Dynamic cluster-scaling in DNA

It is shown that the nucleotide sequences in DNA molecules have cluster-scaling properties (discovered for the first time in turbulent processes [K.R. Sreenivasan, A. Bershadskii, J. Stat. Phys. 125 (2006) 1141]. These properties are relevant to both types of nucleotide pair-bases interactions: hydrogen bonds and stacking interactions. It is shown that taking into account the cluster-scaling properties can help to improve heterogeneous models of the DNA dynamics. Two human genes: BRCA2 and NRXN1, have been considered as examples.     

Interaction of dopant atoms with stacking faults in silicon

The width of a stacking fault ribbon bound by a pair of partial dislocations in silicon crystals was unchanged when boron and gallium atoms of p-type dopant were agglomerated nearby the ribbon by annealing, even though the width increased when n-type dopant atoms were agglomerated as previously reported [Y. Ohno, Y. Tokumoto, I. Yonenaga, Thin Solid Films, accepted for publication]. The origin of the width-increase in n-type crystals was proposed as the reduction of the stacking fault energy, from 58±5 down to 46±5 mJ/m², due to an electronic interaction between the ribbon and the n-type dopant atoms, and the interaction energy was estimated to be 0.15±0.05 eV. On the other hand, the interaction of p-type dopant atoms with stacking faults was not detected.     

Coherence and oscillations of cosmic neutrinos

For cosmic neutrinos we study the conditions and the effects of the coherence loss as well as coherent broadening of the spectrum. We evaluate the width of the neutrino wavepacket produced by charged particles under various circumstances: in an interaction-free environment, in a radiation-dominated medium (typical of the sources of the gamma ray bursts) and in the presence of a magnetic field. The effect of the magnetic field on the wavepacket size appears to be more important than the scattering. If the magnetic field at the source is larger than 10 Gauss, the coherence of neutrinos will be lost while traveling over cosmological distances. Various applications of these results have been considered. We find that for large magnetic fields (B>10⁹ Gauss) and high energies (E_ν>PeV), “coherent broadening” can modify the energy spectrum of neutrinos. In the coherent case, averaging out the oscillatory terms of the probabilities does not induce any statistical uncertainty beyond what expected in the absence of these terms. A deviation from the standard quantum mechanics that preserves average energy and unitarity cannot alter the picture.     

Coherence and squeezing in superpositions of spin coherent states

We consider the superpositions of spin coherent states and study the coherence properties and spin squeezing in these states. The spin squeezing is examined using a new version of spectroscopic squeezing criteria. The results show that the antibuching effect can be enhanced and spin squeezing can be generated in the superpositions of two spin coherent states.     

谐振腔内非均匀介质和增益饱和引起的谐振模式的耦合和相干

建立了腔内的非均匀介质和增益饱和引起的谐振模式之间的耦合和相干理论。     

Coherence and the statistics of the phase difference between partially polarized electromagnetic waves

Coherence between two vectorial harmonic light vibrations is analyzed in terms of the statistics of their phase difference. This provides a natural and simple extension of second-order coherence to cover more complicate situations. In particular this assigns large coherence to quantum light states providing the most accurate interferometric measurements allowed by the quantum theory, even if they are incoherent according to the standard second-order approach.     

Coherence and stochastic resonance in a delayed bistable system

Both coherence resonance (CR) and stochastic resonance (SR) in a delayed bistable system driven by additive and multiplicative white noises and a weak harmonic excitation are studied by using the theory of two-state model. For the weak noise intensity and delayed feedback, the analytic expressions of power-spectrum and linear-spectrum amplification are derived to quantify the CR and the SR, respectively. The study shows that the peak in the power spectrum at the frequency corresponding to the time delay attains the maximum for an appropriate amount of additive noise intensity and the CR manifests. The feedback gain plays an important role in the SR. For example, the positive feedback gain enhances the SR, but the negative feedback gain suppresses the system output and makes the SR disappear. Moreover, the system also exhibits the frequency SR.     

Coherence resonance in an excitable potential well

The excitable behaviour is considered as motion of a particle in a potential field in the presence of dissipation. The dynamics of the oscillator proposed in the present paper corresponds to the excitable behaviour in a potential well under condition of positive dissipation. Type-II excitability of the offered system results from intrinsic peculiarities of the potential well, whose shape depends on a system state. Concept of an excitable potential well is introduced. The effect of coherence resonance and self-oscillation excitation in a state-dependent potential well under condition of positive dissipation are explored in numerical experiments.     

