Exploring consensus mRNA secondary (folding) structure units by stochastic sampling and folding simulation

It is extremely difficult to explore mRNA folding structure by biological experiments. In this report, we use stochastic sampling and folding simulation to test the existence of the stable secondary structural units of-mRNA, look for the folding units, and explore the probabilistic stabilization of the units. Using this method, We made simulations for all possible local optimum secondary structures of a single strand mRNA within a certain range, and searched for the common parts of the secondary structures. The consensus secondary structure units (CSSUs) extracted from the above method are mainly hairpins, with a few single strands. These CSSUs suggest that the mRNA folding units could be relatively stable and could perform specific biological function. The significance of these observations for the mRNA folding problem in general is also discussed. (c) 2004 Elsevier B.V. All rights reserved.

Comparison of stochastic methods for control in air traffic management

This paper provides a direct comparison of two stochastic optimisation techniques (Markov Chain Monte Carlo and Sequential Monte Carlo) when applied to the problem of conflict resolution and aircraft trajectory control in air traffic management. The two methods are then also compared to another existing technique of Mixed-Integer Linear Programming which is also popular in distributed control. © 2011 IFAC.

A Stochastic Model for Electron Multiplication Charge-Coupled Devices - From Theory to Practice

Electron multiplication charge-coupled devices (EMCCD) are widely used for photon counting experiments and measurements of low intensity light sources, and are extensively employed in biological fluorescence imaging applications. These devices have a complex statistical behaviour that is often not fully considered in the analysis of EMCCD data. Robust and optimal analysis of EMCCD images requires an understanding of their noise properties, in particular to exploit fully the advantages of Bayesian and maximum-likelihood analysis techniques, whose value is increasingly recognised in biological imaging for obtaining robust quantitative measurements from challenging data. To improve our own EMCCD analysis and as an effort to aid that of the wider bioimaging community, we present, explain and discuss a detailed physical model for EMCCD noise properties, giving a likelihood function for image counts in each pixel for a given incident intensity, and we explain how to measure the parameters for this model from various calibration images. © 2013 Hirsch et al.

Visualising a stochastic model of California Water Resources Using Sankey Diagrams

This paper describes a novel approach to the analysis of supply and demand of water in California. A stochastic model is developed to assess the future supply of and demand for water resources in California. The results are presented in the form of a Sankey diagram where present and stochastically-varying future fluxes of water in California and its sub-regions are traced from source to services by mapping the various transformations of water from when it is first made available for use, through its treatment, recycling and reuse, to its eventual loss in a variety of sinks. This helps to highlight the connections of water with energy and land resources, including the amount of energy used to pump and treat water, the amount of water used for energy production, and the land resources that create a water demand to produce crops for food. By mapping water in this way, policy-makers can more easily understand the competing uses of water, through the identification of the services it delivers (e.g. sanitation, food production, landscaping), the potential opportunities for improving themanagement of the resource and the connections with other resources which are often overlooked in a traditional sector-based management strategy. This paper focuses on a Sankey diagram for water, but the ultimate aim is the visualisation of linked resource futures through inter-connected Sankey diagrams for energy, land and water, tracking changes from the basic resources for all three, their transformations, and the final services they provide.

A PDE viewpoint on basic properties of coordination algorithms with symmetries

Several recent control applications consider the coordination of subsystems through local interaction. Often the interaction has a symmetry in state space, e.g. invariance with respect to a uniform translation of all subsystem values. The present paper shows that in presence of such symmetry, fundamental properties can be highlighted by viewing the distributed system as the discrete approximation of a partial differential equation. An important fact is that the symmetry on the state space differs from the popular spatial invariance property, which is not necessary for the present results. The relevance of the viewpoint is illustrated on two examples: (i) ill-conditioning of interaction matrices in coordination/consensus problems and (ii) the string instability issue. ©2009 IEEE.

The stochastic implicit Euler method - A stable coupling scheme for Monte Carlo burnup calculations

Existing Monte Carlo burnup codes use various schemes to solve the coupled criticality and burnup equations. Previous studies have shown that the coupling schemes of the existing Monte Carlo burnup codes can be numerically unstable. Here we develop the Stochastic Implicit Euler method - a stable and efficient new coupling scheme. The implicit solution is obtained by the stochastic approximation at each time step. Our test calculations demonstrate that the Stochastic Implicit Euler method can provide an accurate solution to problems where the methods in the existing Monte Carlo burnup codes fail. © 2013 Elsevier Ltd. All rights reserved.

