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     

Effects of an attractive wall on the translocation of polymer under driving

The effects of an attractive wall at the trans side on the translocation of an eight-site bond-fluctuation model (BFM) polymer through a pore in a membrane under driving are simulated by the dynamic Monte Carlo method. The attractive wall shows two contrary effects: its excluded volume effect reduces configuration entropy and thus hinders the translocation of the polymer, while its attraction decreases the energy and thus accelerates the translocation. At a critical polymer-wall interaction ε*?≈-?1, we find that the two effects compensate each other and the translocation time τ is roughly independent of the separation distance between the wall and the pore. The value ε*?≈-?1 is roughly equal to the critical adsorption point for the BFM polymer. Moreover, the value of the critical attraction is roughly independent of chain length N and chemical potential difference Δμ. At last, a scaling relation τ?～?N(α) is observed for polymer translocation at a high value of NΔμ. Though the translocation time is highly dependent on the polymer-wall interaction and pore-wall separation distance, the exponent α is always about 1.30?±?0.05 so long as NΔμ is large enough.     

Theoretical study on adsorption properties of methyl methacrylate and its molecular chain within metal‐organic frameworks

Utilizing metal‐organic frameworks (MOFs) as a “polymerization container” is a very effective method to prepare oriented and therefore birefringent polymer materials. In particular, the adsorption of polymer monomers and molecular chains within MOFs has a profound impact on the orientation of polymer chains. In this work, a theoretical study on the adsorption properties of methyl methacrylate (MMA) and its molecular chain within MOFs has been conducted by employing a combination of molecular dynamics, density functional theory, and Monte Carlo method, where 2 MOFs, [Zn₂(1,4‐benzenedicarboxylate)₂triethylenediamine]_n and [Zn₂(4,4′‐biphenyldicarboxylate)₂triethylenediamine]_n, were chosen. The corresponding number and degree of orientation of adsorbed molecules in these 2 MOFs were obtained from the simulations. The calculation results revealed 3 factors that affect the adsorption and orientation of MMA monomers in MOF pore channels. First, as the walls of the MOF pores are polar surfaces and consist of metal ions and organic ligands, the electrostatic interaction between the MOF channels and polar MMA molecules promotes the adsorption and orientation of the MMA monomers within the pore channel. Second, the electrostatic interactions between monomers can reduce the intermolecular gaps, which similarly assist in their orientation. Last, the relative sizes of the MOF pores and the monomers are also relevant. When the sizes of the MOF channels and monomers are similar, the molecular chains show a higher degree of orientation. The results and the findings of this work could provide predictive methods for selecting polymeric monomers or MOFs that may be ideal for the control of polymer chain orientation.     

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.     

Polymer translocation in a double-force arrangement

Using Langevin dynamics simulations, we investigate the translocation dynamics of an externally driven polymer chain through a nanopore, where a pulling force F is exerted on the first monomer whilst there is an opposing force F _E < F within the pore. Such a double-force arrangement has been proposed recently to allow better dynamical control of the translocation process in order to sequence biopolymers. We find that in the double-force arrangement translocation becomes slower as compared to the case under a single monomer pulling force of magnitude F - F _E , but scaling of the translocation time as a function of the chain length ∼ N ² does not change. The waiting time (m) for monomer m to exit the pore is found to be a monotonically increasing function of the bead number almost until m N , which indicates relatively well-defined slowing down and control of the chain velocity during translocation. We also study the waiting time distributions for the beads in the chain, and characterize in detail fluctuations in the bead positions and their transverse position coordinates during translocation. These data should be useful in estimating position-dependent sequencing errors in double-force experiments.     

