Further Discussion on Polaron Existence in Dry DNA

We study the interaction between holes and molecular vibrations on dry DNA by using the extended Firsov＇s model. The ground state energy, calculated by using two Hilbert spaces, Fock state space and coherent state space, is confirmed. The polaron binding energy, defined with the ground state energy, is 0.014eV, much less than the thermal energy 0.026eV at room temperature 300K, which means that polarons are difficult to form self-trapping at room temperature and Anderson localization will prevent a metallic state on dry DNA. The results are consistent with the available experiments.     

Small polarons in dry DNA

We report ab initio calculations for positively charged fragments of dry poly(dC)-poly(dG) DNA, with up to 4 C-G pairs. We find a strong hole-lattice coupling and clear evidence for the formation of small polarons. The largest geometry distortions occur in only one or two base pairs. They involve the stretching of weak bonds within each base pair, increasing the distance of positive hydrogens, and decreasing that of negative oxygens, to the region in which the hole localizes. We obtain an energy of approximately 0.30 eV for the polaron formation, nearly independent of the chain size. From it, we can estimate an activation energy for polaron hopping of approximately 0.15 eV, consistent with the available experimental value.     

A Mechanism for the Self-Organization of Colloidal Gold Nanoparticles

We report a two-stage mechanism of formation of the two-dimensional surperlattices in colloidal gold nanoparticles. The first stage is the formation and growth of holes. When the film is thinner than the “pancake“ thickness and because the solvent volatility holes nucleate and grow, the dry solid surface is exposed. The second stage corresponds to the reorganization of the colloids in the impacted areas between several holes, in which the particles gathering along the rims order due to the van der Waals-type attraction between colloids and the confinement by the length of dodecanethiol. Then at a compromised distance and perfect position giving the minimum free energy, ordering occurs in small domains along the boundary of the hole. When the ordered domains become closer because of the hole growth, they rotate at certain angles and the further ordering appears.     

Spin states of holes in Ge/Si nanowire quantum dots

We investigate tunable hole quantum dots defined by surface gating Ge/Si core-shell nanowire heterostructures. In single level Coulomb-blockade transport measurements at low temperatures spin doublets are found, which become sequentially filled by holes. Magnetotransport measurements allow us to extract a g factor g approximately 2 close to the value of a free spin-1/2 particle in the case of the smallest dot. In less confined quantum dots smaller g factor values are observed. This indicates a lifting of the expected strong spin-orbit interaction effects in the valence band for holes confined in small enough quantum dots. By comparing the excitation spectrum with the addition spectrum we tentatively identify a hole exchange interaction strength chi approximately 130 microeV.     

Microdrilling for fabricating micrometer-scale holes in soft matter

Probing the response of soft materials at small scales requires examining fundamental behaviors that are often distinct from large-scale interactions. In the development of micrometer- and nanometer-sized holes in soft materials, understanding failure modes becomes essential. We observe fracture behavior in a soft material through a novel method, which leads to the fabrication of small-scale holes in polydimethylsiloxane. We utilize an ultra-sharp tungsten needle to drill this soft elastomeric polymer; this results in controlled hole size and exhibits fracture characteristics observed in brittle materials at larger length scales. We also examine the macroscopic characteristics known to contribute to brittleness and hardness for this material’s response with respect to curing times. This understanding will contribute to many applications including the development of porous materials and DNA sequencing efforts. PACS 81.05.Lg; 81.40.Np; 82.35.Lr     

DNA分子链的电子局域性质及电导的研究

将一维随机二元固体模型应用于DNA分子链，利用传输矩阵方法来研究系统电子态的局域性质并进而讨论系统的导电性质.对一个链长为50000个碱基对的DNA序列，数值分析了局域长度和电导随碱基对的摩尔百分数、本征能量和无序度的变化关系.结果表明，系统的局域长度和电导强烈地依赖于能量，在能带中心部分局域长度大于边沿部分.无序度也在一定程度上影响着局域长度，双方成反向变化的关系.对有限长度的DNA分子链，局域长度体现出明显的对碱基对摩尔百分数的依赖关系，对正常成分比例的随机DNA序列，在所有能量范围内系统的态都是局域的，系统的电导很小，系统呈现绝缘体行为.仅当一种碱基对在序列中所占比例很小时，系统中可以发现与特定分立能量值相对应的“扩展态”存在，处在这些态下的系统有较大的电导，但这些扩展态是不稳定的，在热力学极限之下会消失. 关键词： DNA分子链 电子局域 局域长度 电导     

多孔硅材料光学Anderson局域的研究

本文基于Anderson局域效应和有限时域差分(FDTD)计算方法,对具有一定无序性的多孔硅材料内光的横向局域进行了理论分析,考察了不同无序度、孔洞排列的不同方式对硅材料光学性质的影响。计算结果表明,多孔硅内光的行为和多孔硅的结构参数有很大关系。当结构参数合适时,光束可以呈现比较明显的横向局域效果。适当改变材料中孔道的排列方式,可以有效的调节光在材料中的传播方式与局域效果。设计了具有"边墙"效果的孔洞排列方式,不仅能够固定光斑的位置,而且还可实现光束的局域增强效果。     

