Stochastic Resonance of Single （Independent of Each Other） Protein Motor System with Fluctuating Potential Barrier

A single （independent of each other） protein motor system with fluctuating potential barrier and subject to sine electric field is investigated. We first derive the approximate Langevin equation of this system with fluctuating potential barrier. Then from this approximate Langevin equation, we calculate the signal-to-noise ratio （SNR） in the adiabatic limit. The phenomenon of stochastic resonance is found for this protein motor system with fluctuating potential barrier.     

The mean first passage time of a three-level atomic optical bistable system subjected to noise

The transient properties of a three-level atomic optical bistable system in the presence of multiplicative and additive noises are investigated. The explicit expressions of the mean first-passage time (MFPT) of the transition from the high intracavity intensity state to the low one are obtained by numerical computations. The impacts of the intensities of the multiplicative noise D M and the additive noise D A , the intensity of correlation between two noises λ , and the intensity of the incident light y on the MFPT are discussed, respectively. Our results show: (i) for the case of no correlation between two noises (λ = 0.0), the increase in D M and D A can lead to an increase in the probability of the transition to the low intracavity intensity state, while the increase in y can lead to a retardation of the transition; and (ii) for the case of correlation between two noises (λ = 0.0), the increase in λ can cause an increase in the probability of the transition, and the increase in D A can cause a retardation of the transition firstly and then an increase in the probability of the transition, i.e., the noise-enhanced stability is observed for the case of correlation between two noises.     

非关联噪声驱动的单稳系统的平均首次穿越时间

基于非对称双稳系统的理论研究了偏单稳系统的平均首次穿越时间问题,并基于势函数分析了参数对平均首次穿越时间的影响.得出结论:1)当偏稳系数为零时,随着加性噪声强度和参数a的增加,两个方向的平均首次穿越时间相等且均单调减小,2)随着偏稳系数b的增加,势阱的对称性被破坏,粒子由xs1跃迁到xs2的时间线性地减小,而粒子由xs2跃迁到xs1的时间线性地增加.3)随着乘性噪声强度和加性噪声强度比率R的增加,两个方向平均首次穿越时间均单调增加.     

Colored Noises-Induced Regime Shifts in a Vegetation Ecological System

In this paper, we investigate the stationary probability distribution and mean first passage time in a vegetation ecological system, which is driven by cross-correlation between intrinsic and extrinsic colored noises as well as the nonzero cross-correlation in between. The impacts of the self-correlation time τ₁ and τ₂, the cross-correlation time τ₃ and intensity k on the stationary probability distribution and mean first passage time are discussed, respectively. Our main results show that: (#em/em#) the self-correlation time τ₁ can induce regime shifts from the desert state to the sustainable vegetation state, while the self-correlation time τ₂, cross-correlation time τ₃ and intensity k can induce regime shifts from the sustainable vegetation state to the desert state; and (ii) the self-correlation time τ₁ or τ₂ can enhance the stability of the sustainable vegetation biomass, while the cross-correlation time τ₃ or strength k weakens the stability of the sustainable vegetation biomass.     

Escape statistics for systems driven by dichotomous noise. II. The imperfect pitchfork bifurcation as a case study

We use the general results for the escape probabilities and mean exit times obtained in an accompanying paper to analyze in detail a nonlinear system presenting an imperfect (subcritical) pitchfork bifurcation. We redraw the bifurcation diagram to show the effect of the noise. To avoid spurious results we introduce the concept ofextinction level as the minimum possible value for the system, and discuss its effect on the bifurcation diagram.     

