Semiflexible polymer confined to a spherical surface

We develop a formalism for describing the kinematics of a wormlike chain confined to the surface of a sphere that simultaneously satisfies the spherical confinement and the inextensibility of the chain contour. We use this formalism to study the statistical behavior of the wormlike chain on a spherical surface. In particular, we provide an exact, closed-form expression for the mean square end-to-end distance that is valid for any value of chain length L, persistence length l(p), and sphere radius R. We predict two qualitatively different behaviors for a long polymer depending on the ratio R/l(p). For R/l(p)>4, the mean square end-to-end distance increases monotonically with the chain length, whereas for R/l(p)<4, a damped oscillatory behavior is predicted.     

Dynamics of a polymer chain confined in a membrane

We present a Brownian dynamics theory with full hydrodynamics (Stokesian dynamics) for a Gaussian polymer chain embedded in a liquid membrane which is surrounded by bulk solvent and walls. The mobility tensors are derived in Fourier space for the two geometries, namely, a free membrane embedded in a bulk fluid, and a membrane sandwiched by the two walls. Within the preaveraging approximation, a new expression for the diffusion coefficient of the polymer is obtained for the free-membrane geometry. We also carry out a Rouse normal mode analysis to obtain the relaxation time and the dynamical structure factor. For large polymer size, both quantities show Zimm-like behavior in the free-membrane case, whereas they are Rouse-like for the sandwiched membrane geometry. We use the scaling argument to discuss the effect of excluded-volume interactions on the polymer relaxation time.     

Translocation of knotted proteins through a pore

We report the results of molecular dynamics simulations of translocation of knotted proteins through pores. The protein is pulled into the pore with a constant force, which in many cases leads to the tightening of the knot. Since the radius of tightened knot is larger than that of the pore opening, the tight knot can block the pore thus preventing further translocation of the chain. Analyzing six different proteins, we show that the stuck probability increases with the applied force and that final positions of the tightened knot along the protein backbone are not random but are usually associated with sharp turns in the polypeptide chain. The combined effect of the confining geometry of the pore and the inhomogeneous character of the protein chain leads thus to the appearance of topological traps, which can immobilize the knot and lead to the jamming of the pore.     

Transverse migration of a confined polymer driven by an external force

We demonstrate that a polymer confined to a narrow channel migrates towards the center when driven by an external force parallel to the channel walls. This migration results from asymmetric hydrodynamic interactions between polymer segments and the confining walls. A weak pressure-driven flow, applied in the same direction as the external force, enhances the migration. However, when the pressure gradient and the external force act in opposite directions the polymer can migrate towards the boundaries. Nevertheless, for sufficiently strong forces the polymer always migrates towards the center. A dumbbell kinetic theory explains these results qualitatively. A comparison of our results with experimental measurements on DNA suggests that hydrodynamic interactions in polyelectrolytes are only partially screened. We propose new experiments and analysis to investigate the extent of the screening in polyelectrolyte solutions.     

Holographic phase conjugation through a sub-wavelength hole

Holographic phase conjugation is analyzed as a method to create a photo-refractive lens with high numerical aperture. For this purpose a sub-wavelength hole is drilled into a metal surface directly on top of an iron-doped lithium niobate crystal. An interference pattern generated by the light coming from this point source and a plane reference wave is recorded. By using the phase-conjugated reference wave for read-out, a light wave being focused onto the former point source is reconstructed. In principle, a focusing system close to the theoretical diffraction limit could be implemented by this method. The performance of this arrangement is mainly determined by properties of the lithium niobate crystal, especially the crystal symmetry. Experimentally, the tight holographic focusing is demonstrated. The focus width of the reconstructed wave is shown to be below 1.2 μm, which is our spatial resolution. The diffraction efficiency obtained, however, is just 3×10⁻⁵ compared to 3×10⁻² in the plane-wave case. This can be explained by experimental reasons, the inhomogeneous light intensity and limitations originating from the crystal symmetry. We estimate that the diffraction efficiency for phase conjugation through a sub-wavelength hole can be improved by three to four orders of magnitude by addressing the above-mentioned issues.     

