Switching Between Discrete and Continuous Process Models to Predict Molecular Genetic Activity

Two kinds of process models have been used in programs that reason about change: Discrete and continuous models. We describe the design and implementation of a qualitative simulator, PEPTIDE, which uses both kinds of process models to predict the behavior of molecular energetic systems. The program uses a discrete process model to simulate both situations involving abrupt changes in quantities and the actions of small numbers of molecules. It uses a continuous process model to predict gradual changes in quantities. A novel technique, called aggregation, allows the simulator to switch between theses models through the recognition and summary of cycles. The flexibility of PEPTIDE's aggregator allows the program to detect cycles within cycles and predict the behavior of complex situations.

Exponential sensitivity of noise-driven switching in genetic networks

Cells are known to utilize biochemical noise to probabilistically switch between distinct gene expression states. We demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore exponentially sensitive to changes in physiological parameters such as transcription and translation rates. However, provided mRNA lifetimes are short, switching can still be accurately simulated using protein-only models of gene expression. Exponential sensitivity limits the robustness of noise-driven switching, suggesting cells may use other mechanisms in order to switch reliably.

Differential and numerical models of hysteretic systems with stochastic and deterministic inputs

Many deterministic models with hysteresis have been developed in the areas of economics, finance, terrestrial hydrology and biology. These models lack any stochastic element which can often have a strong effect in these areas. In this work stochastically driven closed loop systems with hysteresis type memory are studied. This type of system is presented as a possible stochastic counterpart to deterministic models in the areas of economics, finance, terrestrial hydrology and biology. Some price dynamics models are presented as a motivation for the development of this type of model. Numerical schemes for solving this class of stochastic differential equation are developed in order to examine the prototype models presented. As a means of further testing the developed numerical schemes, numerical examination is made of the behaviour near equilibrium of coupled ordinary differential equations where the time derivative of the Preisach operator is included in one of the equations. A model of two phenotype bacteria is also presented. This model is examined to explore memory effects and related hysteresis effects in the area of biology. The memory effects found in this model are similar to that found in the non-ideal relay. This non-ideal relay type behaviour is used to model a colony of bacteria with multiple switching thresholds. This model contains a Preisach type memory with a variable Preisach weight function. Shown numerically for this multi-threshold model is a pattern formation for the distribution of the phenotypes among the available thresholds.

Sensitivity to switching rates in stochastically switched ODEs

We consider a stochastic process driven by a linear ordinary differential equation whose right-hand side switches at exponential times between a collection of different matrices. We construct planar examples that switch between two matrices where the individual matrices and the average of the two matrices are all Hurwitz (all eigenvalues have strictly negative real part), but nonetheless the process goes to infinity at large time for certain values of the switching rate. We further construct examples in higher dimensions where again the two individual matrices and their averages are all Hurwitz, but the process has arbitrarily many transitions between going to zero and going to infinity at large time as the switching rate varies. In order to construct these examples, we first prove in general that if each of the individual matrices is Hurwitz, then the process goes to zero at large time for sufficiently slow switching rate and if the average matrix is Hurwitz, then the process goes to zero at large time for sufficiently fast switching rate. We also give simple conditions that ensure the process goes to zero at large time for all switching rates. © 2014 International Press.

Stochastic switching in infinite dimensions with applications to random parabolic PDE

© 2015 Society for Industrial and Applied Mathematics.We consider parabolic PDEs with randomly switching boundary conditions. In order to analyze these random PDEs, we consider more general stochastic hybrid systems and prove convergence to, and properties of, a stationary distribution. Applying these general results to the heat equation with randomly switching boundary conditions, we find explicit formulae for various statistics of the solution and obtain almost sure results about its regularity and structure. These results are of particular interest for biological applications as well as for their significant departure from behavior seen in PDEs forced by disparate Gaussian noise. Our general results also have applications to other types of stochastic hybrid systems, such as ODEs with randomly switching right-hand sides.

Idealised operation of zero-voltage-switching series-L/parallel-tuned Class-E power amplifier