Modeling DNA and Virus Trafficking in the Cell Cytoplasm

Cytosol trafficking is a limiting step of viral infection or DNA delivery. Starting from the cell surface, most viruses have to travel through a crowded and risky environment in order to reach a small nuclear pore. This work is dedicated to estimating the probability p _N of a viral arrival success and, in that case, the mean time τ _N it takes. Viral movement is described by a stochastic equation, containing both a drift and a Brownian component. The drift part represents the movement along microtubules, while the Brownian component corresponds to the free diffusion. The success of a viral infection is limited by a killing activity occurring inside the cytoplasm. We model the killing activity by a steady state killing rate k. Because nuclear pores occupy a small fraction of the nuclear area, we use this property to obtain asymptotic estimates of p _N and τ _N as a function of the diffusion constant D, the amplitude of the drift B and the killing rate k. This paper is dedicated to my wife Nathalie Rouach. D. H. is supported by the program “Chaire d’Excellence.” D.H is incumbent to the Haas Russell Chair     

Mean First-Passage Time in the Stochastic Theory of Biochemical Processes. Application to Actomyosin Molecular Motor

Many studies performed in recent years indicate a rich stochastic dynamics of transitions between a multitude of conformational substates in native proteins. A slow character of this dynamics is the reason why the steady-state kinetics of biochemical processes involving protein enzymes cannot be described in terms of conventional chemical kinetics, i.e., reaction rate constants. A more sophisticated language of mean first-passage times has to be used. A technique of summing up the stochastic dynamics diagrams is developed, enabling a calculation of the steady-state fluxes for systems of enzymatic reactions controlled and gated by the arbitrary type stochastic dynamics of the enzymatic complex. For a single enzymatic reaction, it is shown that the phenomenological steady-state kinetics of Michaelis–Menten type remains essentially unaltered but the interpretation of its parameters needs substantial change. A possibility of dynamical rather then structural inhibition of enzymatic activity is supposed. Two coupled enzymatic cycles are studied in the context of the biologically important process of free energy transduction. The theoretical tools introduced are applied to elucidate the mechanism of mechanochemical coupling in actomyosin molecular motor. Relations were found between basic parameters of the flux-force dependences: the force stalling the motor, the degree of coupling between the ATPase and the mechanical cycles as well as the asymptotic turnover number, and the mean first-passage times in a random movement between the particular conformational substates of the myosin head. These times are to be determined within a definite model of conformational transition dynamics. The theory proposed, not contradicting the presently available experimental data, is capable to explain the recently demonstrated multiple stepping produced by a single myosin head during just one ATPase cycle.     

The Influence of Stochastic Layers of Magnetic Field Lines on Transport Barrier Formation in a Stellarator System

The results of local measurements of RF discharge plasma parameters in the process of internal transport barriers (ITB) formation in the vicinity of rational magnetic surfaces in the Uragan-3M torsatron are presented. The following phenomena were observed in the process of ITB formation: widening of the radial density distribution, formation of plateaus on radial density and electron temperature distributions, formation of regions with high shear of poloidal plasma rotation velocity and radial electric field in the vicinity of stochastic layers of magnetic field lines, decrease of density fluctuations and their radial correlation length, decorrelation of density fluctuations, and increase of the bootstrap current.After the ITB formation, the transition to the improved plasma confinement regime takes place. The transition moves to the beginning of the discharge with the increase of heating power. The possible mechanism of ITB formation near rational surfaces is discussed.     

Transmission and Dwell Time Oscillations Caused by Coexistence of Tunneling and Propagating in a Trapezoidal Barrier

Abstract A refined one of our exactly solvable trapezoidal barrier potential model [Thin Solids Films, 414 （2002） 136）] for metal-insulator-metal tunnel junctions has Seen presented. According to the refined model, the longitudinal kinetic energy （ExL） and the effective mass （m^＊L） of the electron8 in the electrode on the left of the barrier distinguish from that on the right. It is found that as ExL is greater than the shorter side of the resultant trapezoidal barrier potential, there will be a coexistence of the tunneling and propagating in the barrier. The results demonstrate that the damped oscillating electron waves localized in the propagating barrier subregion lead to the oscillation and enhancement in the transmission coefficient DT and dwell time TD. For the barrier height φ1=2.6 eV and φ2 = 1.4 eV, the width d=22 A and ExL = 1.0 eV, DT and TD have a maximum of 0.054 and 0.58x10^-15 s at V = 2.04 V and 2.18 V, respectively. This suggests that a real tunneling may be a hybrid.     

