Roles of noise in single and coupled multiple genetic oscillators

The noisy fluctuation of chemical reactions should profoundly affect the oscillatory dynamics of gene circuit. In this paper a prototypical genetic oscillator, repressilator, is numerically simulated to analyze effects of noise on oscillatory dynamics. The oscillation is coherent when the protein number and the rate of the DNA state alteration are within appropriate ranges, showing the phenomenon of coherence resonance. Stochastic fluctuation not only disturbs the coherent oscillation in a chaotic way but also destabilizes the stationary state to make the oscillation relatively stable. Bursting in translation, which is a source of intense stochastic fluctuation in protein numbers, suppresses the destructive effects of the finite leakage rate of protein production and thus plays a constructive role for the persistent oscillation. When multiple repressilators are coupled to each other, the cooperative interactions among repressilators enhance the coherence in oscillation but the dephasing fluctuation among multiple repressilators induces the amplitude fluctuation in the collective oscillation.     

甲酸Pt电极电化学氧化体系中时间自组织导致的可利用功耗失

在电极化学反应步骤为控制步骤的条件下,对甲酸阳极氧化体系中出现的电化学振荡的阈值及跨越阈值后状态演化的极限环路径进行了系统动力学计算.同时,根据非平衡电极过程的耗散-涨落理论,进一步对跨越振荡阈值前后的临界区与电化学震荡区的极化曲线及功耗谱进行了随机热力学分析计算.研究结果表明,跨越临界区后单位电化学反应功耗谱出现突降...     

铜电极阳极溶解过程恒电位电流振荡的动力学模型

研究了铜电极在酸性氯化钠溶液中的恒电位电流振荡行为,分析了电极过程中的非线性步骤及电化学耦合因素,提出了一个可能的电极过程动力学模型,并借助线性稳定性分析及分支分析得到了参数坐标空间中的动力学行为区域图。在此基础上,将极化曲线视为稳定非平衡定态区态函（电流）与外控参数（电位）的关系,同时将恒电位电流振荡模拟为稳定极限环振荡,分别计算出了极化曲线与时间－电流振荡曲线,其结果与实验数据相符,表明该类电     

The formation of cluster vibrations in imperfectly structured materials

The dynamics of cluster formation in imperfectly structured materials is discussed in terms of their evolution from a prepared state fluctuation. It is shown that this is accompanied by the generation of group oscillations of displacements in the centres/axes of motion of the cluster components. A fractional index defining the partitioning of the vibrational/librational energy between the group oscillations and the centre of motion vibrations is shown to be related to the structural regularity of the cluster. The generation of group oscillation has also been related to the change in configurational entropy attendant upon the irreversible formation of imperfectly structured clusters, expressed as the same fraction of the change arising from complete dissociation of the ideal state.     

Isochronicity and limit cycle oscillation in chemical systems

Chemical oscillation is an interesting nonlinear dynamical phenomenon which arises due to complex stability condition of the steady state of a reaction far away from equilibrium which is usually characterised by a periodic attractor or a limit cycle around an interior stationary point. In this context Lienard equation is specifically used in the study of nonlinear dynamical properties of an open system which can be utilized to obtain the condition of limit cycle. In conjunction with the property of limit cycle oscillation, here we have shown the condition for isochronicity for different chemical oscillators with the help of renormalisation group method with multiple time scale analysis from a Lienard system. When two variable open system of equations are transformed into a Lienard system of equation the condition for limit cycle and isochronicity can be stated in a unified way. For any such nonlinear oscillator we have shown the route of a dynamical transformation of a limit cycle oscillation to a periodic orbit of centre type depending on the parameters of the system.     

