Formation and positioning of nucleosomes: Effect of sequence-dependent long-range correlated structural disorder

The understanding of the long-range correlations (LRC) observed in DNA sequences is still an open and very challenging problem. In this paper, we start reviewing recent results obtained when exploring the scaling properties of eucaryotic, eubacterial and archaeal genomic sequences using the space-scale decomposition provided by the wavelet transform (WT). These results suggest that the existence of LRC up to distances ∼ 20-30kbp is the signature of the nucleosomal structure and dynamics of the chromatin fiber. Actually the LRC are mainly observed in the DNA bending profiles obtained when using some structural coding of the DNA sequences that accounts for the fluctuations of the local double-helix curvature within the nucleosome complex. Because of the approximate planarity of nucleosomal DNA loops, we then study the influence of the LRC structural disorder on the thermodynamical properties of 2D elastic chains submitted locally to mechanical/topological constraint as loops. The equilibrium properties of the one-loop system are derived numerically and analytically in the quite realistic weak-disorder limit. The LRC are shown to favor the spontaneous formation of small loops, the larger the LRC, the smaller the size of the loop. We further investigate the dynamical behavior of such a loop using the mean first passage time (MFPT) formalism. We show that the typical short-time loop dynamics is superdiffusive in the presence of LRC. For displacements larger than the loop size, we use large-deviation theory to derive a LRC-dependent anomalous-diffusion rule that accounts for the lack of disorder self-averaging. Potential biological implications on DNA loops involved in nucleosome positioning and dynamics in eucaryotic chromatin are discussed.     

Supercoiling and denaturation of DNA loops

We study the statistical mechanics of small DNA loops emphasizing the competition between elasticity, supercoiling, and denaturation. Motivated by recent experiments and atomistic molecular dynamics simulation, we propose a new coarse-grained phenomenological model of DNA. We extend the classical elastic rod models to include the possibility of denaturation and nonlinear twist elasticity. Using this coarse-grained model, we obtain a phase diagram in terms of fractional overtwist and loop size that can be used to rationalize a number of experimental results which have also been confirmed by atomistic simulations.     

凝血酶适体DNA四螺旋构象去折叠机制的NMR研究

凝血酶适体DNA\[thrombin binding DNA aptamer d (G₁G₂T₃T₄G₅G₆T₇G₈T₉G₁₀G₁₁T₁₂T₁₃G₁₄G₁₅),TBA]是对凝血酶有极高亲和性、并能有效抑制凝血酶凝血功能的单链DNA适体. 凝血酶适体DNA在K⁺等离子存在时呈现出椅式构象,其中2个堆积的四碱基体（G-quartet）构成椅子的主体部分,而1个TGT loop环和2个TT loop环分别构成椅子的靠背和椅脚. 我们测定了在K⁺存在时凝血酶适体DNA中亚氨基质子的交换速率, 发现位于TGT loop环和TT loop环内的亚氨基质子G6、G5和G14由于受TGT loop环和TT loop环的保护有比较小的交换速率,而位于环之外的亚氨基质子G2、G11和G15有较大的交换速率;TGT loop环稳定性同TT loop环相似;碱基T4、T13和T9在稳定凝血酶适体DNA结构中起着很大的作用. 这些证据进一步支持了凝血酶适体DNA的去折叠机制：位于TGT loop环和TT loop环之外的碱基对G1G15、G2G14和G5G11首先断裂其Hoogsteen氢键,而TGT loop环、TT loop环和其内的Hoogsteen氢键保持完好;当温度进一步升高时,TGT loop环和两个TT loop环打开环状结构,凝血酶适体DNA的椅式构象彻底解体,转变为自由单链.      

