单峰高斯分布适应面上的误差阈

在Eigen的单峰适应面模型基础上,提出了生物体的适应值为高斯分布的随机适应面模型。 利用系综平均的方法, 计算了在单峰高斯分布适应面上准物种的浓度分布和误差阈。 结果表明, 对于小的适应面涨落, 准物种分布和误差阈与确定情形相比变化极小,误差阈对于小的涨落是稳定的。 然而, 当适应值涨落较大时,从准物种到误差灾变的转变不再明显。 误差阈变宽, 并且在涨落增加时向大的突变率方向移动。 Based on the Eigen model with a single peak fitness landscape, the fitness values of all sequence types are assumed to be random with Gaussian distribution. By ensemble average method, the concentration distribution and error threshold of quasispecies on single peak Gaussian distributed fitness landscapes were evaluated. It is shown that the concentration distribution and error threshold change little in comparing with deterministic case for small fluctuations, which implies that the error threshold is stable against small perturbation. However, as the fluctuation increases, the situation is quite different. The transition from quasi species to error catastrophe is no longer sharp. The error threshold becomes a narrow band which broadens and shifts toward large values of error rate with increasing fluctuation.     

色散光学双稳系统中的一级相变类比

研究随机过程中由噪声诱导的非平衡相变一直是国际学术界十分关注的课题之一[1, 2].我们从色散光学双稳系统出发,当入射光中的强度涨落和位相涨落分别看作色噪声时,用统一色噪声近似得到它们的定态强度分布.研究结果表明,当入射光仅包含强度涨落时,随着噪声相关时间τ的增加,一级相变类比参数(I,θ)区域图中,定态强度分布函数Qs(I)在I>0处有一相对极大和一相对极小的区域范围变小.     

反铁磁链中Dzyaloshinskii–Moriya机制驱动矢量自旋手征束缚态的研究

Dzyaloshinskii-Moriya(DM)相互作用驱动的矢量自旋手征态,能和声子发生耦合,具备非常丰富的物理现象.本论文以一维反铁磁链中自旋手征-声子耦合模型为基础,研究不同声子环境下,耦合强度对自旋手征动力学演化过程的影响规律.结果表明,对自旋S=1/2的系统,在不同的声子浴(sub-Ohmic(0 1))中,均会在非相干到相干自旋涨落过程中产生无能隙一级相变,其来源是自旋手征束缚态的形成.相变发生的临界自旋-声子耦合强度正比于自旋涨落大小,反比于系统德拜频率.当自旋-声子耦合强度超过其临界值时,自旋手征束缚态的产生将极大地抑制非相干自旋涨落.     

非平衡态相变的两例——光学参量振荡和激光

本文就光学参量振荡和激光两个物理问题,讨论了非平衡态相变过程的动力特点。相变点是由稳定结点状态突变到鞍点时的转变点。说明了涨落和耗散在相变中所起的作用,得到第二类相变的临界指数(β=1/2,γ=1)。 关键词：     

Coherent Resonance for Rate Oscillations During CO Oxidation on Pt(110) Surfaces: Interplay Between Internal and External Noise

用理论和模拟相结合的方法研究了Pt(110)面上CO催化氧化体系中由化学反应随机性所导致的内涨落和参量扰动带来的外涨落对其速率振荡过程的影响,重点考察了内涨落和外涨落的相互作用．在体系的确定性Hopf分岔点附近区域,噪声可以诱导产生随机振荡,其信噪比随噪声强度的变化会出现极大值,即发生了相干共振．运用随机范式理论,研究发现体系的相干共振行为依赖于一\有效噪声",其强度是内涨落和外涨落的加权和．研究结果表明,在内外噪声强度的参数平面内,随机振荡的信噪比呈现屋脊形,太大的内涨落或外涨落条件下相干共振都不能发生．数值模拟的结果和理论分析符合得很好．     

夸克介子模型的相图和表面张力

利用有限温度场论和平均场近似的方法,在考虑夸克真空涨落的情况下,研究了两个夸克味的夸克介子模型的量子色动力学相变的相图结构,得到了当夸克化学势密度较小时,量子色动力学相变是过渡相变,而当夸克化学势密度较大的时候,量子色动力学相变是一级相变.对于一级相变的区域,基于薄壁近似,给出了当温度等于临界温度Tc时,强子相表面张力随夸克化学势密度的变化关系.本研究为相对论重离子对撞实验和中子星早期结构演化提供必要的参考.     

铁电体中极化长程涨落的光子关联谱实验研究

从极化团簇的随机涨落出发, 利用维纳过程模型, 推导了铁电体中极化长程涨落的弛豫规律以及光强自相关函数所可能的表现形式. 阐述了微观极化团簇的弛豫过程与宏观测量弛豫规律之间的联系. 通过对原有氦氖激光光子关联谱实验装置进行改进, 观测了BaTiO₃和0.71Pb(Mg_1/3Nb_2/3)O₃-0.29PbTiO₃单晶中极化团簇长程涨落在居里点和立方到四方相变点附近的弛豫过程. 在BaTiO₃中发现极化团簇长程涨落在居里点之上4 K存在双弛豫现象, 此现象与其有序无序相变机理相联系. 在Pb(Mg_1/3Nb_2/3)O₃-0.29PbTiO₃中发现极化团簇长程涨落在相变点两侧都存在双弛豫现象. 利用推导的理论结果很好地拟合了实验结果并提取了极化团簇长程涨落的弛豫时间. 两种样品中极化团簇长程涨落的弛豫时间都在相变点出现突变, 并呈现临界慢化现象.     

