Non-coding RNAs and a layered architecture of genetic networks

In eukaryotic cells, protein-coding sequences constitute a relatively small part of the genome. The rest of the genome is transcribed to non-coding RNAs (ncRNAs). Such RNAs form the cornerstone of a regulatory network that operates in parallel with the protein network. Their biological functions are based primarily on the ability to pair with and deactivate target messenger RNAs (mRNAs). To clarify the likely role of ncRNAs in complex genetic networks, we present and comprehensively analyze a kinetic model of one of the key counterparts of the network architectures. Specifically, the genes transcribed to ncRNAs are considered to interplay with a hierarchical two-layer set of genes transcribed to mRNAs. The genes forming the bottom layer are regulated from the top and negatively self-regulated. If the former regulation is positive, the dependence of the RNA populations on the governing parameters is found to be often non-monotonous. Specifically, the model predicts bistability. If the regulation is negative, the dependence of the RNA populations on the governing parameters is monotonous. In particular, the population of the mRNAs, corresponding to the genes forming the bottom layer, is nearly constant.     

Non-coding RNAs and complex distributed genetic networks

In eukaryotic cells, the mRNA-protein interplay can be dramatically influenced by non-coding RNAs (ncRNAs). Although this new paradigm is now widely accepted, an understanding of the effect of ncRNAs on complex genetic networks is lacking. To clarify what may happen in this case, we propose a mean-field kinetic model describing the influence of ncRNA on a complex genetic network with a distributed architecture including mutual protein-mediated regulation of many genes transcribed into mRNAs. ncRNA is considered to associate with mRNAs and inhibit their translation and/or facilitate degradation. Our results are indicative of the richness of the kinetics under consideration. The main complex features are found to be bistability and oscillations. One could expect to find kinetic chaos as well. The latter feature has however not been observed in our calculations. In addition, we illustrate the difference in the regulation of distributed networks by mRNA and ncRNA.     

Switches in gene expression including microRNA and a large number of distinct mRNAs

In eukaryotic cells, the kinetics of gene expression depends on the interplay of messenger RNAs (mRNAs), proteins, and nonprotein coding RNAs, or, more specifically, microRNAs. Some microRNAs may target hundreds of mRNAs. To describe this case, the author proposes a kinetic model implying that the microRNA synthesis is suppressed by the protein produced via the translation of one of the target mRNAs. With physically reasonable model parameters, the model predicts bistability or, in other words, switches in the expression of hundreds of genes. The text was submitted by the author in English.     

Different Types of Synchronization in Time-Delayed Systems

We investigate different types of synchronization between two unidirectionally nonlinearly coupled identical delay- differential systems related to optical bistable or hybrid optical bistable devices. This system can represent some kinds of delay-differential models, i.e. Ikeda model, Vall~e model, sine-square model, Mackey Glass model, and so on. We find existence and sufficient stability conditions by theoretical analysis and test the correctness by＂ numerical simulations. Lag, complete and anticipating synchronization are observed, respectively. It is found that the time-delay system can be divided into two parts~ one is the instant term and the other is the delay term. Synchronization between two identical chaotic systems can be derived by adding a coupled term to the delay term in the driven system.     

A random walker on a ratchet

We analyze a model for a walker moving on a ratchet potential. This model is motivated by the properties of transport of motor proteins, like kinesin and myosin. The walker consists of two feet that are represented as two particles coupled nonlinearly through a bistable potential. In contrast to linear coupling, the bistable potential admits a richer dynamics, where the ordering of the particles can alternate during the walking. The transitions between the two stable states on the bistable potential correspond to a walking with alternating particles. We distinguish between two main walking styles: alternating and no alternating, resembling the hand-over-hand and the inchworm walking in motor proteins, respectively. When the equilibrium distance between the two particles divided by the periodicity of the ratchet is an integer, we obtain a maximum for the current, indicating optimal transport.     

Optical bistability and signal processing in a microstructured fiber ring resonator

We explore theoretically the effects of bistability in a microstructured fiber-based ring resonator. Numerical simulations indicate that bistable behavior of the fiber cavity can be observed with a short length of fiber. Feasibility of all-optical processing using this type of cavity is also investigated. In particular, we show that a ring cavity including a microstructured fiber should allow one to perform flip-flop and time-division demultiplexing functions. The analysis presented here will be useful for future design of bistable microstructured fiber device.     

Resonance phenomena in discrete systems with bichromatic input signal

We undertake a detailed numerical study of the twin phenomenon of stochastic and vibrational resonance in a discrete model system in the presence of bichromatic input signal. A two parameter cubic map is used as the model that combines the features of both bistable and threshold systems. In addition to the results already shown for continuous systems, our analysis brings out several interesting features both for vibrational and stochastic resonance, including the existence of a cross over behavior between the two. In the regime of vibrational resonance, it is shown that the additional high frequency forcing can change the effective value of the system parameter resulting in the shift of the bistable window. In the case of stochastic resonance, the study reveals a fundamental difference between the bistable and threshold mechanisms in the response, with respect to multisignal input.     