An analysis of a modified series-L/parallel-tuned Class-E power amplifier is presented, which includes the effects that a shunt capacitance placed across the switching device will have on Class-E behaviour. In the original series L/parallel-tuned topology in which the output transistor capacitance is not inherently included in the circuit, zero-current switching (ZCS) and zero-current derivative switching (ZCDS) conditions should be applied to obtain optimum Class-E operation. On the other hand, when the output transistor capacitance is incorporated in the circuit, i.e. in the modified series-L/parallel-tuned topology, the ZCS and ZCDS would not give optimum operation and therefore zero-voltage-switching (ZVS) and zero-voltage-derivative switching (ZVDS) conditions should be applied instead. In the modified series-L/parallel-tuned Class-E configuration, the output-device inductance and the output-device output capacitance, both of which can significantly affect the amplifier's performance at microwave frequencies, furnish part, if not all, of the series inductance L and the shunt capacitance COUT, respectively. Further, when compared with the classic shunt-C/series-tuned topology, the proposed Class-E configuration offers some advantages in terms of 44% higher maximum operating frequency (fMAX) and 4% higher power-output capability (PMAX). As in the classic topology, the fMAX of the proposed amplifier circuit is reached when the output-device output capacitance furnishes all of the capacitance COUT, for a given combination of frequency, output power and DC supply voltage. It is also shown that numerical simulations agree well with theoretical predictions.

Free-space optoelectronic switching cores with MPLS for SANs over WDM ring networks

With increasing demands on storage devices in the modern communication environment, the storage area network (SAN) has evolved to provide a direct connection allowing these storage devices to be accessed efficiently. To optimize the performance of a SAN, a three-stage hybrid electronic/optical switching node architecture based on the concept of a MPLS label switching mechanism, aimed at serving as a multi-protocol label switching (MPLS) ingress label edge router (LER) for a SAN-enabled application, has been designed. New shutter-based free-space multi-channel optical switching cores are employed as the core switch fabric to solve the packet contention and switching path conflict problems. The system-level node architecture design constraints are evaluated through self-similar traffic sourced from real gigabit Ethernet network traces and storage systems. The extension performance of a SAN over a proposed WDM ring network, aimed at serving as an MPLS-enabled transport network, is also presented and demonstrated.

Prey field switching based on preferential behaviour can induce Lévy flights

Using the foraging movements of an insectivorous bat, Myotis mystacinus, we describe temporal switching of foraging behaviour in response to resource availability. These observations conform to predictions of optimized search under the Lévy flight paradigm. However, we suggest that this occurs as a result of a preference behaviour and knowledge of resource distribution. Preferential behaviour and knowledge of a familiar area generate distinct movement patterns as resource availability changes on short temporal scales. The behavioural response of predators to changes in prey fields can elicit different functional responses, which are considered to be central in the development of stable predator-prey communities. Recognizing how the foraging movements of an animal relate to environmental conditions also elucidates the evolution of optimized search and the prevalence of discrete strategies in natural systems. Applying techniques that use changes in the frequency distribution of movements facilitates exploration of the processes that underpin behavioural changes. © 2012 The Author(s) Published by the Royal Society. All rights reserved.

Real-space mapping of dynamic phenomena during hysteresis loop measurements: Dynamic switching spectroscopy piezoresponse force microscopy

Dynamic switching spectroscopy piezoresponse force microscopy is developed to separate thermodynamic and kinetic effects in local bias-induced phase transitions. The approaches for visualization and analysis of five-dimensional data are discussed. The spatial and voltage variability of relaxation behavior of the a-c domain lead zirconate-titanate surface suggest the interpretation in terms of surface charge dynamics. This approach is applicable to local studies of dynamic behavior in any system with reversible bias-induced phase transitions ranging from ferroelectrics and multiferroics to ionic systems such as batteries, fuel cells, and electroresistive materials. (C) 2011 American Institute of Physics. [doi:10.1063/1.3590919]

Lorentz TEM investigation of the switching behavior in artificial spin ice building blocks