Monte Carlo simulation of overdamped motion in a double well potential under the influence of coloured noise

We present a Monte Carlo simulation algorithm for evaluating the stationary probability and the mean and the variance of first passage times in any dynamical system under the influence of additive coloured Gaussian and Marcovian noise (Ornstein-Uhlenbeck process). Our algorithm generates the Ornstein-Uhlenbeck process by a superposition of a finite number of random telegraph processes. We obtain our results from a direct evaluation of the trajectories. We apply our method to the overdamped motion of a particle in a double well potential. We compare our simulation results with various analytic approximations for the stationary probability and the mean first passage times.     

Global and exploding solutions in a model of self-gravitating systems

We study asymptotic properties of solutions to an extension to arbitrary dimensions of the astrophysical model proposed by Chavanis et al. to explain phenomena of gravitational collapse in clouds of self-gravitating particles. In particular, we show that in the two-dimensional case the solutions can be continued to global ones, while in three space dimensions large data of negative energy blow up in a finite time. Relations between isothermal, Streater's energy-transport and the present models are also studied.     

Critical Analyses of Order Parameter and Phase Transitions at High Density in Gross-Neveu Model

By critical analyses of the order parameter of symmetry breaking, we have researched the phase transitionsat high density in D = 2 and D = 3 Gross-Neveu (GN) model and shown that the gap equation obeyed by the dynamicalfermion mass has the same effectivenesss as the effective potentials for such analyses of all the second order and somespecial first order phase transitions. In the meantime we also further ironed out a theoretical divergence and proventhat in D = 3 GN model a first order phase transition does occur in the case of zero temperature and finite chemicalpotential.     

频率变化场J-C模型中的量子态保真度

利用Jaynes-Cummings模型,考虑场频率受微扰的情况,在旋波近似下研究了二能级原子与单模辐射场相互作用系统中量子态保真度的演化.利用数值计算方法给出量子态保真度随时间的演化曲线.研究了场频率随时间正弦函数形式变化对系统、光场和原子的量子态保真度演化的影响.结果表明:场频率随时间正弦函数形式变化对系统和光场的量子态保真度的演化的影响很小,但对原子的量子态保真度的演化有显著影响.     

Critical Analyses of Order Parameter and Phase Transitions at High Density in Gross－Neveu Model

By critical analyses of the order parameter of symmetry breaking, we have researched the phase transitions at high density in D = 2 and D = 3 Gross-Neveu (GN) model and shown that the gap equation obeyed by the dynamical fermion mass has the same effectivenesss as the effective potentials for such analyses of all the second order and some specJal first order phase transitions. In the meantime we also further ironed out a theoretical divergence and proven that in D = 3 GN model a first order phase transition does occur in the case of zero temperature and finite chemical potential.     

原子与频率随时间变化场相互作用系统中场熵的演化

利用多光子Jaynes-Cummings模型,考虑场频率随时间以正弦函数形式作小量变化,在旋波近似下,研究了二能级原子通过多光子跃迁与单模辐射场相互作用系统中场熵的演化规律.利用数值计算方法给出场熵随时间的演化曲线.研究结果表明:场熵的演化受场频率随时间正弦函数形式变化的调制,场频率振荡的幅值u越大调制作用越强,在场频率振荡的幅值u大于一定值后,场熵将按场频率周期性的变化规律作周期性振荡.     

多光子J-C模型中频率随时间变化场的反聚束效应

利用多光子J-C模型,考虑场频率随时间以正弦函数形式作小量变化,在旋波近似下,研究了二能级原子通过多光子跃迁与单模辐射场相互作用系统中场的反聚束效应.利用数值计算方法给出反映场反聚束效应的二阶关联函数随时间的演化曲线.研究结果表明:场二阶关联函数的演化受场频率随时间正弦函数形式变化的调制,场频率振荡的幅值 u越大调制作用越强,在场频率振荡的幅值u大于一定值后,场二阶关联函数随时间的演化呈现出周期性振荡特性,其振荡周期与场频率变化的周期一致.     

