On the Role of Delays in Biological Systems : Analysis and Design

This work quantifies the nature of delays in genetic regulatory networks and their effect on system dynamics. It is known that a time lag can emerge from a sequence of biochemical reactions. Applying this modeling framework to the protein production processes, delay distributions are derived in a stochastic (probability density function) and deterministic setting (impulse function), whilst being shown to be equivalent under different assumptions. The dependence of the distribution properties on rate constants, gene length, and time-varying temperatures is investigated. Overall, the distribution of the delay in the context of protein production processes is shown to be highly dependent on the size of the genes and mRNA strands as well as the reaction rates. Results suggest longer genes have delay distributions with a smaller relative variance, and hence, less uncertainty in the completion times, however, they lead to larger delays. On the other hand large uncertainties may actually play a positive role, as broader distributions can lead to larger stability regions when this formalization of the protein production delays is incorporated into a feedback system.

Furthermore, evidence suggests that delays may play a role as an explicit design into existing controlling mechanisms. Accordingly, the reccurring dual-feedback motif is also investigated with delays incorporated into the feedback channels. The dual-delayed feedback is shown to have stabilizing effects through a control theoretic approach. Lastly, a distributed delay based controller design method is proposed as a potential design tool. In a preliminary study, the dual-delayed feedback system re-emerges as an effective controller design.

The evolution of cooperation in asymmetric systems

Explaining "Tragedy of the Commons" of evolution of cooperation remains one of the greatest problems for both biology and social science. Asymmetrical interaction, which is one of the most important characteristics of cooperative system, has not been sufficiently considered in the existing models of the evolution of cooperation. Considering the inequality in the number and payoff between the cooperative actors and recipients in cooperation systems, discriminative density-dependent interference competition will occur in limited dispersal systems. Our model and simulation show that the local but not the global stability of a cooperative interaction can be maintained if the utilization of common resource remains unsaturated, which can be achieved by density-dependent restraint or competition among the cooperative actors. More intense density dependent interference competition among the cooperative actors and the ready availability of the common resource, with a higher intrinsic contribution ratio of a cooperative actor to the recipient, will increase the probability of cooperation. The cooperation between the recipient and the cooperative actors can be transformed into conflict and, it oscillates chaotically with variations of the affecting factors under different environmental or ecological conditions. The higher initial relatedness (i.e. similar to kin or reciprocity relatedness), which is equivalent to intrinsic contribution ratio of a cooperative actor to the recipient, can be selected for by penalizing less cooperative or cheating actors but rewarding cooperative individuals in asymmetric systems. The initial relatedness is a pivot but not the aim of evolution of cooperation. This explains well the direct conflict observed in almost all cooperative systems.

Feedback mechanisms for global oscillations in Lure systems

The paper presents two mechanisms for global oscillations in feedback systems, based on bifurcations in absolutely stable systems. The external characterization of the oscillators provides the basis for a (energy-based) dissipativity theory for oscillators, thereby opening new possibilities for rigorous stability analysis of high-dimensional systems and interconnected oscillators. © 2004 Elsevier B.V. All rights reserved.