An ionic force-field study of monomers, dimers and higher polymers in pentafluoride vapors

Pentafluoride compounds such as NbF₅ and TaF₅ have been reported in the literature to admit various states of polymerization coexisting with monomers in their vapor phase, in relative concentrations that vary with temperature and pressure. We construct a microscopic interionic force-field model for the molecular monomer of these compounds (including VF₅, SbF₅ and MoF₅ in addition to NbF₅ and TaF₅), the stable form of the monomer being in the shape of a D_3h trigonal bipyramid in all cases. The model emulates chemical bonds by allowing for electrical and short-range overlap polarizabilities of the fluorines, and is used to evaluate the structure and the stability of (MF₅)_n molecules with n running from 2 to 6. The dimer is formed by two distorted edge-sharing octahedral, while the trimer and the higher polymers can form rings of distorted corner-sharing octahedra. A chain-like configuration is also found for the trimer of NbF₅, which consists of a seven-fold coordinated Nb bonded to two distorted octahedra via edge sharing. Comparison of calculated vibrational frequencies and bond lengths with experimental data is made whenever possible. We find that there is a small net gain of energy in the formation of a dimer, while otherwise the static energy of the n-mer is very close to that of n separated monomers. High sensitivity of the state of molecular aggregation to the thermodynamic conditions of the vapor is clearly indicated by our calculations.     

Theory of transport of long polymer molecules through carbon nanotube channels

A theory of transport of long chain polymer molecules through carbon nanotube (CNT) channels is developed using the Fokker-Planck equation and direct molecular dynamics simulations. The mean transport or translocation time tau is found to depend on the chemical potential energy, the entropy, and the diffusion coefficient. A power law dependence tau approximately N2 is found, where N is the number of monomers in a molecule. For 10(5)-unit long polyethylene molecules, tau is estimated to be approximately 1 micros. The diffusion coefficient of long polymer molecules inside CNTs, like that of short ones, is found to be a few orders of magnitude larger than in ordinary silicate based zeolite systems.     

Free energy evaluation in polymer translocation via Jarzynski equality

We perform, with the help of cloud computing resources, extensive Langevin simulations, which provide free energy estimates for unbiased three-dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite-size scaling properties.     

Reaction kinetics in polymer melts

We study the reaction kinetics of end-functionalized polymer chains dispersed in an unreactive polymer melt. Starting from an infinite hierarchy of coupled equations for many-chain correlation functions, a closed equation is derived for the 2nd order rate constant k after postulating simple physical bounds. Our results generalize previous 2-chain treatments (valid in dilute reactants limit) by Doi [#!doi:inter2!#], de Gennes [#!gennes:polreactionsiandii!#], and Friedman and O'Shaughnessy [#!ben:interdil_all_aip!#], to arbitrary initial reactive group density n₀ and local chemical reactivity Q. Simple mean field (MF) kinetics apply at short times, .For high Q, a transition occurs to diffusion-controlled (DC) kinetics with (where x_t is rms monomer displacement in time t) leading to a density decay . If n₀ exceeds the chain overlap threshold, this behavior is followed by a regime where during which k has the same power law dependence in time, , but possibly different numerical coefficient. For unentangled melts this gives while for entangled cases one or more of the successive regimes ,t ^-3/8 and t ^-3/4 may be realized depending on the magnitudes of Q and n₀. Kinetics at times longer than the longest polymer relaxation time are always MF. If a DC regime has developed before then the long time rate constant is where R is the coil radius. We propose measuring the above kinetics in a model experiment where radical end groups are generated by photolysis. Received: 2 June 1998 / Revised: 9 July 1998 / Accepted: 10 July 1998     

Mechanism for the formation of molecular clusters under ion sputtering

The mechanism for the formation of molecular Si _n O _2n+1 ^? clusters above the surface during the recombination of ions, atoms, and molecules independently sputtered in individual cascades is presented. Clusters form when sputtering products Si, O, SiO and SiO₂ (monomers) join the active anion O^? successively as a result of pair collisions between them. The joining of monomers involves different combinations of them; in this case, the (Si _n O_2n+1)^? group is formed and consists of monomers with the same masses, but with different monomer compositions in the chain (combinatorial synthesis).     

Dual Gas-responsive Fluorescent Diblock Copolymer Synthesized via RAFT Polymerization

Stimulus-responsive polymers with luminescence properties have a wide range of applications in the fields of controlled drug release, fluorescent probes, and biological stents. In this paper, carbon dioxide (CO₂)/oxygen (O₂) dual-responsive fluorescent diblock copolymers were synthesized by the reversible addition-fragmentation chain transfer (RAFT) polymerization method with two fluorescent monomers synthesized as its luminescence source, DEAEMA (CO₂ responsive monomer) and tFMA (O₂ responsive monomer). An experimental study demonstrated that the synthesized stimulus-responsive fluorescent polymer had a high sensitivity to CO₂; the double-responsive fluorescent diblock copolymer could form and achieve the reversal of polymer micelles in the aqueous solution when it was sequentially subjected to the introduction of CO₂ and O₂.