高阶高温超导量子干涉器件平面式梯度计的设计

设计了一种高温超导平面式梯度计的探测线圈，利用这种探测线圈与超导量子干涉器件(SQ UID)耦合，可以制成二阶或更高阶的高温超导SQUID平面式磁场梯度计.设计的探测线 圈由两个闭合环路组成，每个闭合环路是由若干个环路通过细小的连接通道连接而成.两个 闭合环路由一条超导窄带分割，将SQUID与这条超导窄带耦合可以测出超导窄带上的电流大 小.通过调整各个环路的形状、面积和位置，可以使超导窄带上的电流与磁场的高阶梯度成 正比，从而测得磁场的高阶梯度. 通过计算，得到了各个环路的面积、电感以及位置的关 系，在理 关键词： 高阶平面式磁场梯度计 高温超导薄膜     

Constrained thermal denaturation of DNA under fixed linking number

A DNA molecule with freely fluctuating ends undergoes a sharp thermal denaturation transition upon heating. However, in circular DNA chains and some experimental setups that manipulate single DNA molecules, the total number of turns (linking number) is constant at all times. The consequences of this additional topological invariant on the melting behaviour are nontrivial. Below, we investigate the melting characteristics of a homogeneous DNA where the linking number along the melting curve is preserved by supercoil formation in duplex portions. We obtain the mass fraction and the number of loops and supercoils below and above the melting temperature. We also argue that a macroscopic loop appears at T _c and calculate its size as a function of temperature.     

Melting and unzipping of DNA

Existing experimental studies of the thermal denaturation of DNA yield sharp steps in the melting curve suggesting that the melting transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic configurations of a DNA molecule consist of an alternating sequence of non-interacting bound segments and denaturated loops. Studies of these models neglect the repulsive, self-avoiding, interaction between different loops and segments and have invariably yielded continuous denaturation transitions. In the present study we take into account in an approximate way the excluded-volume interaction between denaturated loops and the rest of the chain. This is done by exploiting recent results on scaling properties of polymer networks of arbitrary topology. We also ignore the heterogeneity of the polymer. We obtain a first-order melting transition in d = 2 dimensions and above, consistent with the experimental results. We also consider within our approach the unzipping transition, which takes place when the two DNA strands are pulled apart by an external force acting on one end. We find that the under equilibrium condition the unzipping transition is also first order. Although the denaturation and unzipping transitions are thermodynamically first order, they do exhibit critical fluctuations in some of their properties. For instance, the loop size distribution decays algebraically at the transition and the length of the denaturated end segment diverges as the transition is approached. We evaluate these critical properties within our approach. Received 21 August 2001 and Received in final form 26 January 2002     

Direct visualization of the formation and structure of RecA/dsDNA complexes

A direct visualization of the construction of RecA/DNA nucleofilament complexes was obtained using high-resolution atomic force microscopy (AFM). It showed that the complex consisted of helical loops, with each helical loop composed of units of size equivalent to ～six monomers. The contour of stretched DNA that was embedded beneath RecA monomers was also observed directly. Images of RecA/DNA complexes showed both left- and right-handed helices, with a range of helical pitches. This was considered to imply that the complexes were flexible enough such that they are prone to compression forces that occur during sample preparation.     

Modeling DNA beacons at the mesoscopic scale

We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; alternative calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported. Stem formation is modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of opening and closing is described in terms of a diffusion-controlled motion in an effective free-energy landscape. Melting profiles, dependence of melting temperature on loop length, and kinetic time scales are in semiquantitative agreement with experimental data obtained from fluorescent DNA beacons forming poly(T) loops. Variation in strand rigidity is not sufficient to account for the large activation enthalpy of closing and the strong loop length dependence observed in hairpins forming poly(A) loops. Implications for modeling single strands of DNA or RNA are discussed.     

Scattering amplitudes with open loops

We introduce a new technique to generate scattering amplitudes at one loop. Traditional tree algorithms, which handle diagrams with fixed momenta, are promoted to generators of loop-momentum polynomials that we call open loops. Combining open loops with tensor-integral and Ossola-Papadopoulos-Pittau reduction results in a fully flexible, very fast, and numerically stable one-loop generator. As demonstrated with nontrivial applications, the open-loop approach will permit us to obtain precise predictions for a very wide range of collider processes.     