Manipulating a micro-cantilever between its optomechanical bistable states in a lever-based Fabry-Pérot cavity

In this paper, we demonstrate experimentally switching a cantilever between its optomechanical bistable states in a low finesse optical cavity. Our experiment shows that the deformation of cantilever can be manipulated by tuning the cavity resonance. When the laser power increases across the threshold value of 110 ?W, optomechanical bistability is induced by strong static photothermal backaction at room temperature. Numerical calculation revealed that the bistable effect originates from the multi-well potential created via the optomechanical interaction. Switching of the cantilever between the bistable states was achieved by tuning the cavity to the corresponding boundaries of the bistable region, where the barrier between the bistable states vanishes.     

Optical bistability via amplitude and phase control of a microwave field

We investigate the steady-state optical bistability behavior in a three-level Λ-type atomic system closed by a microwave field under the condition that the applied fields are in resonance with corresponding atomic transitions. It is shown that the bistable hysteresis cycles can be controlled by both the amplitude and the phase of the microwave field.     

一种实现二进制加法符号替换规律的光逻辑系统

为了实现二进制加法符号替换规律,本文提出了一种简单的光逻辑系统,它仅包括一片二维列阵光学双稳器件.本实验采用同时具有NXOR和OR逻辑功能的透反射型ZnS光学双稳干涉滤光片作光逻辑器件.该光学逻辑系统完成了二进制加法四个符号替换规律的并行替换.光学系统采用固定的自由空间互连方法,具有光学硬件少,光功率损耗低,结构简单、实用的优点.     

双稳随机动力系统信号调制噪声效应的数值分析

用数值方法研究了双稳随机动力系统的信号调制噪声效应.结果表明，正弦信号在系统输出中的效应仍为正弦信号，白噪声的效应则为维纳过程，通过选择合适的系统参数，可以减小系统输出中信号和噪声之间的耦合效应，系统可以大大抑制噪声，从而在双稳系统中可以产生信号调制噪声效应. 关键词： 双稳系统 信号调制噪声效应 随机共振     

Oscillatory dynamics in a simple gene regulatory network mediated by small RNAs

More and more experiments show that small RNAs regulate gene expression by repressing translation of messenger RNAs (mRNAs) or degrading mRNAs. In this paper, we incorporate the small RNAs into a simple gene regulatory network and investigate its dynamical behaviors. In addition, we also derive the theoretical results of globally asymptotic stability and provide the sufficient conditions for the oscillation of the simple gene regulatory network, and further demonstrate that the amplitudes against the change of delay in the gene regulatory network are robust.     

Stochastic resonance on paced genetic regulatory small-world networks: effects of asymmetric potentials

We study the phenomenon of stochastic resonance on small-world networks consisting of bistable genetic regulatory units, whereby the external subthreshold periodic forcing is introduced as a pacemaker trying to impose its rhythm on the whole network through the single unit to which it is introduced. Without the addition of additive spatiotemporal noise, however, the whole network remains forever trapped in one of the two stable steady states of the local dynamics. We show that the correlation between the frequency of subthreshold pacemaker activity and the response of the network is resonantly dependent on the intensity of additive noise. The reported pacemaker driven stochastic resonance depends significantly on the asymmetry of the two potential wells characterizing the bistable dynamics, which can be tuned via a single system parameter. In particular, we show that the ratio between the clustering coefficient and the characteristic path length is a suitable quantity defining the ability of a small-world network to facilitate the outreach of the pacemaker-emitted subthreshold rhythm, but only if the asymmetry between the potentials is practically negligible. In case of substantially asymmetric potentials the impact of the small-world topology is less profound and cannot warrant an enhancement of stochastic resonance by units that are located far from the pacemaker.     

Hybrid Optoelectronic Bistability in Frequency-Domain and Its Potential Application in FBG Sensors

We propose a novel optical bistable device （OBD） in frequency-domain with which we can perform optical bistable operations in a number of fibre Bragg gratings （FBGs） which are included in the same OBD. Such an OBD may bring more opportunities in applications and, as an example, we show the possibility of using it in an FBG sensor demodulating system. By use of a tunable light source, consisting of a broad band source and a scanning fibre F-P （FFP）, we demonstrate the above-mentioned operations experimentally.     

四稳系统的双重随机共振特性

提出了一类8次势函数并讨论了其分岔特性,得到由左、右2个小尺度双稳势和中间势垒构成的对称四稳系统.建立了在周期力和随机力共同作用下四稳系统输出响应的近似解析表达式,并从能量角度引入功这一过程量来刻画大、小不同尺度双稳势之间的作功能力,发现四稳势中存在着双重随机共振现象.理论分析与数值仿真结果表明,当中间势垒高度大于左右...     

Incoherent optical switching of semiconductor resonator solitons

We demonstrate experimentally the bistable nature of the bright resonator solitons in a semiconductor microresonator with mixed absorptive/defocusing nonlinearity and show that they can be written and erased by incoherent local optical injection. Received: 22 February 2001 / Published online: 27 April 2001     

Hysteresis and memory of the magnetic resonance of conduction electrons in solids. From bistability to stochastic resonance

The magnetic resonance line of conduction electrons in solids may exhibit bistable hysteresis if several conditions are fulfilled. Its mechanism is presented and the manifestation of bistability in the ESR of conduction electrons in single crystal and polycrystalline samples is discussed. The characteristics of the dynamics of the bistability show that bistable resonance can be assimilated to one-dimensional overdamped motion of the spin system in the nuclear field space, driven by a bistable potential. It is shown for the first time that noise acting on this bistable resonance can create order, by the phenomenon of stochastic resonance.