Discrete nonlinear Schrödinger equation dynamics in complex networks

We investigate dynamical aspects of the discrete nonlinear Schrödinger equation in finite lattices. Starting from a periodic chain with nearest neighbor interactions, we insert randomly links connecting distant pairs of sites across the lattice. Using localized initial conditions we focus on the time averaged probability of occupation of the initial site as a function of the degree of complexity of the lattice and nonlinearity. We observe that selftrapping occurs at increasingly larger values of the nonlinearity parameter as the lattice connectivity increases, while close to the fully coupled network limit, localization becomes more preferred. For nonlinearity values above a certain threshold we find a reentrant localization transition, viz. localization when the number of long distant bonds is small followed by delocalization and enhanced transport at intermediate bond numbers while close to the fully connected limit localization reappears.     

不同构型(In,Al)GaN合金发光机理的第一性原理研究

基于第一性原理的密度泛函理论,研究了纤锌矿（In,Al）GaN合金的4种构型（均匀、短链、小团簇、团簇-链共存模型）的电子结构和发光微观机理。结果表明,在InGaN合金中,短In-N-链和小In-N团簇都局域电子在价带顶（VBM）态。当小团簇与短链共存时,前者局域电子的能力明显强于后者,是辐射复合发光中心。然而,在AlGaN合金中,电子在VBM态的局域受短Al-N链和小Al-N团簇的影响并不显著。合金微观结构的不同会引起电子局域的改变,从而影响材料的发光性能,并对带隙和弯曲系数有重要影响。     

Analysis of DNA elasticity

With a model that incorporates hydrodynamics directly, we show that flow experiments can be used for detecting some characteristics of the DNA elasticity which manifest themselves clearly at large length scales but cannot be observed by mechanical forcing experiments even at very small length scales. By systematic analysis, the conclusiveness of different experimental methods is evaluated. For the wormlike chain, confirmed as the correct model for DNA, we find an underlying scaling relation between its extension and flow velocity of the form L(p) approximately v(0.155), which emphasizes the significance of hydrodynamics.     

Complete transmission through a periodically perforated rigid slab

The propagation of a normally incident plane acoustic wave through a three-dimensional rigid slab with periodically placed holes is modeled and analyzed. The spacing of the holes A and B, the wavelength lambda, and the thickness of the slab L are order one parameters compared to the characteristic size D of the holes, which is a small quantity. Scattering matrix techniques are used to derive expressions for the transmission and reflection coefficients of the lowest mode. These expressions depend only on the transmission coefficient, tau(0), of an infinitely long slab with the same configuration. The determination of tau(0) requires the solution of an infinite set of algebraic equations. These equations are approximately solved by exploiting the small parameter D/square root(AB). Remarkably, this structure is transparent at certain frequencies and opaque for all others. Such a structure may be useful in constructing narrow-band filters and resonators.     

Crystal plasticity simulations of microstructure-induced uncertainty in strain concentration near voids in brass

The uncertainty in mechanical response near a cylindrical hole in polycrystalline alpha brass was simulated as a function of variations in the crystallographic orientations of the grains near the hole. A total of 4 hole sizes were examined, including the case of a microstructure without a hole, and 45 simulations were performed for each case (yielding 180 simulations total) to acquire statistical data. For a hole larger than the grain size, the deformation resembles the homogenous solution but with perturbations due to the local microstructural environment. For a hole approximately equal to or smaller than the grain size, the deformation deviates substantially from the continuum behaviour, and depends strongly on the local microstructural environment surrounding the hole. Each population of simulations was analysed statistically to determine the effect of micro structural variability on strain localization near each of the four defect sizes. The coefficient of variation in the maximum plastic strain around microstructure-scale holes is about 37%, and the largest values of plastic strain are about twice those in the absence of microstructure. These results have significant implications for analyses of the margin of failure due to defects of this class (e.g. voids or small bolt holes).     

Elastic rod model of a supercoiled DNA molecule

We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod-like chain, involving two elastic constants, the bending and the twist rigidities. Writing this model in terms of Euler angles, we show that the corresponding Hamiltonian is singular and needs a small distance cut-off, which is a natural length scale giving the limit of validity of the model, of the order of the double-helix pitch. The rod-like chain in the presence of the cut-off is able to reproduce quantitatively the experimentally observed effects of supercoiling on the elongation-force characteristics, in the small supercoiling regime. An exact solution of the model, using both transfer matrix techniques and its mapping to a quantum mechanics problem, allows to extract, from the experimental data, the value of the twist rigidity. We also analyse the variation of the torque and the writhe-to-twist ratio versus supercoiling, showing analytically the existence of a rather sharp crossover regime which can be related to the excitation of plectoneme-like structures. Finally we study the extension fluctuations of a stretched and supercoiled DNA molecule, both at fixed torque and at fixed supercoiling angle, and we compare the theoretical predictions to some preliminary experimental data. Received 1 April 1999 and Received in final form 4 January 2000     