Identifying the mean residence time of soil water for different vegetation types in a water source area of the Yuanyang Terrace,southwestern China

The mean residence time of soil water (MRT_sw) for forestland and shrubland in a water source area of Yuanyang Terrace, southwestern China, was estimated using stable isotope tracer tests and the sine-wave regression model. Stable isotope analyses from precipitation and soil water were performed in 2015. The δ²H/δ¹⁸O relationship of precipitation resulted in δ²H?=?7.31δ¹⁸O?+?1.49, which is nearly identical to the local meteoric water line in Kunming, southwestern, China. The MRT_sw was simulated at five depth ranges (0–20, 20–40, 40–60, 60–80, 80–100?cm) of the two vegetation types by precipitation δ¹⁸O input data and soil water δ¹⁸O output data. The results showed that the MRT_sw values of the forestland and shrubland both increased with soil depth. However, differences in the MRT_sw of the forestland (between day 53 and 94) and of the shrubland (between day 76 and 142) were discussed. Regarding the physical properties of the soil profiles from the sample plots, non-capillary porosity decreased with soil depth in the forestland (from 48.5 to 20.5?%), and was clearly higher than that in the shrubland (from 38.8 to 18.7?%). Therefore, non-capillary porosity (macropores) could be a factor that shortens the mean residence time of soil water.     

一类具时滞的厄尔尼诺-南方涛动充电-放电振子模型的Hopf分岔与周期解问题

研究了一类具时滞的厄尔尼诺-南方涛动充电-放电振子模型. 给出了产生Hopf分岔的临界时滞条件, 利用Mawhin重合度理论,探讨了该模型的周期解问题. 关键词： 时滞 厄尔尼诺-南方涛动模型 Hopf分岔 周期解     

Fluorosolvatochromism of monomethyl indoles: further evidence in support of a new photophysical model for the indole chromophore

In this study, we investigated whether a change exists in the emitting state of the monomethyl indoles, dissolved in 1‐chlorobutane (ClB) and 2‐methylbutane (2MB), resulting from a dipolarity increase of the solvent. Analysis of the solvatochromism of monomethyl indoles in ClB at 343–133 K and in 2MB at 293–113 K leads to the following conclusions: (i) the state S₁ is the greatest contributor to the structured emission of 4‐Me‐, 5‐Me‐, and 7‐MeIndole; (ii) lowering the temperature of solutions of these compounds in ClB or 2MB below 113 K leads not to a structureless emission or bathochromic shift typical for an S₁′ state; (iii) 1‐Me‐, 2‐Me‐, 3‐Me‐, and 6‐MeIndole exhibit a structured emission typical for an S₁ state in 2MB but show an invariably structureless emission, subject to a red shift in ClB as the temperature is lowered, which is suggestive for an S₁′ emitting state; and (iv) lowering the temperature of solutions of the previous compounds below 133 K causes their emission spreading to become structured and blueshifted (two typical features for an emission from their S₁ state). Copyright © 2015 John Wiley & Sons, Ltd.     

Static dissolution rate of tungsten film versus chemical adjustments of a reused slurry for chemical mechanical polishing

Tungsten is widely used as deposited layer for the multi-level interconnection structures of wafers. The chemical composition of abrasive slurry plays an important role in chemical mechanical polishing (CMP) process. Removal of tungsten is driven by complex oxidation mechanisms between slurry components. The slurry for tungsten CMP generally contains oxidizer, iron catalyst, complexing agents and stabilizers in a pH adjusted solution of abrasive particles. Interaction between iron complex and H₂O₂ in the slurry is the main factor governing the chemical mode of material removal, oxidation potencies and kinetics.In this study, we investigate the effects of chemical additives in silica (SiO₂)-based slurry on the removal rate of the tungsten film. Experiments were carried out in static batch as a preliminary study to understand and optimize chemical mechanisms in CMP-Tungsten process. Experiment designs were conducted to understand the influence of the chemical additives on the main performances of W-CMP. Used slurry, concentrated and retreated with chemical adjustments, is compared to the original slurry as a reference.