一种新的振荡体系的研究 Ⅰ. 在铑膦催化剂存在条件下的丙烯氢甲酰化振荡现象

丙烯氢甲酰化过程(以下简称氢甲酰化过程),可以用如下反应式表示: 作者在进行氢甲酰化动力学研究中发现,在接近工业生产条件,特别是使用了适当聚合度的正丁醛做溶剂时,只要控制一定的操作条件,即可在反应的母体转化期和诱导期内检测出反应体系的气相中各组分浓度的振荡变化。据作者了解,目前尚未有关于该体系气相组分中浓度振荡的报道。     

Understanding (sessile/constrained) bubble and drop oscillations

The diffuse literature on drop oscillation is reviewed, with an emphasis on capillary wave oscillations of constrained drops. Based on the review, a unifying conceptual framework is presented for drop and bubble oscillations, which considers free and constrained drops/bubbles, oscillation of the surface or the bulk (i.e. center of mass) of the drop/bubble, as well as different types of restoring forces (surface tension, gravity, electromagnetic, etc). Experimental results (both from literature and from a new set of experiments studying sessile drops in cross flowing air) are used to test mathematical models from literature, using a novel whole profile analysis technique for the new experiments. The cause of oscillation (cross flowing air, vibrated surface, etc.) is seen not to affect oscillation frequency. In terms of models, simplified models are seen to poorly predict oscillation frequencies. The most advanced literature models are found to be relatively accurate at predicting frequency. However it is seen that no existing models are reliably accurate across a wide range of contact angles, indicating the need for advanced models/empirical relations especially for drops undergoing the lowest frequency mode of oscillation (the order 1 degree 1 non-axisymmetric ‘bending’ mode that corresponds to a lateral ‘rocking’ motion of the drop).     

Combustion measurement of thermoacoustic oscillating flames by diode-laser absorption spectroscopy sensors

Diode-laser absorption spectroscopy has been applied to a swirl-stabilized turbulent combustor to detect high frequency combustion oscillation and combustion state related to combustion noise. Two diode-laser absorption spectroscopy techniques of scanned-wavelength method and fixed-wavelength method are adopted. In the scanned-wavelength method, fluctuations of temperature and H₂O mole fraction up to 1 kHz are detected. Two dominant peak frequencies of power spectra of these fluctuations, which are about 125 Hz and 140 Hz, coincide with those of pressure fluctuation in the combustor. In the case of control by secondary fuel injection, the energy at peak frequency of temperature and H₂O mole fraction decreases in accordance with noise reduction. Similar to the combustion noise, temperature fluctuation shows a minimal value at the appropriate frequency of secondary fuel injection. By analysing transmitted signals, the fixed-wavelength method provides power spectra similar to those obtained by the scanned-wavelength method. The advantage of the fixed-wavelength method is capability of detection of high frequency combustion oscillation more than 1 kHz. These results prove that the diode-laser absorption spectroscopy has great applicability as sensors for the combustion measurement of thermoacoustic oscillating flames and active control of turbulent combustion.     

多定态转变化学反应体系与环境传热-扩散耦合导致的环面型化学振荡

以Schlögl模型作为多定态转变化学反应体系的范例, 研究了通过传热及扩散与环境耦合的多定态转变化学反应体系中诱发的新动力学行为, 其中特别重要的是沿慢变量方向的环面型化学振荡的出现. 建立了慢流型上的准定态的线形化稳定性分析法, 揭示了由极限环振荡蜕变为环面型振荡的动力学机制, 不同于小寄生参数存在引起的非连续极限环振荡. 通过以慢流型上准定态稳定性分区为基础的定性分析, 进一步揭示了该类体系中可能出现间歇性、反复持续式和骤发式3种亚类环面振荡. 最后以第三亚类作为示例, 以相应的计算机模拟证实理论分析的正确性.     