Direct or indirect semiconductor: The role of stacking fault in h-BN

Electronic properties of hexagonal boron nitride (h-BN) with stacking fault have been systematically studied using the first-principles method. The formation energy of a single layer stacking fault in five typical stacking h-BN (AA, AB, AD, AE and AF) ranges from −58 to 55 meV, which indicates that the stacking fault can be easily introduced into the material. Amazingly, we find that as long as AA, AB, AD and AF stacking h-BN with AE-liked stacking fault they are similar to AE stacking with or without stacking fault behaving as quasi-direct or direct semiconductor. We predict that the AE-liked stacking sequence may be the primary reason for the inconsistency between theoretical and experimental reports according to the type of the band gap of h-BN.     

倒Y型四能级系统中自发辐射诱导相干对弱探测场的色散和吸收特性的影响

本文研究了倒Y型四能级系统中自发辐射诱导相干对探测场的色散和吸收特性的影响。在稳态条件下利用密度矩阵微扰理论推导出了密度矩阵的迭代解。数值分析了自发辐射诱导相干对线性和非线性折射率和吸收系数的影响,分析了泵浦场和耦合场偏离双光子共振对弱探测场色散和吸收特性的影响。研究发现自发辐射诱导相干使弱探测光的线性和非线性折射率增强,同时形成一个较宽的透明窗。在没有自发辐射诱导相干的情况下,泵浦场和耦合场偏离双光子共振对探测场的线性和非线性折射率影响明显,在有自发辐射诱导相干的情况下,泵浦场和耦合场偏离双光子共振使得探测场的线性透明窗变窄,非线性吸收增加。     

捕光复合物中起源于电子-振动耦合的长时间相干

We theoretically investigate the evolutions of two-dimensional, third-order, nonlinear pho-ton echo rephasing spectra with population time by using an exact numerical path integral method. It is shown that for the same system, the coherence time and relaxation time of excitonic states are short, however, if the couplings of electronic and intra-pigment vibra-tional modes are considered, the coherence time and relaxation time of this vibronic states are greatly extended. It means that the couplings between electronic and vibrational modes play important roles in keeping long-lived coherence in light-harvesting complexes. Particularly, by using the method we can fix the transition path of the energy transfer in bio-molecular systems.     

Global transposable characteristics in the complete DNA sequence of the yeast

Global transposable characteristics in the complete DNA sequence of the Saccharomyces cevevisiae yeast is determined by using the metric representation and recurrence plot methods. On the basis of the correlation distance of nucleotide strings, 16 chromosome sequences of the yeast, which are divided into 5 groups, display 4 kinds of the fundamental transposable characteristics: a short increasing period, a long increasing quasi-period, a long major value and hardly relevant.     

时空非相干光孤子的传播和相干特性

研究了时空非相干椭圆形高斯光束在饱和对数型非线性介质中的自陷行为,得到了孤子的形成条件并分析了其相干特性,讨论了光束自陷的变化形式,发现光束的初态和材料非线性对其有决定性的影响, 并进一步获得了光束半径和光束相干半径的解析表达式,发现光束的相干特性不但会随传播距离产生周期性的变化,且随组份频率的增大而减弱.     

Coherence and polarization properties of a three-dimensional, primary, quasi-homogeneous, and isotropic source and its far field

We study the spatial coherence properties of a three-dimensional, primary, quasi-homogeneous, and isotropic source and the far field that it generates. We assess the spectrum, degree of polarization, electromagnetic degree of coherence, and effective degree of coherence of the source and of the far field. We also demonstrate the formalism for a spherical Gaussian Schell-model current source. The polarization properties of light are fully accounted for in the analysis, and it is found that certain results pertaining to scalar coherence theory are reproduced also within the electromagnetic treatment.     