     

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.     

Diffusion of a Heteropolymer in a Multi-Interface Medium

We consider a heteropolymer, consisting of an i.i.d. concatenation of hydrophilic and hydrophobic monomers, in the presence of water and oil arranged in alternating layers. The heteropolymer is modelled by a directed path ( $\left( {i,S_i } \right)_{i \in \mathbb{N}_0 }$ , where the vertical component lives on $\mathbb{Z}$ , and the layers are horizontal with equal width. The path measure for the vertical component is given by that of simple random walk multiplied by an exponential weight factor that favors matches and disfavors mismatches between the monomers and the medium. We study the vertical motion of the heteropolymer as a function of its total length n when the width of the layers is d _n and the parameters in the exponential weight factor are such that the heteropolymer tends to stay close to an interface (“localized regime”). In the limit as n→∞ and under the condition that lim _n→∞ d _n /log log n=∞ and lim _n→∞ d _n /log n=0, we show that the vertical motion is a diffusive hopping between neighboring interfaces on a time scale exp[χd _n (1+o(1))], where χ is computed explicitly in terms of a variational problem. An analysis of this variational problem sheds light on the optimal hopping strategy.     

Preparation of Liquid Crystalline Molecularly Imprinted Polymer Coated Metal Organic Framework for Capecitabine Delivery

A novel molecularly imprinted polymer (MIP) coated metal organic framework (MOF) containing a liquid crystalline (LC) monomer is successfully synthesized for use in drug delivery systems. In this study, [Cu₃(BTC)₂(H₂O)₃] _n (HKUST‐1) is chosen as the MOF support owing to its large pore volume, good diffusion, and thermostability. 4‐Methyl phenyl dicyclohexyl ethylene (MPDE) is used as a LC monomer to increase the solvent‐responsive floating of the composite. The preparation conditions of HKUST‐1@LC‐MIP with capecitabine (CAPE) as a template, including the types of functional monomer, the ratio between template and functional monomer, as well as the content of MPDE, are investigated. Characterizations of the HKUST‐1@LC‐MIP are explored using scanning electron microscopy and transmission electron microscope images, Fourier transform infrared spectroscopy, thermal gravimetric analysis, X‐ray diffraction, and nitrogen adsorption. Compared to the HKUST‐1, the HKUST‐1@LC‐MIP shows better stability in aqueous solution. In vitro release studies of CAPE of HKUST‐1@LC‐MIP show zero‐order release of profiles at the loaded concentration of 500 µg mL^?1. From in vivo pharmacokinetic studies, the HKUST‐1@LC‐MIP displays higher relative bioavailability. It turns out that the HKUST‐1@LC‐MIP possesses the properties of controlled release and has the potentials for oral administration.     

Non-equilibrium effects in chaperone-assisted translocation of a stiff polymer

Chaperone-assisted biopolymer translocation is the main model proposed for translocation in vivo. A dynamical Monte Carlo method is used to simulate the translocation of a stiff homopolymer through a nanopore driven by chaperones. Chaperones are proteins that bind to the polymer near the wall and prevent its backsliding through Cis side. The important parameters include binding energy, size and the local concentration of the chaperones. The profile of these local concentrations, build up the chaperones distribution. Here we investigate the effects of binding energy, size and the exponential distribution of chaperones in their equilibration in each step of the polymer translocation needed for stable translocation time. The simulation results show that in case of chaperones with the size of a monomer ($\lambda =1$) and/or positive effective binding energy and/or uniform distribution, the chaperones binding equilibration rate/frequency is less than 5 times per monomer. However, in some special cases in the exponential distribution of chaperones with size $\lambda >1$ and negative effective binding energy the equilibration rate will diverge to more than 20 times per monomer. We show that this non-equilibrium effect results in supper diffusion, seen before. Moreover, we confirm the equilibration process theoretically.     