Micro－area Infrared Spectroanalysis of Inclusions in Lithium Triborate Crystals

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Adsorption of Zn2+ from Synthetic Wastewater Using Dried Watermelon Rind (D-WMR): An Overview of Nonlinear and Linear Regression and Error Analysis

Sustainable wastewater treatment is one of the biggest issues of the 21st century. Metals such as Zn²⁺ have been released into the environment due to rapid industrial development. In this study, dried watermelon rind (D-WMR) is used as a low-cost adsorption material to assess natural adsorbents’ ability to remove Zn²⁺ from synthetic wastewater. D-WMR was characterized using scanning electron microscope (SEM) and X-ray fluorescence (XRF). According to the results of the analysis, the D-WMR has two colours, white and black, and a significant concentration of mesoporous silica (83.70%). Moreover, after three hours of contact time in a synthetic solution with 400 mg/L Zn²⁺ concentration at pH 8 and 30 to 40 °C, the highest adsorption capacity of Zn²⁺ onto 1.5 g D-WMR adsorbent dose with 150 μm particle size was 25 mg/g. The experimental equilibrium data of Zn²⁺ onto D-WMR was utilized to compare nonlinear and linear isotherm and kinetics models for parameter determination. The best models for fitting equilibrium data were nonlinear Langmuir and pseudo-second models with lower error functions. Consequently, the potential use of D-WMR as a natural adsorbent for Zn²⁺ removal was highlighted, and error analysis indicated that nonlinear models best explain the adsorption data.     

Dynamic charge fluctuation of endohedral fullerene with coencapsulated Be atom and H2

As one of the typical examples of characteristic reaction field generated in inclusion (enclosure) compounds, the dynamics of an endohedral metallofullerene, (Be+nH2)@C60(n=1,2), is studied with Be atom serving as a test probe. A very large dynamical and thermal fluctuation of electronic state of Be has been found, which is surprising since the highest occupied molecular orbital-lowest unoccupied molecular orbital gap of Be is so wide that such a large fluctuation in a low temperature is never expected. This finding demonstrates one of the special features of endohedral reaction field offered by the fullerene. The physical origin of this phenomenon is analyzed.     

Environmental plutonium: Reference states and alpha coefficients

The results of plutonium oxidation state distribution calculations do not depend on special attention to any oxidation state as has been incorrectly supposed in some literature sources. Experimentally determined alpha coefficients for natural water could make the distribution of environmental plutonium easy to estimate with a programmable pocket calculator.Mound is operated for the U.S. Department of Energy by EG&G Mound Applied Technologies, Inc., under Contract No. DE-AC04-88DP43495.     

Electrically driven oscillations of a mercury-droplet electrode

The resonance frequencies of 13 polygonal vibrations plus 11 axisymmetric vibrations have been observed for a 4.0-mg sessile mercury droplet submerged in 0.10 N KCl solution. When an input voltage with suitable dc and ac components was applied between the mercury droplet and a Ag/AgCl counter electrode, the mercury droplet could be observed under a microscope to oscillate. The mechanism that drives this droplet into oscillation differs from past electrokinetic mechanisms. Basically, the oscillating input voltage causes periodic changes in the interfacial surface tension which, at specific input frequencies, induce resonant vibrations within the droplet by interacting with its expanding and contracting surface area. Because there are two cycles of surface-area variation and two cycles of surface-tension variation per cycle of droplet oscillation, the most effective driving frequency (but not the only driving frequency) is twice the frequency of the droplet oscillation. This work was performed at the Oak Ridge Y-12 Plant, Oak Ridge, Tennessee.     

Establishment of a confluent cardiomyocyte culture in a cylindrical microchannel

We established a confluent cardiomyocyte culture method using an 800-μm diameter cylindrical microchannel in this report. This was realized by introducing cardiomyocytes 2 times before and after turning over a microchip. The optimum condition was starting the flowing medium 2.0 h after seeding and flowing the medium at 1.0 μL/min. By applying this technology to a cardiomyocyte-based spherical heart pump device, one may develop self-fluid regulated devices that could be applied for implantable or circulation analysis device on a chip.     

