven by the effective force due to free energy difference.     

Effect of channel-protein of a protein-like chain interaction on translocation through a finite channel

We study the translocation of a protein-like chain through a finite cylindrical channel using the pruned-enriched Rosenbluth method(PERM) and the modified orientation-dependent monomer-monomer interaction(ODI) model.Attractive channels(ε cp = 2.0,1.0,0.5),repulsive channels(ε cp = 0.5,1.0,2.0),and a neutral channel(ε cp = 0) are discussed.The results of the chain dimension and the energy show that Z0 = 1.0 is an important case to distinguish the types of the channels.For the strong attractive channel,more contacts form during the process of translocation.It is also found that an external force is needed to drive the chain outside of the channel with the strong attraction.While for the neutral,the repulsive,and the weak attractive channels,the translocation is spontaneous.     

Polymer translocation in the presence of excluded volume and explicit hydrodynamic interactions

Molecular Dynamics simulations of polymer translocation are hereby reported. No external force was applied to the polymer during translocation, and the dynamics was dominated by polymer–pore interactions. It was found that hydrodynamic interactions play an important role in the relaxation of the polymer on each side of the membrane but have a negligible impact on the translocation process itself. Also, the scaling laws obtained for the relaxation and translocation times indicate that long translocating polymers may be considered to be following a quasi-equilibrium anomalous diffusion process in the absence of external forces.     

Passage times for unbiased polymer translocation through a narrow pore

We study the translocation process of a polymer in the absence of external fields for various pore diameters b and membrane thickness L. The polymer performs Rouse and reptation dynamics. The mean translocation time (tau(t)) that the polymer needs to escape from a cell and the mean dwell time (tau(d)) that the polymer spends in the pore during the translocation process obey scaling relations in terms of the polymer length N, L, and b/R(g), where R(g) is the radius of gyration for the polymer. We explain these relations using simple arguments based on polymer dynamics and the equilibrium properties of polymers.     

Dynamics of polyelectrolyte transport through a protein channel as a function of applied voltage

We study the transport of dextran sulfate through a protein channel as a function of applied voltage. Below 60 mV, the chain's entrance to the pore is hindered by an entropic barrier; above 60 mV, the strong local electric field forces the chain entrance. The effective charge of the polyelectrolyte inside the pore is reduced. We observe two types of blockades which have durations that decrease when the applied voltage increases. The shortest is a straddling time between the polyelectrolyte and the pore; the longest is the translocation time. The translocation time obeys an exponential dependence upon applied voltage.     

Effect of channelben protein interaction on translocation of a protein-like chain through a finite channel

We study the translocation of a protein-like chain through a finite cylindrical channel using the pruned-enriched Rosenbluth method (PERM) and the modified orientation-dependent monomer-monomer interaction (ODI) model. Attractive channels (ε_cp=-2.0, -1.0, -0.5), repulsive channels (ε_cp=0.5, 1.0, 2.0), and a neutral channel (ε_cp =0) are discussed. The results of the chain dimension and the energy show that Z₀=1.0 is an important case to distinguish the types of the channels. For the strong attractive channel, more contacts form during the process of translocation. It is also found that an external force is needed to drive the chain outside of the channel with the strong attraction. While for the neutral, the repulsive, and the weak attractive channels, the translocation is spontaneous.     

Translocation of Single Polymer Chain from Nanopore on a Membrane： Solvent Effect

We investigate the translocation of single polymer chain through a nanopore located on a membrane with different solvents in the two sides of the membrane. For the case under study, the effect of solvents on the translocation dynamics is significant, and as a result, the mean first passage time shortens remarkably compared with that calculated in the case of good solvents on both the sides of the membrane. In addition, we also discuss the condition such that the present result holds true.     

Interface water-induced hydrophobic carbon chain unfolding in water

The folding and unfolding of the carbon chain, which is the basic constitutional unit of polymers,are important to the performance of the material. However, it is difficult to regulate conformational transition of the carbon chain, especially in an aqueous environment. In this paper, we propose a strategy to regulate the conformational transition of the carbon chain in water based on the all-atom molecular dynamics simulations. It is shown that the unfolded carbon chain will spontaneously collapse into the folded state, while the folded carbon chain will unfold with an external electric field. The regulation ability of the electric field is attributed to the electric field-induced redistribution of interface water molecules near the carbon chain. The demonstrated method of regulating conformational transition of the carbon chain in water in this study provides an insight into regulating hydrophobic molecules in water, and has great potential in drug molecule design and new polymer material development.     

Dynamics of Polaron at Polymer/Polymer Interface

The migration of a polaron at polymer/polymer interface is believed to be of fundamental importance for the transport and light-emitting properties of conjugated polymer-based light emitting diodes. Based on the one- dimensional tight-binding Su-Schrieffer-Heeger （SSH） model, we have investigated polaron dynamics in a one- dimensional polymer/polymer system by using a nonadiabatic evolution method. In particular, we focus on how a polaron migrates through the conjugated polymer/polymer interface in the presence of external electric field. The results show that the migration of polaron at the interface depends sensitively on the hopping integrals, the potential barrier induced by the energy mismatch, and the strength of applied electric field which increases the polaron kinetic energy.