Frustration – the inability to simultaneously satisfy all interactions – occurs in a wide range of systems including neural networks, water ice and magnetic systems. An example of the latter is the so called spin-ice in pyrochlore materials [1] which have attracted a lot of interest not least due to the emergence of magnetic monopole defects when the ‘ice rules’ governing the local ordering breaks down [2]. However it is not possible to directly measure the frustrated property – the direction of the magnetic moments – in such spin ice systems with current experimental techniques. This problem can be solved by instead studying artificial spin-ice systems where the molecular magnetic moments are replaced by nanoscale ferromagnetic islands [3-8]. Two different arrangements of the ferromagnetic islands have been shown to exhibit spin ice behaviour: a square lattice maintaining four moments at each vertex [3,8] and the Kagome lattice which has only three moments per vertex but equivalent interactions between them [4-7]. Magnetic monopole defects have been observed in both types of lattices [7-8]. One of the challenges when studying these artificial spin-ice systems is that it is difficult to arrive at the fully demagnetised ground-state [6-8].
Here we present a study of the switching behaviour of building blocks of the Kagome lattice influenced by the termination of the lattice. Ferromagnetic islands of nominal size 1000 nm by 100 nm were fabricated in five island blocks using electron-beam lithography and lift-off techniques of evaporated 18 nm Permalloy (Ni80Fe20) films. Each block consists of a central island with four arms terminated by a different number and placement of ‘injection pads’, see Figure 1. The islands are single domain and magnetised along their long axis. The structures were grown on a 50 nm thick electron transparent silicon nitride membrane to allow TEM observation, which was back-coated with a 5 nm film of Au to prevent charge build-up during the TEM experiments.
To study the switching behaviour the sample was subjected to a magnetic field strong enough to magnetise all the blocks in one direction, see Figure 1. Each block obeys the Kagome lattice ‘ice-rules’ of “2-in, 1-out” or “1-in, 2-out” in this fully magnetised state. Fresnel mode Lorentz TEM images of the sample were then recorded as a magnetic field of increasing magnitude was applied in the opposite direction. While the Fresnel mode is normally used to image magnetic domain structures [9] for these types of samples it is possible to deduce the direction of the magnetisation from the Lorentz contrast [5]. All images were recorded at the same over-focus judged to give good Lorentz contrast.
The magnetisation was found to switch at different magnitudes of the applied field for nominally identical blocks. However, trends could still be identified: all the blocks with any injection pads, regardless of placement and number, switched the direction of the magnetisation of their central island at significantly smaller magnitudes of the applied magnetic field than the blocks without injection pads. It can therefore be concluded that the addition of an injection pad lowers the energy barrier to switching the connected island, acting as a nucleation site for monopole defects. In these five island blocks the defects immediately propagate through to the other side, but in a larger lattice the monopoles could potentially become trapped at a vertex and observed [10].
References

[1] M J Harris et al, Phys Rev Lett 79 (1997) p.2554.
[2] C Castelnovo, R Moessner and S L Sondhi, Nature 451 (2008) p. 42.
[3] R F Wang et al, Nature 439 (2006) 303.
[4] M Tanaka et al, Phys Rev B 73 (2006) 052411.
[5] Y Qi, T Brintlinger and J Cumings, Phys Rev B 77 (2008) 094418.
[6] E Mengotti et al, Phys Rev B 78 (2008) 144402.
[7] S Ladak et al, Nature Phys 6 (2010) 359.
[8] C Phatak et al, Phys Rev B 83 (2011) 174431.
[9] J N Chapman, J Phys D 17 (1984) 623.
[10] The authors gratefully acknowledge funding from the EPSRC under grant number EP/D063329/1.

Performance analysis of switch-and-stay combining in two-way relay systems with analog network coding and time-division broadcast protocols

In this paper, weconsider switch-and-stay combining (SSC) in two-way relay systems with two amplify-and-forward relays, one of which is activated to assist the information exchange between the two sources. The system operates in either analog network coding (ANC) protocol where the communication is only achieved with the help of the active relay or timedivision broadcast (TDBC) protocol where the direct link between two sources can be utilized to exploit more diversity gain. In both cases, we study the outage probability and bit error rate (BER) for Rayleigh fading channels. In particular, we derive closed-form lower bounds for the outage probability and the average BER, which remain tight for different fading conditions. We also present asymptotic analysis for both the outage probability and the average BER at high signalto-noise ratio. It is shown that SSC can achieve the full diversity order in two-way relay systems for both ANC and TDBC protocols with proper switching thresholds. Copyright © 2014 John Wiley & Sons, Ltd.

Fluorescent Logic Systems for Sensing and Molecular Computation: Structure-Activity Relationships in Edge-Detection

Molecular logic-based computation continues to throw up new applications in sensing and switching, the newest of which is the edge detection of objects. The scope of this phenomenon is mapped out by the use of structure-activity relationships, where several structures of the molecules and of the objects are examined. The different angles and curvatures of the objects are followed with good-fidelity in the visualized edges, even when the objects are in reverse video.

Enhanced ethernet switching technology for adaptive hard real-time applications: Tecnologia de comutação ethernet melhorada para aplicações adaptativas e críticas de tempo-real