Nonlinear phenomena in thermoacoustic systems with premixed flames

Nonlinear analysis of thermoacoustic instability is essential for prediction of frequencies, amplitudes and stability of limit cycles. Limit cycles in thermoacoustic systems are reached when the energy input from driving processes and energy losses from damping processes balance each other over a cycle of the oscillation. In this paper an integral relation for the rate of change of energy of a thermoacoustic system is derived. This relation is analogous to the well-known Rayleigh criterion in thermoacoustics, but can be used to calculate the amplitudes of limit cycles, as well as their stability. The relation is applied to a thermoacoustic system of a ducted slot-stabilized 2-D premixed flame. The flame is modelled using a nonlinear kinematic model based on the G-equation, while the acoustics of planar waves in the tube are governed by linearised momentum and energy equations. Using open-loop forced simulations, the flame describing function (FDF) is calculated. The gain and phase information from the FDF is used with the integral relation to construct a cyclic integral rate of change of energy (CIRCE) diagram that indicates the amplitude and stability of limit cycles. This diagram is also used to identify the types of bifurcation the system exhibits and to find the minimum amplitude of excitation needed to reach a stable limit cycle from another linearly stable state, for single- mode thermoacoustic systems. Furthermore, this diagram shows precisely how the choice of velocity model and the amplitudedependence of the gain and the phase of the FDF influence the nonlinear dynamics of the system. Time domain simulations of the coupled thermoacoustic system are performed with a Galerkin discretization for acoustic pressure and velocity. Limit cycle calculations using a single mode, as well as twenty modes, are compared against predictions from the CIRCE diagram. For the single mode system, the time domain calculations agree well with the frequency domain predictions. The heat release rate is highly nonlinear but, because there is only a single acoustic mode, this does not affect the limit cycle amplitude. For the twenty-mode system, however, the higher harmonics of the heat release rate and acoustic velocity interact resulting in a larger limit cycle amplitude. Multimode simulations show that in some situations the contribution from higher harmonics to the nonlinear dynamics can be significant and must be considered for an accurate and comprehensive analysis of thermoacoustic systems. Copyright © 2012 by ASME.

Observation of locked phase dynamics and enhanced frequency stability in synchronized micromechanical oscillators

Even though synchronization in autonomous systems has been observed for over three centuries, reports of systematic experimental studies on synchronized oscillators are limited. Here, we report on observations of internal synchronization in coupled silicon micromechanical oscillators associated with a reduction in the relative phase random walk that is modulated by the magnitude of the reactive coupling force between the oscillators. Additionally, for the first time, a significant improvement in the frequency stability of synchronized micromechanical oscillators is reported. The concept presented here is scalable and could be suitably engineered to establish the basis for a new class of highly precise miniaturized clocks and frequency references. © 2013 American Physical Society.

Predictions of the Pt(8)Ti phase in unexpected systems.

The binary A(8)B phase (prototype Pt(8)Ti) has been experimentally observed in 11 systems. A high-throughput search over all the binary transition intermetallics, however, reveals 59 occurrences of the A(8)B phase: Au(8)Zn(dagger), Cd(8)Sc(dagger), Cu(8)Ni(dagger), Cu(8)Zn(dagger), Hg(8)La, Ir(8)Os(dagger), Ir(8)Re, Ir(8)Ru(dagger), Ir(8)Tc, Ir(8)W(dagger), Nb(8)Os(dagger), Nb(8)Rh(dagger), Nb(8)Ru(dagger), Nb(8)Ta(dagger), Ni(8)Fe, Ni(8)Mo(dagger)*, Ni(8)Nb(dagger)*, Ni(8)Ta*, Ni(8)V*, Ni(8)W, Pd(8)Al(dagger), Pd(8)Fe, Pd(8)Hf, Pd(8)Mn, Pd(8)Mo*, Pd(8)Nb, Pd(8)Sc, Pd(8)Ta, Pd(8)Ti, Pd(8)V*, Pd(8)W*, Pd(8)Zn, Pd(8)Zr, Pt(8)Al(dagger), Pt(8)Cr*, Pt(8)Hf, Pt(8)Mn, Pt(8)Mo, Pt(8)Nb, Pt(8)Rh(dagger), Pt(8)Sc, Pt(8)Ta, Pt(8)Ti*, Pt(8)V*, Pt(8)W, Pt(8)Zr*, Rh(8)Mo, Rh(8)W, Ta(8)Pd, Ta(8)Pt, Ta(8)Rh, V(8)Cr(dagger), V(8)Fe(dagger), V(8)Ir(dagger), V(8)Ni(dagger), V(8)Pd, V(8)Pt, V(8)Rh, and V(8)Ru(dagger) ((dagger) = metastable, * = experimentally observed). This is surprising for the wealth of new occurrences that are predicted, especially in well-characterized systems (e.g., Cu-Zn). By verifying all experimental results while offering additional predictions, our study serves as a striking demonstration of the power of the high-throughput approach. The practicality of the method is demonstrated in the Rh-W system. A cluster-expansion-based Monte Carlo model reveals a relatively high order-disorder transition temperature.