Transmission of light through a single rectangular hole

We show that a single rectangular hole in a metallic film exhibits transmission resonances that appear near the cutoff wavelength of the hole waveguide. For light polarized with the electric field pointing along the hole's short axis, it is shown that the normalized-to-area transmittance at resonance is proportional to the ratio between the long and short sides, and to the dielectric constant inside the hole. Importantly, this resonant transmission process is accompanied by a huge enhancement of the electric field at both entrance and exit interfaces of the hole.     

Electron–hole transition energy for a spherical quantum dot confined in a nano-cylindrical wire

A single-band constant confining potential is applied to InAs spherical quantum dot confined in a GaAs cylindrical nano-wire to determine the electronic structure. The energy eigenvalues and transition energies are numerically calculated as a function of the dot radius. The calculations were performed within the effective mass approximation, using the finite element method. The effect of both spherical and cylindrical confinement, the size dependence of the ground and first excited state energies for electron and heavy hole and transition energies are reported and compared with experimental and theoretical results in relevant conditions.     

Orbits through the ergosphere of a Kerr black hole

We study the positions of orbits around a Kerr black hole with respect to its ergosphere. Ther– motions of zero-energy (E=0) null geodesies are inside truncated circular sectors, whose outer corners are on the static limit. Timelike geodesies with the same constants of motion are restricted inside a smaller area. For certain parameter values there are also orbits inside the inner horizon not reaching the center. Then we study the various types of orbits on the plane of symmetry for all the values of the angular momentum of the black hole 0aM, and of the angular momentum of the photons, or particles,L, and for all the values of the energyE. In particular we find the possible positions of the turning points with respect to the ergosphere. A restriction imposed by physical considerations is that the coordinate time increases when the proper time increases. This allows us to distinguish between positive and negative energy orbits. All negative energy orbits enter the horizon of the black hole.     

Translocation of closed polymers through a nanopore under an applied external field

The dynamic behaviours of the translocations of closed circular polymers and closed knotted polymers through a nanopore, under the driving of an applied field, are studied by three-dimensional Langevin dynamics simulations. The power-law scaling of the translocation time τ with the chain length N and the distribution of translocation time are investigated separately. For closed circular polymers, a crossover scaling of translocation time with chain length is found to be τ～ N α , with the exponent α varying from α = 0.71 for relatively short chains to α = 1.29 for longer chains under driving force F = 5. The scaling behaviour for longer chains is in good agreement with experimental results, in which the exponent α = 1.27 for the translocation of double-strand DNA. The distribution of translocation time D(τ) is close to a Gaussian function for duration time τ < τ p and follows a falling exponential function for duration time τ > τ p . For closed knotted polymers, the scaling exponent α is 1.27 for small field force (F = 5) and 1.38 for large field force (F = 10). The distribution of translocation time D(τ) remarkably features two peaks appearing in the case of large driving force. The interesting result of multiple peaks can conduce to the understanding of the influence of the number of strands of polymers in the pore at the same time on translocation dynamic process and scaling property.     

Kinetics of water flow through a polymer gel

The water flow through the poly(acrylamide) gel under a constant water pressure is measured by newly designed apparatus. The Young modulus and Poisson’s ratio of the rod shape gels are measured by the uni-axial elongation experiments, which determine the longitudinal modulus independently from the water flow experiments. The time evolution of the water flow in the dilute gel is calculated based on the collective diffusion model of the polymer network coupled with the friction between the polymer network and the water. The calculated results are compared with the time evolution of the flow experiments, and the values of the longitudinal modulus and the friction coefficient are estimated. The estimated values are consistent with the results of our mechanical-response experiments and the light scattering experiments reported previously. We find that the time evolution of the water flow is well described by a single characteristic relaxation time predicted by our model for dilute gels.     

受限于圆柱体内半刚性高分子链的螺旋结构转变

采用非格点珠簧球链模型, 结合Monte Carlo方法, 研究了半刚性高分子链受限于无限长圆柱体的构象性质. 模拟结果表明: 在圆柱体内表面附近具有吸附能的情况下, 当弯曲能b由小到大变化时, 发现半刚性高分子链由开始时的无规则被吸附在圆柱体内表面, 到逐渐出现螺旋结构, 最后伸展成类似棒状的结构. 同时计算了不同弯曲能b时的半刚性高分子链的平均螺旋数N_t, 平均每条链单体的螺旋百分比P_h和能量涨落. 发现高分子链螺旋结构的形成与转变, 不仅与圆柱体半径R的大小有关, 还与弯曲能b的大小有关. 研究结果能有助于加深对受限生物大分子构象的认识.     