冲击条件下含纳米空洞的单晶铜的塌缩

利用分子动力学方法研究了单晶铜中不同大小的球形空洞在冲击波下的演化过程.模拟结果表明不同大小空洞的塌缩过程不同.模拟中冲击波由空洞左边扫向空洞右边.在较大尺寸的空洞塌缩过程中会产生系列的位错环.当空洞半径较小时,先在空洞的右侧形成位错环,当空洞半径增大到某一临界大小时,在空洞左右两侧同时产生位错环,当空洞半径较大时,先在空洞左侧形成位错环.当空洞左右两侧的位错环均形成以后,其右侧位错环前端的生长速度大于其左侧的.空洞半径增大,相应的位错环前端的生长速度变化不大.当空洞半径增大时,空洞中心指向位错源的矢量方 关键词： 纳米空洞 位错环 冲击波 塑性变形     

On the stochastic confinement in SU(2) lattice gauge theory

We extend the Olesen approach to confinement, originally proposed for SU(∞) gauge theory, to the SU(2) group. We perform Monte Carlo calculations of the spectral density, which describes the distribution of eigenvalues of the Wilson loop in the SU(2) lattice gauge theory (LGT), for square loops up to size 4 × 4. Our results indicate the onset of disorder in the 4-dimensional LGT so that at weak coupling confinement is due to non-abelian fluctuations of the gauge field. We describe the Monte Carlo data by formulae of the 2-dimensional LGT with some effective coupling constant. We formulate how this effective coupling constant should depend on the size of the loop in order that the Olesen hypothesis about the dimensional reduction (i.e. approximate reduction of the 4-dimensional LGT to the effective 2-dimensional LGT in the confinement region) would be held. Using the strong-coupling expansion where the Olesen hypothesis holds in fourteen orders, we perform quantitative estimates. The density of simple vortices up to size 4 × 4 is calculated. A connection between the definitions of spectral densities for the SU(∞) and SU(2) groups is considered. Explicit formulae for the spectral density in the 2-dimensional SU(2) LGT are derived.     

DNA 环化时间的半经验计算方法

DNA 分子是生命遗传信息的主要物质载体。DNA 环化是DNA 不同位置所携带信息的 一种协同实现方式。典型的例子是转录调控，增强子通过DNA 环化与启动子相互作用，从而 实现了对基因表达水平的调控。因此，破译DNA 的环化动力学是解读基础生命过程的重要课 题。本文在介绍DNA 结构和力学性质的基础上，综述DNA 环化时间的计算方法。在生理条件 下，DNA 的主要性质特点是弯折柔性强，而扭转和拉伸刚性强；据此，DNA 环化可视作自发 的熵减过程。运用热力学统计理论，可获得计算DNA 环化时间的半经验公式。公式中的参数可 由单分子光谱共聚焦技术测得的数据确定。该公式表明，空间拓扑决定了环化概率，DNA 长度 决定了环化时间。该公式适用于计算DNA 上的顺式元件之间、顺式元件与启动子之间的相互作 用。其优点在于避开了DNA 结构和细胞核环境的复杂性。     

Loop-space hamiltonians and numerical methods for large-N gauge theories (II)

We generalize our numerical loop-space methods to consider the full large-N Yang-Mills problem. First we study the weak-coupling phase in loop space and derive the equation obeyed by spacelike Wilson loops. We then consider the problem of topological reduction and derive the effective potential for topologically distinct loops. In connection with numerical computations we discuss the issues of truncation of the system. We present an initial numerical result for a simplest truncation of the full (2+1)-dimensional Yang-Mills theory.     

Elastic-energy relaxation in heterostructures with strained nanoinclusions

Elastic-energy relaxation in systems with nanoinclusions is considered. The relaxation is related to the formation of the following dislocation loops: a single misfit dislocation loop or a group of such loops on the matrix-nanoinclusion interface and/or a satellite dislocation loop near the inclusion. The critical inclusion sizes beginning from which misfit dislocation loops and satellite dislocation loops can nucleate are determined for various models of relaxation processes. The dependences of the satellite-dislocation-loop diameter on the inclusion size are calculated and compared with experimental data.     