A COMPARISON OF MARKET CLEARING TOOLS IN ELECTRICITY SYSTEMS

To maintain a strict balance between demand and supply in the US power systems, the Independent System Operators (ISOs) schedule power plants and determine electricity prices using a market clearing model. This model determines for each time period and power plant, the times of startup, shutdown, the amount of power production, and the provisioning of spinning and non-spinning power generation reserves, etc. Such a deterministic optimization model takes as input the characteristics of all the generating units such as their power generation installed capacity, ramp rates, minimum up and down time requirements, and marginal costs for production, as well as the forecast of intermittent energy such as wind and solar, along with the minimum reserve requirement of the whole system. This reserve requirement is determined based on the likelihood of outages on the supply side and on the levels of error forecasts in demand and intermittent generation. With increased installed capacity of intermittent renewable energy, determining the appropriate level of reserve requirements has become harder. Stochastic market clearing models have been proposed as an alternative to deterministic market clearing models. Rather than using a fixed reserve targets as an input, stochastic market clearing models take different scenarios of wind power into consideration and determine reserves schedule as output. Using a scaled version of the power generation system of PJM, a regional transmission organization (RTO) that coordinates the movement of wholesale electricity in all or parts of 13 states and the District of Columbia, and wind scenarios generated from BPA (Bonneville Power Administration) data, this paper explores a comparison of the performance between a stochastic and deterministic model in market clearing. The two models are compared in their ability to contribute to the affordability, reliability and sustainability of the electricity system, measured in terms of total operational costs, load shedding and air emissions. The process of building the models and running for tests indicate that a fair comparison is difficult to obtain due to the multi-dimensional performance metrics considered here, and the difficulty in setting up the parameters of the models in a way that does not advantage or disadvantage one modeling framework. Along these lines, this study explores the effect that model assumptions such as reserve requirements, value of lost load (VOLL) and wind spillage costs have on the comparison of the performance of stochastic vs deterministic market clearing models.

Intelligent technologies for nuclear power systems: heuristic and neural tools

The consecutive, partly overlapping emergence of expert systems and then neural computation methods among intelligent technologies, is reflected in the evolving scene of their application to nuclear engineering. This paper provides a bird's eye view of the state of the application in the domain, along with a review of a particular task, the one perhaps economically more important: refueling design in nuclear power reactors.

Disturbance attenuation in linear systems via dynamical compensators: A parametric eigenstructure assignment approach

A simple approach is proposed for disturbance attenuation in multivariable linear systems via dynamical output compensators based on complete parametric eigenstructure assignment. The basic idea is to minimise the H-2 norm of the disturbance-output transfer function using the design freedom provided by eigenstructure assignment. For robustness, the closed-loop system is restricted to be nondefective. Besides the design parameters, the closed-loop eigenvalues are also optimised within desired regions on the left-half complex plane to ensure both closed-loop stability and dynamical performance. With the proposed approach, additional closed-loop specifications can be easily achieved. As a demonstration, robust pole assignment, in the sense that the closed-loop eigenvalues are as insensitive as possible to open-loop system parameter perturbations, is treated. Application of the proposed approach to robust control of a magnetic bearing with a pair of opposing electromagnets and a rigid rotor is discussed.