Contribution to the study of regularly alternating copolymers confined to strips and capillaries

Recurrence equations are proposed to calculate C_n, the total number of configurations, and x _n, the mean x projection of the end-to-end separation, for regularly alternating copolymers confined to strips and capillaries. We suppose that the monomer units are incompatible in solution and investigate the asymptotic behavior of x _n according to the solubility of the constituent monomers.     

Extended Huckel calculations on azo and azine analogues of polyacetylene

Extended Huckel calculations on the pi systems of polyazine, ?CHNNCH?_x, and polyazoethene, ?CHCHNN?_x, are reported. Two methods were used to find polymer band properties: extrapolation to infinite length of a series of long chain molecules and by the tightbinding method using a basis set derived from monomer (four atom) molecular orbitals. For both polymers in the all trans configuration, four pi bands are found with the lower two filled and the upper two empty. The band gap in polyazoethene is found to be 0.4 to 0.7 eV, while the band gap in polyazine is 1.9 to 2.3 eV implying that polyazoethene is expected to be a substantially better semiconductor than polyazine. Analysis of the long chain wave functions shows that the bonding and antibonding functions of the dimers CC and NN for polyazoethene or CN for polyazine are the appropriate orbitals to consider for describing the band properties of these polymers, and this is the starting point for the tightbinding calculation.     

Hydrogen bonds and polymerization in acrylamide under pressure

Acrylamide (C₃H₅NO), a hydrogen‐bonded amide, is an important compound from the point of view of basic and material research. It can be used as a model system for studying hydrogen bonding interactions in amides under pressure. As it is a monomer of polyacrylamide, an important polymer, high pressure investigation of polymerization in this material is also of interest. Our in‐situ high pressure Raman spectroscopic investigations of acrylamide carried out up to 17 GPa under quasi‐hydrostatic conditions indicate possible structural variations through the reconstruction of the N‐H‐‐‐O hydrogen bonds at pressures above 2.6 GPa. Emergence of several new spectral features at higher pressures indicate onset of polymerization. The characteristic polymer band becomes discernible at ~17 GPa. The increase in the relative intensity of the polymer peaks with respect to the monomer peaks on release to ambient conditions suggests that higher fraction of polymer is obtained on decompression. Copyright © 2013 John Wiley & Sons, Ltd.     

Plasma-based introduction of monosort functional groups of different type and density onto polymer surfaces. Part 2: Pulsed plasma polymerization

This new functionalization method consists of the deposition of very thin plasma polymer layers (20 to 100 nm) of functional group bearing monomers in pulsed plasma. With allylalcohol, a maximum of 30 OH groups per 100 C atoms was measured with a selectivity of about 90% and a significant stability at long-time exposure to air. Allylamine was used to produce primary amino groups, with a maximum of 18 NH₂groups per 100 C atoms. Side reactions were observed during the storage in air, such as oxidation of the amino groups. Carboxylic groups could be produced using acrylic acid with a maximum concentration of 24 COOH groups per 100 C atoms. The most prominent side reaction was the decarbonylation/ decarboxylation of the acid group during plasma deposition. The variation of the density of functional groups using the pulsed-plasma polymerization of functional-group-bearing monomers was possible by the chemically-initiated radical copolymerization with either a chain-extending monomer, such as ethylene, or a cross linker, such as butadiene, in plasma. The density of functional groups could be adjusted continuously (0 to 30 OH, 0 to 18 NH₂ and 0 to 24 COOH groups per 100 C atoms). The successful application of these densely functionalized polymer surfaces for producing biocompatible surfaces and for use in metal–polymer composites is proposed.     

Casimir force between two Aharonov-Bohm solenoids

The vacuum structure for the massive charged scalar field in the region of two parallel, infinitely long and thin solenoids confining the fluxesn ₁ andn ₂ is studied. By using the Green function method, it is found that the vacuum expectation value of the system's energy has a finite mutual interaction term depending on the distance a between the solenoids, which implies an attractive force per unit length given by F _n1n2 =–(c/²)(n ₁ n ₂)²/a ³.