Stochastic resonance for modulated gain in a single-mode laser

Stochastic resonance (SR) induced by the signal modulation is investigated, by introducing the signal-modulated gain into a single-mode laser system. Using the linear approximation method, we detailedly calculate the signal-to-noise ratio (SNR) of a gain-noise model of the single-mode laser, taking the cross-correlation between the quantum noise and pump noise into account. We find that, SR appears in the dependence of the SNR on the intensities of the quantum and the pump noises when the correlation coefficient between both the noises is negative; moreover, when the cross-correlation between the two noises is strongly negative, SR exhibits a resonance and a suppression versus the gain coefficient, meanwhile, the single-peaked SR and multi-peaked SR occur in the behaviors of the SNR as functions of the loss coefficient and the deterministic steady-state intensity. (c) 2005 Elsevier B.V. All rights reserved.

Stochastic resonance in single-mode semiconductor lasers

Owing to the considerable virtues of semiconductor lasers for applications, they have become the main optical source for fiber communication systems recently. The behavior of stochastic resonance (SR) in direct-modulated semiconductor laser systems is investigated in this article. Considering the carrier and photon noises and the cross-correlation between the two noises, the power spectrum of the photon density and the signal-to-noise ratio (SNR) of the modulated laser system were calculated using the linear approximation method. We found that the SR always appears in the dependence of the SNR upon the bias current density, and is strongly affected by the cross-correlation coefficient of the carrier and photon noises, the frequency of modulation signal and the photon lifetime in the laser cavity. Hence, it is promising to use the SR mechanism to enhance the SNR of direct-modulated semiconductor laser systems and improve the quality of optical communication. (c) 2006 Elsevier B.V. All rights reserved.

Stochastic resonance in quantum-well semiconductor lasers

The quantum well (QW) semiconductor lasers have become main optical sources for optical fibre communication systems because of their higher modulation speed, broader modulation bandwidth and better temperature characteristics. In order to improve the quality of direct-modulation by means of the stochastic resonance (SR) mechanism in QW semiconductor lasers, we investigate the behaviour of the SR in direct-modulated QW semiconductor laser systems. Considering the cross-correlated carrier noise and photon noise, we calculate the power spectrum of the photon density and the signal-to-noise ratio (SNR) of the direct-modulated laser system by using the linear approximation method. The results indicate that the SR always appears in the dependence of the SNR on the bias current density, and is strongly affected by the cross-correlation coefficient of the carrier and photon noises, the frequency of modulation signal, and the photon lifetime in the laser cavity.

Ultrafast sum-frequency polarization beats in twin Markovian stochastic correlation

An analytic closed form for the second- order or fourth- order Markovian stochastic correlation of attosecond sum- frequency polarization beat ( ASPB) can be obtained in the extremely Doppler- broadened limit. The homodyne detected ASPB signal is shown to be particularly sensitive to the statistical properties of the Markovian stochastic light. fields with arbitrary bandwidth. The physical explanation for this is that the Gaussian- amplitude. field undergoes stronger intensity. fluctuations than a chaotic. field. On the other hand, the intensity ( amplitude). fluctuations of the Gaussian- amplitude. field or the chaotic. field are always much larger than the pure phase. fluctuations of the phase-diffusion field. The field correlation has weakly influence on the ASPB signal when the laser has narrow bandwidth. In contrast, when the laser has broadband linewidth, the ASPB signal shows resonant- nonresonant cross correlation, and the sensitivities of ASPB signal to three Markovian stochastic models increase as time delay is increased. A Doppler- free precision in the measurement of the energy- level sum can be achieved with an arbitrary bandwidth. The advantage of ASPB is that the ultrafast modulation period 900as can still be improved, because the energy- level interval between ground state and excited state can be widely separated.

Two-photon asymmetric color-locking second-order stochastic correlation of attosecond polarization beats

Based on the phase-conjugation polarization interference between two two-photon processes, we theoretically investigated the attosecond scale asymmetry sum-frequency polarization beat in four-level system (FASPB). The field correlation has weak influence on the FASPB signal when the laser has narrow bandwidth. Conversely, when the laser has broadband linewidth, the FASPB signal shows resonance-nonresonance cross correlation. The two-photon signal exhibits hybrid radiation-matter detuning terahertz; damping oscillation, i.e., when the laser frequency is off resonance from the two-photon transition, the signal exhibits damping oscillation and the profile of the two-photon self-correlation signal also exhibits zero time-delay asymmetry of the maxima. We have also investigated the asymmetry of attosecond polarization beat caused by the shift of the two-photon self-correlation zero time-delay phenomenon, in which the maxima of the two two-photon signals are shifted from zero time-delay point to opposite directions. As an attosecond ultrafast modulation process, FASPB can be intrinsically extended to any level-summation systems of two dipolar forbidden excited states.