In situ study of self-ion irradiation damage in W and W–5Re at 500 °C

In situ self-ion irradiations (150?keV?W⁺) have been carried out on W and W–5Re at 500?°C, with doses ranging from 10¹⁶ to 10¹⁸ W⁺m^?2 (～1.0?dpa). Early damage formation (10¹⁶W⁺m^?2) was observed in both materials. Black–white contrast experiments and image simulations using the TEMACI software suggested that vacancy loops were formed within individual cascades, and thus, the loop nucleation mechanism is likely to be ‘cascade collapse’. Dynamic observations showed the nucleation and growth of interstitial loops at higher doses, and that elastic loop interactions may involve changes in loop Burgers vector. Elastic interactions may also promote loop reactions such as absorption or coalescence or loop string formation. Loops in both W and W–5Re remained stable after annealing at 500?°C. One-dimensional hopping of loops (b?=?1/2 ?111>) was only seen in W. At the final dose (10¹⁸W⁺m^?2), a slightly denser damage microstructure was seen in W–5Re. Both materials had about 3–4?×?10¹⁵ loops m^?2. Detailed post-irradiation analyses were carried out for loops of size???4?nm. Both b?=?1/2 ?111? (～75%) and b?= ?100> (～25%) loops were present. Inside–outside contrast experiments were performed under safe orientations to determine the nature of loops. The interstitial-to-vacancy loop ratio turned out close to unity for 1/2 ?111? loops in W, and for both 1/2 ?111? and ?100? loops in W–5Re. However, interstitial loops were dominant for ?100? loops in W. Re seemed to restrict loop mobility, leading to a smaller average loop size and a higher number density in the W-Re alloy.     

Torus destruction in a nonsmooth noninvertible map

We consider here a nonsmooth noninvertible map and report new route to chaos from a resonance loop torus which is not homeomorphic to circle but only endomorphic to it. We have found that cusp torus cannot develop before the onset of chaos, though the loop torus appears. The destruction of the loop torus occurs through homoclinic bifurcation in the presence of an infinite number of nonsmooth loops. We show that owing to the nonsmooth noninvertible nature of the map, the stable sets can bifurcate to form nonsmooth closed loops. However, that cannot be interpreted directly as basin bifurcation.     

Effect of interaction between loop bases and ions on stability of G-quadruplex DNA

G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics(MD), and steered MD(SMD)simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions(K⁺/Na⁺)is about the base stacking free energies indicates that there will be a competition among the binding of M⁺-base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K+was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K+, such an interaction was unable to promote the stability of the loop with the sequence Cyt.     

Renormalization of loop functions in QCD

We give a short overview of the renormalization properties of rectangular Wilson loops, the Polyakov loop correlator and the cyclic Wilson loop. We then discuss how to renormalize loops with more than one intersection, using the simplest non-trivial case as an illustrative example. Our findings expand on previous treatments. The generalized exponentiation theorem is applied to the Polyakov loop correlator and used to renormalize linear divergences in the cyclic Wilson loop.     

Two-dimensional wetting with binary disorder: a numerical study of the loop statistics

We numerically study the wetting (adsorption) transition of a polymer chain on a disordered substrate in 1+1 dimension. Following the Poland-Scheraga model of DNA denaturation, we use a Fixman-Freire scheme for the entropy of loops. This allows us to consider chain lengths of order N ∼10⁵ to 10⁶, with 10⁴ disorder realizations. Our study is based on the statistics of loops between two contacts with the substrate, from which we define Binder-like parameters: their crossings for various sizes N allow a precise determination of the critical temperature, and their finite size properties yields a crossover exponent φ=1/(2-α) ≃0.5. We then analyse at criticality the distribution of loop length l in both regimes l ∼O(N) and 1 ≪l ≪N, as well as the finite-size properties of the contact density and energy. Our conclusion is that the critical exponents for the thermodynamics are the same as those of the pure case, except for strong logarithmic corrections to scaling. The presence of these logarithmic corrections in the thermodynamics is related to a disorder-dependent logarithmic singularity that appears in the critical loop distribution in the rescaled variable λ=l/N as λ↦1.     

The Circular Loop Equation of a Cosmic String with Time-Varying Tension in de Sitter Spacetimes

In this work the equation of circular loops of cosmic string possessing time-dependent tension is studied in the de Sitter spacetime. We find that the cosmic string loops with initial radius r(t ₀)>0.707L, L de Sitter radius, should not collapse to form a black hole. It is also found that in the case of r(t ₀)<0.707L a loop of cosmic string whose tension depends on some power of cosmic time can not become a black hole if the power is lower than a critical value which is associated with the initial size of the loop. Our research gives rise to some important corrections to the conclusion in the case of loops of cosmic string with constant tension in the same background.