Enhanced and confined light transmission through a funnel-type aperture with a sub-wavelength outlet

Enhanced transmission through sub-wavelength hole arrays and a single sub-wavelength aperture with periodic corrugations surrounded have been investigated extensively. We report the similar phenomenon through a funnel-type aperture with a sub-wavelength outlet in a thick silver film, which was obtained numerically by using finite-difference time-domain method. Properties of the transmission spectrum can be modulated by geometric parameters of the funnel-type aperture. With periodic grooves or dielectric gratings on the output surface of the structure, beaming light emission can be obtained.     

The influence of hole shape on enhancing transmission through subwavelength hole arrays

The extraordinary light transmission through a 200-nm thick gold film when passing through different subwavelength hole arrays is observed experimentally. The sample is fabricated by electron beam lithography and reactive ion etching system. A comparison between light transmissions shows that the hole shape changing from rectangular to diamond strongly affects the transmission intensity although both structures possess the same lattice constant of 600,nm. Moreover, the position of the transmission maximum undergoes a spectral red-shift of about 63,nm. Numerical simulations by using a transfer matrix method reproduce the observed transmission spectrum quite well.     

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     

Scaling exponents of forced polymer translocation through a nanopore

We investigate several properties of a translocating homopolymer through a thin pore driven by an external field present inside the pore only using Langevin Dynamics (LD) simulations in three dimensions (3D). Motivated by several recent theoretical and numerical studies that are apparently at odds with each other, we estimate the exponents describing the scaling with chain length (Nof the average translocation time \(\ensuremath \langle\tau\rangle\) , the average velocity of the center of mass \(\ensuremath \langle v_{{\rm CM}}\rangle\) , and the effective radius of gyration \(\ensuremath \langle {R}_g\rangle\) during the translocation process defined as \(\ensuremath \langle\tau\rangle \sim N^{\alpha}\) , \(\ensuremath \langle v_{{\rm CM}} \rangle \sim N^{-\delta}\) , and \(\ensuremath {R}_g \sim N^{\bar{\nu}}\) respectively, and the exponent of the translocation coordinate (s -coordinate) as a function of the translocation time \(\ensuremath \langle s^2(t)\rangle\sim t^{\beta}\) . We find \(\ensuremath \alpha=1.36 \pm 0.01\) , \(\ensuremath \beta=1.60 \pm 0.01\) for \(\ensuremath \langle s^2(t)\rangle\sim \tau^{\beta}\) and \(\ensuremath \bar{\beta}=1.44 \pm 0.02\) for \(\ensuremath \langle\Delta s^2(t)\rangle\sim\tau^{\bar{\beta}}\) , \(\ensuremath \delta=0.81 \pm 0.04\) , and \(\ensuremath \bar{\nu}\simeq\nu=0.59 \pm 0.01\) , where \( \nu\) is the equilibrium Flory exponent in 3D. Therefore, we find that \(\ensuremath \langle\tau\rangle\sim N^{1.36}\) is consistent with the estimate of \(\ensuremath \langle\tau\rangle\sim\langle R_g \rangle/\langle v_{{\rm CM}} \rangle\) . However, as observed previously in Monte Carlo (MC) calculations by Kantor and Kardar (Y. Kantor, M. Kardar, Phys. Rev. E 69, 021806 (2004)) we also find the exponent α = 1.36 ± 0.01 < 1 + ν. Further, we find that the parallel and perpendicular components of the gyration radii, where one considers the “cis” and “trans” parts of the chain separately, exhibit distinct out-of-equilibrium effects. We also discuss the dependence of the effective exponents on the pore geometry for the range of N studied here.     

Dynamic instability of strongly confined thin polymer films in spinodal dewetting

We present a general criterion for determining the dynamic instability of a thin polymer film that is strongly confined to a substrate. When such a polymer film is heated above its glass transition temperature, it dewets from the substrate by a spinodal dewetting scenario, in which the onset of the instability is governed by dispersion force and residual thermal stress. It turns out that the thermal stress plays an important role when there is a special interaction between a polymer and a substrate.