Coherence resonance induced by non-Gaussian noise in a deterministic Hodgkin-Huxley neuron

In this paper, we report a novel effect of a particular kind of non-Gaussian noise (NGN), especially its deviation from Gaussian noise, on the spiking activity in a deterministic Hodgkin-Huxley (HH) neuron. It is found via numerical simulations that the coefficient of variation (CV), characterizing the spiking regularity, nonlinearly changes with varying deviation and passes through a minimum at an optimal deviation value, representing the presence of the coherence resonance (CR). This phenomenon shows that, when the NGN is optimal, the neuron can exhibit the most regular firing behavior. This result provides a constructive role of the NGN in the timing precision of information processing and signal transduction in neural systems.     

光学相干层析成像色散补偿研究

针对通过增加光源谱宽度来提高光学相干层析成像系统分辨率时样品色散特性的限制作用,分析了色散与光学相干层析成像系统纵向光程分辨率的约束关系.根据物质色散特性,采用数值变换方法对光学相干层析成像相干成像信号进行了色散补偿.实验使用了中心波长1 550 nm 自激发辐射光源和光纤迈克尓逊干涉结构,对水和光学快速扫描延迟线引入的二阶和三阶色散进行了数值补偿并通过相位修正因子来改善补偿效果.确定了一种普适的、快速的数值色散补偿方法.在对水中盖玻片和生物组织和的光学相干层析成像图像的色散补偿实验中取得了良好的效果,证明了方法的可行性.     

Breaking a novel image fusion encryption algorithm based on DNA sequence operation and hyper-chaotic system

Recently, a novel image fusion encryption algorithm based on DNA sequence operation and hyper-chaotic system was proposed. It was reported that the scheme can be broken with 4mn/3 +1 chosen plain-images and the corresponding cipher-images, where mn is the size of the plain-image. This paper re-evaluates the security of the encryption scheme and finds that the encryption scheme can be broken with less than ⌈ log ₂(4mn)/2 ⌉ +1 chosen plain-images, even three in many cases. The effectiveness of the proposed chosen-plaintext attack is supported by theoretical analysis, and verified by experimental results.     

Molecular dynamics simulation of the interaction between a mixed dislocation and a stacking fault tetrahedron

A high number-density of nanometer-sized stacking fault tetrahedra are commonly found during irradiation of low stacking fault energy metals. The stacking fault tetrahedra act as obstacles to dislocation motion leading to increased yield strength and decreased ductility. Thus, an improved understanding of the interaction between gliding dislocations and stacking fault tetrahedra are critical to reliably predict the mechanical properties of irradiated materials. Many studies have investigated the interaction of a screw or edge dislocation with a stacking fault tetrahedron (SFT). However, atomistic studies of a mixed dislocation interaction with an SFT are not available, even though mixed dislocations are the most common. In this paper, molecular dynamics simulation results of the interaction between a mixed dislocation and an SFT in face-centered cubic copper are presented. The interaction results in shearing, partial absorption, destabilization or simple bypass of the SFT, depending on the interaction geometry. However, the SFT was not completely annihilated, absorbed or collapsed during a single interaction with a mixed dislocation. These observations, combined with simulation results of edge or screw dislocations, suggest that defect-free channel formation in irradiated copper is not likely by a single dislocation sweeping or destruction process, but rather by a complex mix of multiple shearing, partial absorption and defect cluster transportation that ultimately reduces the size of stacking fault tetrahedra within a localized region.     

时域光学相干层析系统噪音分析和实验研究

本文从理论和实验上分析了存在拍频噪音时时域光学相干层析系统的噪音特性,给出了拍频噪音的具体估算方法.建立了描述一般时域光学相干层析系统实际噪音的简化模型,并给出了测量和寻找平衡探测光学相干层析系统最佳工作状态的方法.理论计算表明,平衡探测光学相干层析系统的信噪比受限于拍频噪音,理想情况下,最大信噪比可达100 dB左右|同时实验表明,如果实际的系统不能完全消除冗余噪音,其信噪比可能要比理论值小10~20 dB.本文的主要结果将可直接用于时域光学相干层析系统工作状态的测试和诊断当中,对频域光学相干层析系统噪音性能的分析和优化也将有所裨益.     

囚禁粒子在热库型驻波场中的量子相干特性

研究囚禁粒子与热库型(热辐射)驻波场的相互作用,通过外加驱动场,分析置于热库型驻波场中的囚禁粒子约化密度算符非对角元的时间演化,得到囚禁粒子在热库型驻波场中的相干特性.当外加驱动场的时间演化满足一定条件时,可保持囚禁粒子的相干性.