Os Sistemas Embarcados Distribuídos (SEDs) estão, hoje em dia, muito difundidos em vastas áreas, desde a automação industrial, a automóveis, aviões, até à distribuição de energia e protecção do meio ambiente. Estes sistemas são, essencialmente, caracterizados pela integração distribuída de aplicações embarcadas, autónomas mas cooperantes, explorando potenciais vantagens em termos de modularidade, facilidade de manutenção, custos de instalação, tolerância a falhas, entre outros. Contudo, o ambiente operacional onde se inserem estes tipos de sistemas pode impor restrições temporais rigorosas, exigindo que o sistema de comunicação subjacente consiga transmitir mensagens com garantias temporais. Contudo, os SEDs apresentam uma crescente complexidade, uma vez que integram subsistemas cada vez mais heterogéneos, quer ao nível do tráfego gerado, quer dos seus requisitos temporais. Em particular, estes subsistemas operam de forma esporádica, isto é, suportam mudanças operacionais de acordo com estímulos exteriores. Estes subsistemas também se reconfiguram dinamicamente de acordo com a actualização dos seus requisitos e, ainda, têm lidar com um número variável de solicitações de outros subsistemas. Assim sendo, o nível de utilização de recursos pode variar e, desta forma, as políticas de alocação estática tornam-se muito ineficientes. Consequentemente, é necessário um sistema de comunicação capaz de suportar com eficácia reconfigurações e adaptações dinâmicas. A tecnologia Ethernet comutada tem vindo a emergir como uma solução sólida para fornecer comunicações de tempo-real no âmbito dos SEDs, como comprovado pelo número de protocolos de tempo-real que foram desenvolvidos na última década. No entanto, nenhum dos protocolos existentes reúne as características necessárias para fornecer uma eficiente utilização da largura de banda e, simultaneamente, para respeitar os requisitos impostos pelos SEDs. Nomeadamente, a capacidade para controlar e policiar tráfego de forma robusta, conjugada com suporte à reconfiguração e adaptação dinâmica, não comprometendo as garantias de tempo-real. Esta dissertação defende a tese de que, pelo melhoramento dos comutadores Ethernet para disponibilizarem mecanismos de reconfiguração e isolamento de tráfego, é possível suportar aplicações de tempo-real críticas, que são adaptáveis ao ambiente onde estão inseridas.Em particular, é mostrado que as técnicas de projecto, baseadas em componentes e apoiadas no escalonamento hierárquico de servidores de tráfego, podem ser integradas nos comutadores Ethernet para alcançar as propriedades desejadas. Como suporte, é fornecida, também, uma solução para instanciar uma hierarquia reconfigurável de servidores de tráfego dentro do comutador, bem como a análise adequada ao modelo de escalonamento. Esta última fornece um limite superior para o tempo de resposta que os pacotes podem sofrer dentro dos servidores de tráfego, com base unicamente no conhecimento de um dado servidor e na hierarquia actual, isto é, sem o conhecimento das especifidades do tráfego dentro dos outros servidores. Finalmente, no âmbito do projecto HaRTES foi construído um protótipo do comutador Ethernet, o qual é baseado no paradigma “Flexible Time-Triggered”, que permite uma junção flexível de uma fase síncrona para o tráfego controlado pelo comutador e uma fase assíncrona que implementa a estrutura hierárquica de servidores referidos anteriormente. Além disso, as várias experiências práticas realizadas permitiram validar as propriedades desejadas e, consequentemente, a tese que fundamenta esta dissertação.

Fuel switching

The present Master dissertation is a project whose main objective is to identify value creation opportunities through fuel switching in the Portuguese industry, services, agriculture and fishing sectors. Fuel switching opportunities are characterized by type of fuel transition, type of technology transition, economy subsectors prone to have fuel switching and value created through fuel shift. Results suggest tomato concentrate, dairy, beer manufacturing and sugar refining subsectors is where prevalence of fuel oil steam boilers is high, for such cases conversion to natural gas steam boilers should result in operations having a ratio of NPV over CAPEX larger than ten and a payback period just under one year. Results further suggest food, beverages, textile, chemicals and wood subsectors currently operate between ten and twenty cogeneration Diesel engines that can be either modified to operate with natural gas or replaced by new natural gas cogeneration systems. Financial modeling indicates that both options have great value creation potential. The current analysis aims to be used by natural gas suppliers and energy project promoters to identify new potential deals as well as by heavy energy consumers to mitigate their energy related costs.

Lead free heterogeneous multilayers with giant magneto electric coupling for microelectronics/microelectromechanical systems applications

Lead free magneto electrics with a strong sub resonant (broad frequency range) magneto electric coupling coefficient (MECC) is the goal of the day which can revolutionise the microelectronics and microelectromechanical systems (MEMS) industry. We report giant resonant MECC in lead free nanograined Barium Titanate–CoFe (Alloy)-Barium Titanate [BTO-CoFe-BTO] sandwiched thin films. The resonant MECC values obtained here are the highest values recorded in thin films/ multilayers. Sub-resonant MECC values are quite comparable to the highest MECC reported in 2-2 layered structures. MECC got enhanced by two orders at a low frequency resonance. The results show the potential of these thin films for transducer, magnetic field assisted energy harvesters, switching devices, and storage applications. Some possible device integration techniques are also discussed