Molecular recoiling in polymer thin film dewetting

The molecular recoiling force stemming from nonequilibrium chain conformation was found to play a very important role in the dewetting stability of polymer thin films. Correct measurements and inclusion of this molecular force into thermodynamic consideration are crucial for analyzing dewetting phenomena and nanoscale polymer chain physics. This force was measured using a simple method based on contour relaxation at the incipient dewetting holes. The recoiling stress was found to increase dramatically with molecular weight and decreasing film thickness. The corresponding forces were calculated to be in the range from 9.0 to 28.2 mN/m, too large to be neglected when compared to the dispersive forces (approximately 10 mN/m) commonly operative in thin polymer films.     

Self-assembly of a colloidal interstitial solid with tunable sublattice doping

We determine the phase diagram of a binary mixture of small and large hard spheres with a size ratio of 0.3 using free-energy calculations in Monte Carlo simulations. We find a stable binary fluid phase, a pure face-centered-cubic (fcc) crystal phase of the small spheres, and binary crystal structures with LS and LS(6) stoichiometries. Surprisingly, we demonstrate theoretically and experimentally the stability of a novel interstitial solid solution in binary hard-sphere mixtures, which is constructed by filling the octahedral holes of an fcc crystal of large spheres with small spheres. We find that the fraction of octahedral holes filled with a small sphere can be completely tuned from 0 to 1. Additionally, we study the hopping of the small spheres between neighboring octahedral holes, and interestingly, we find that the diffusion increases upon increasing the density of small spheres.     

Conduction transition of nano-scaled molecular wires driven by environment coupling

We propose a hybridization model to simulate a molecular wire coupling with the environmental molecules. Results reveal that the conduction transition from conducting to semiconducting depends on the coupling strength. In our simulations, the non-equilibrium Green's function method is employed to calculate the current-voltage relationship for the molecular wire through metallic contacts. Our calculations show that the band gap can be manipulated from the outside molecules coupling. Temperature dependence of the conductivity is represented in our results with strong dependence in high temperature range, which is qualitatively comparable with the experimental results of DNA. In our results, with small coupling, the current is enhanced by the exchange. On the contrary, too large a coupling results in localization of the transport carriers, leading to a semiconducting like property. We try to associate this study with the conducting property of DNA, which can be manipulated by environmental modulation.     

Stretching DNA: Role of electrostatic interactions

The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent variational approach. For small values of the external force f, we find the extension scales as where is the Debye screening length. In the limit of large force the electrostatic effects can be accounted for within the semiflexible chain model of DNA by assuming that only small excursions from rod-like conformations are possible. In this regime the extension approaches the contour length as where f is the magnitude of the external force. The theory is used to analyze experiments that have measured the extension of double-stranded DNA subject to tension at various salt concentrations. The theory reproduces nearly quantitatively the elastic response of DNA at small and large values of f and for all concentration of the monovalent counterions. The limitations of the theory are also pointed out. Received 13 October 1998 and Received in final form 9 June 1999     

Electron-hole duality and vortex rings in quantum dots

In a quantum-mechanical system, particle-hole duality implies that instead of studying particles, we can get equivalent information by studying the missing particles, the so-called holes. Using this duality picture for fermions in a rotating trap the vortices appear as holes in the Fermi sea. Here we predict that the formation of vortices in quantum dots at high magnetic fields causes oscillations in the energy spectrum which can be experimentally observed using accurate tunneling spectroscopy. We use the duality picture to show that these oscillations are caused by the localization of vortices in rings.     

Proposal for a chaotic ratchet using cold atoms in optical lattices

We investigate a new type of quantum ratchet which may be realized by cold atoms in a double-well optical lattice, pulsed with unequal periods. The classical dynamics is chaotic and we find the classical diffusion rate D is asymmetric in momentum up to a finite time t(r). The quantum behavior produces a corresponding asymmetry in the momentum distribution which is "frozen-in" by dynamical localization provided the break time t(*)>or=t(r). We conclude that the cold atom ratchets require Db/ variant Planck's over 2pi approximately 1, where b is a small deviation from period-one pulses.     

Heterogeneous hole nucleation in electron-charged 4He wetting films

4He wetting layers on Cs exhibit an unusually long-lived metastable state upon undercooling to temperatures well below the wetting temperature T(w) approximately 1.9 K. The decay of this state by homogeneous thermal nucleation of holes is disfavored by the incipient divergence of the free energy barrier separating the metastable thick film from the stable thin-film state. We propose that interface deformations ("dimples") created by electrons bound at the 4He liquid-vapor interface can be used as nuclei for the heterogeneous nucleation of holes. The size and excess free energy of the dimple can be tuned by an applied electric field E which allows the lifetime of the metastable film to be controlled.