单光子调制频谱用于量子点荧光寿命动力学的研究

本文开展了基于单光子调制频谱测量量子点荧光寿命动力学特性的研究.在脉冲激光激发下,对探测到的量子点单光子荧光信号进行频谱分析以获得荧光调制频谱,研究发现特征频谱信号幅值与荧光寿命之间存在确定的非线性对应关系.这种单光子调制频谱方法能有效消除背景噪声和单光子探测器暗计数的影响,用于分析量子点荧光寿命动力学特性时在准确度以及时间分辨率方面都较目前普遍采用的荧光衰减曲线寿命拟合方法呈现出明显优势:当涨落误差为5%时,寿命测量准确度提高了一个数量级;当涨落误差和偏离误差均为5%时,对动力学测量效率以及时间分辨率提高了四倍以上.因此单光子调制频谱可以作为获取量子点在短时间尺度内激发态动力学信息的一种有效技术手段.     

含时驱动的Dicke模型的混沌特性

依据Dicke量子相变首次被观测的实验装置,我们通过调节抽运激光强度来实现原子-场集体耦合强度的单频非绝热调制,即实现含时驱动的Dicke模型.当驱动的耦合强度为零时,系统回退到标准的Dicke模型.从刻画的庞加莱截面图观测到:在临近相变点附近系统由经典规则轨道向混沌变化,超辐射区对应着相空间的完全混沌;当静态耦合和驱动耦合同时存在时,系统显示出丰富的混沌运动.通过调节振荡频率,系统可在正常相区间从经典规则轨道变到混沌再变到经典规则轨道.     

Jaynes-Cummings晶格模型和Rabi晶格模型的量子相变

采用平均场近似的方法,分别研究了Jaynes-Cummings晶格模型和Rabi晶格模型的量子相变:Mott绝缘体相-超流体相量子相变,探索了光的聚束-反聚束行为,研究了Kerr非线性作用对量子相变与光子统计特征的影响.研究结果表明,在Rabi晶格模型中二能级原子和光子相互作用强度g和格点之间光子跃迁强度J的增大会使晶格体系从Mott绝缘体相向超流体相转变,同时,光子统计行为由聚束转变为反聚束,而Kerr非线性强度的增大抑制了Mott绝缘体相-超流体相相变,但促进了光子聚束与反聚束之间的转变.     

Error Thresholds in Single-Peak Gaussian Distributed Fitness Landscapes

Based on the Eigen and Crow-Kimura models with a single-peak fitness landscape, we propose the fitness values of all sequence types to be Gausslan distributed random variables to incorporate the effects of the fluctuations of the fitness landscapes （noise of environments） and investigate the concentration distribution and error threshold of quasispecies by performing an ensemble average within this theoretical framework. We find that a small fluctuation of the fitness landscape causes only a slight change in the concentration distribution and error threshold, which implies that the error threshold is stable against small perturbations. However, for a sizable fluctuation, quite different from the previous deterministic models, our statistical results show that the transition from quasi-species to error catastrophe is not so sharp, indicating that the error threshold is located within a certain range and has a shift toward a larger value. Our results are qualitatively in agreement with the experimental data and provide a new implication for antiviral strategies.     

Phase diagrams of quasispecies theory with recombination and horizontal gene transfer

We consider how transfer of genetic information between individuals influences the phase diagram and mean fitness of both the Eigen and the parallel, or Crow-Kimura, models of evolution. In the absence of genetic transfer, these physical models of evolution consider the replication and point mutation of the genomes of independent individuals in a large population. A phase transition occurs, such that below a critical mutation rate an identifiable quasispecies forms. We show how transfer of genetic information changes the phase diagram and mean fitness and introduces metastability in quasispecies theory, via an analytic field theoretic mapping.     

Relaxation Property and Stability Analysis of the Quasispecies Models

The relaxation property of both Eigen model and Crow-Kimura model with a single peak fitness landscape is studied from phase transition point of view. We first analyze the eigenvalue spectra of the replication mutation matrices. For sufficiently long sequences, the almost crossing point between the largest and second-largest eigenvalues locates the error threshold at whichcritical slowing down behavior appears. We calculate the critical exponent in the limit of infinite sequence lengths and compare it with the result from numerical curve fittings at sufficiently long sequences. We find that for both models the relaxation time diverges with exponent 1 at the error (mutation) threshold point. Results obtained from both methods agree quite well. From the unlimited correlation length feature, the first order phase transition isfurther confirmed. Finally with linear stability theory, we show that the two model systems are stable for all ranges of mutation rate. The Eigen model is asymptotically stable in terms of mutant classes, and the Crow-Kimura model is completely stable.     