Study of oxidative desulphurization process of coal with different metamorphism degrees

The oxidative desulphurization process of coal with different metamorphism degrees treated by an air-steam mixture has been studied.It has been shown that the pyrite present in black coal and anthracite is oxidized with the sulphur dioxide formation,and the process chemical mechanism does not depend on the quality of organic matter.The medium-metamorphized coal,capable of turning into a plastic state and cake in the range of investigated temperatures(350～450 ℃),is desulphurized with the greatest difficulty.The chemical mechanism dealing with the transformations of pyritic sulphur present in brown coal differs from similar processes taking place in black coal and anthracite,because FeS2 is converted with hydrogen sulphide formation at desulphurization.     

Oscillating fluorescence in an unstable colloidal dispersion of CdSe/ZnS core/shell quantum dots

Fluorescence oscillation is observed in an ensemble of colloidal CdSe/ZnS core/shell quantum dots (QDs) dispersed in nonpolar solvent under continuous irradiation. The QDs dispersed in toluene gradually aggregate and change their fluorescence intensity, even in the dark. During the aggregation, the QD/toluene suspension is unstable, that is, overdispersed. The fluorescence oscillation is found only in this unstable state before the system reaches steady state. In addition, the aggregation rate is promoted by irradiation and strongly correlates with the oscillation amplitude. Our experimental results indicate that the dispersion instability plays an important role in both linear and nonlinear dynamics of the fluorescence. It is inferred from the experimental results and previous studies that the complex time evolution of fluorescence in the QD/toluene dispersion is possibly due to adsorption and desorption of surface ligand molecules over the course of QD aggregation.     

Vibrations of microscopic mercury droplets on glass

Personnel at the Oak Ridge Y-12 Plant, Oak Ridge, Tennessee, and at the University of Tennessee, Knoxville, have measured two types of oscillations for individual, microscopic mercury droplets within a sealed glass cell under partial vacuum. Droplet dimensions were determined by measuring the displacement of a microscope stage as the edges of either the base or the maximum diameter of a pendant droplet were sighted at high magnification. Resonance frequencies were measured by varying the input frequency until droplet oscillation was observed under a microscope. One type of vibration was identified as a special type of polygonal vibration in which the droplet is bound to a solid surface. Another type is an axisymmetric vibration of a bound droplet for which an eigenvalue notation has previously been derived. For 12 microscopic mercury droplets, each less than 9 nl in volume, the agreement between measured and calculated frequencies was within ±4.5%, but ±1% was common. This excellent agreement is consistent with assumptions that the surface tension corresponded to that of pure mercury, that these microscopic droplets were spherical sections, and that these droplets had fixed contact lines. Alternative analytical applications of resonance-frequency measurements on bound droplets are also described.     

Statistical mechanical theory for steady state systems. VII. Nonlinear theory

The second entropy theory for nonequilibrium thermodynamics is extended to the nonlinear regime and to systems of mixed parity (even and odd functions of molecular velocities). The steady state phase space probability density is given for systems of mixed parity. The nonlinear transport matrix is obtained and it is shown to yield the analog of the linear Onsager-Casimir reciprocal relations. Its asymmetric part contributes to the flux and to the production of second entropy. The nonlinear transport matrix is not simply expressible as a Green-Kubo fluctuation equilibrium time correlation function. However, here the first nonlinear correction to the transport coefficient is given explicitly as a type of the Green-Kubo equilibrium time correlation function. The theory is illustrated by application to chemical kinetics.     

Atom für Atom

Using the tip of a scanning tunnelling microscope a metal‐free phthalocyanine has been transformed into a silver‐phthalocyanine on a surface. The individual reactions have been performed atom by atom. Each product has been imaged with the scanning tunnelling microscope. Along with the transformation of the molecule, controlled tautomerization and H hopping have been induced by injection of electrons and demonstrate the precision a state‐of‐the‐art scanning tunnelling microscope has reached.