Electrical energy storage and Smart Grid technologies to integrate the next generation of Renewable Power Systems

The growth of renewable power sources, distributed generation and the potential for alternative fuelled modes of transport such as electric vehicles has led to concerns over the ability of existing grid systems to facilitate such diverse portfolio mixes in already congested power systems. Internationally the growth in renewable energy sources is driven by government policy targets associated with the uncertainties of fossil fuel supplies, environmental issues and a move towards energy independence. Power grids were traditionally designed as vertically integrated centrally managed entities with fully dispatchable generating plant. Renewable power sources, distributed generation and alternative fuelled vehicles will place these power systems under additional stresses and strains due to their different operational characteristics. Energy storage and smart grid technologies are widely proposed as the tools to integrate these future diverse portfolio mixes within the more conventional power systems. The choice in these technologies is determined not only by their location on the grid system, but by the diversification in the power portfolio mix, the electricity market and the operational demands. This paper presents a high level technical and economic overview of the role and relevance of electrical energy storage and smart grid technologies in the next generation of renewable power systems.

Characterisation of protein stability in rod-insert vaginal rings

A major goal in vaccine development is elimination of the ‘cold chain’, the transport and storage system for maintenance and distribution of the vaccine product. This is particularly pertinent to liquid formulation of vaccines. We have previously described the rod-insert vaginal ring (RiR) device, comprising an elastomeric body into which are inserted lyophilised, rod-shaped, solid drug dosage forms, and having potential for sustained mucosal delivery of biomacromolecules, such as HIV envelope protein-based vaccine candidates. Given the solid, lyophilised nature of these insert dosage forms, we hypothesised that antigen stability may be significantly increased compared with more conventional solubilised vaginal gel format. In this study, we prepared and tested vaginal ring devices fitted with lyophilised rod inserts containing the model antigen bovine serum albumin (BSA). Both the RiRs and the gels that were freeze-dried to prepare the inserts were evaluated for BSA stability using PAGE, turbidimetry, microbial load, MALDI-TOF and qualitative precipitate solubility measurements. When stored at 4 oC, but not when stored at 40 oC / 75% RH, the RiR formulation offered protection against structural and conformational changes to BSA. The insert also retained matrix integrity and release characteristics. The results demonstrate that lypophilised gels can provide relative protection against degradation at lower temperatures compared to semi-solid gels. The major mechanism of degradation at 40 oC / 75% RH was shown to be protein aggregation. Finally, in a preliminary study, we found that addition of trehalose to the formulation significantly reduces the rate of BSA degradation as compared to the original formulation when stored at 40 oC /75% RH. Establishing the mechanism of degradation, and finding that degradation is decelerated in the presence of trehalose, will help inform further development of RiRs specifically and polymer based freeze-dried systems in general.

Tripping Control for Transient Stability in Coordinated Hydro and Wind Generation

Over-frequency generator tripping (OFGT) is used to cut off extra generation to balance power and loads in an isolated system. In this paper the impact of OGFT as a consequence of grid-connected wind farms and under-frequency load shedding (UFLS) is analysed. The paper uses a power system model to demonstrate that wind power fluctuations can readily render OFGT and UFLS maloperation. Using combined hydro and wind generation, the paper proposes a coordinated strategy which resolves problems associated with OFGT and UFLS and preserves system stability.

Voltage Dip Benchmarking in Power Quality and Disturbance Monitoring

This paper examines power quality benchmarks in the electricity supply industry (ESI) and impact of standards for the reduction of voltage dip incidents. The paper considers adherence to particular standards and is supported by several case studies from incidents where voltage dips have been detected and assessed by the power systems division of Scottish Power and where improvements have been implemented to help militate against subsequent incidents.

Managing adaptivity in parallel systems

The management of non-functional features (performance, security, power management, etc.) is traditionally a difficult, error prone task for programmers of parallel applications. To take care of these non-functional features, autonomic managers running policies represented as rules using sensors and actuators to monitor and transform a running parallel application may be used. We discuss an approach aimed at providing formal tool support to the integration of independently developed autonomic managers taking care of different non-functional concerns within the same parallel application. Our approach builds on the Behavioural Skeleton experience (autonomic management of non-functional features in structured parallel applications) and on previous results on conflict detection and resolution in rule-based systems. © 2013 Springer-Verlag Berlin Heidelberg.