Quasispecies distribution of Eigen model

We have studied sharp peak landscapes of the Eigen model from a new perspective about how the quasispecies are distributed in the sequence space. To analyse the distribution more carefully, we bring in two tools. One tool is the variance of Hamming distance of the sequences at a given generation. It not only offers us a different avenue for accurately locating the error threshold and illustrates how the configuration of the distribution varies with copying fidelity $q$ in the sequence space, but also divides the copying fidelity into three distinct regimes. The other tool is the similarity network of a certain Hamming distance $d_{0}$, by which we can gain a visual and in-depth result about how the sequences are distributed. We find that there are several local similarity optima around the centre (global similarity optimum) in the distribution of the sequences reproduced near the threshold. Furthermore, it is interesting that the distribution of clustering coefficient $C(k)$ follows lognormal distribution and the curve of clustering coefficient $C$ of the network versus $d_{0}$ appears to be linear near the threshold.     

Solution of the Crow-Kimura and Eigen Models for Alphabets of Arbitrary Size by Schwinger Spin Coherent States

To represent the evolution of nucleic acid and protein sequence, we express the parallel and Eigen models for molecular evolution in terms of a functional integral representation with an h-letter alphabet, lifting the two-state, purine/pyrimidine assumption often made in quasi-species theory. For arbitrary h and a general mutation scheme, we obtain the solution of this model in terms of a maximum principle. Euler’s theorem for homogeneous functions is used to derive this ‘thermodynamic’ formulation of evolution. The general result for the parallel model reduces to known results for the purine/pyrimidine h=2 alphabet and the nucleic acid h=4 alphabet for the Kimura 3 ST mutation scheme. Examples are presented for the h=4 and h=20 cases. We also derive the maximum principle for the Eigen model for general h. The general result for the Eigen model reduces to a known result for h=2. Examples are presented for the nucleic acid h=4 and the amino acid h=20 alphabet. An error catastrophe phase transition occurs in these models, and the order of the phase transition changes from second to first order for smooth fitness functions when the alphabet size is increased beyond two letters to the generic case. As examples, we analyze the general analytic solution for sharp peak, linear, quadratic, and quartic fitness functions.     

Eigen model version of evolution with directed migration

We consider the two-habitat quasispecies model, which describes evolutionary process with migration on the basis of the Eigen model. In the first habitat there is only one genotype, and here is an influx of the replicators from the first habitat to the second one with the rate h. We solve exactly the case of a single-peak fitness landscape in both habitats, when in the first habitat there are no mutations. The Eigen model version of the model is more adequately describes the real biological experiments than the Crow-Kimura model, as can be related to the serial transfer experiments in chemical reactor.     

Coevolution of quasispecies: B-cell mutation rates maximize viral error catastrophes

Coevolution of two coupled quasispecies is studied, motivated by the competition between viral evolution and adapting immune response. In this coadaptive model, besides the classical error catastrophe for high virus mutation rates, a second "adaptation" catastrophe occurs, when virus mutation rates are too small to escape immune attack. Maximizing both regimes of viral error catastrophes is a possible strategy for an optimal immune response, reducing the range of allowed viral mutation rates to a minimum. From this requirement, one obtains constraints on B-cell mutation rates and receptor lengths, yielding an estimate of somatic hypermutation rates in the germinal center in accordance with observation.     

Schwinger Boson Formulation and Solution of the Crow-Kimura and Eigen Models of Quasispecies Theory

We express the Crow-Kimura and Eigen models of quasispecies theory in a functional integral representation. We formulate the spin coherent state functional integrals using the Schwinger Boson method. In this formulation, we are able to deduce the long-time behavior of these models for arbitrary replication and degradation functions. We discuss the phase transitions that occur in these models as a function of mutation rate. We derive for these models the leading order corrections to the infinite genome length limit.     

Einstein——Podolsky——Rosen entanglement in time-dependent periodic pumping non-degenerate optical parametric amplifier

The solution of the time-dependent periodic pumping non-degenerate optical parametric amplifier (NOPA) is derived when the pump depletion is considered both above and below thresholds. Based on this solution, the quantum fluctuation calculated shows that a high entanglement and a good squeezing degree of the parametric light beams are achieved near and above thresholds. We adopt two kinds of pump fields: (i) a continuously modulated pump with a sinusoidal envelope; (ii) a sequence of laser pulses with Gaussian envelopes. We analyse the time evolution of continuous variable entanglement by analytical and numerical calculations, and show that the periodic driven pumping also improves the degree of entanglement. The squeezing and Einstein-Podolsky-Rosen (EPR) entanglement by using the two pumping driven functions are investigated from below to above the threshold regions, the tendencies are nearly the same, and the Gaussian driven function is superior to that of the sine driven function, when the maximum squeezing and the minimum variance of quantum fluctuation are considered. In the meantime, the generalization of frequency degenerate OPA to frequency non-degenerated OPA problem is investigated.