Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

An introduction to Biomodel engineering, illustrated for signal transduction pathways

BioModel Engineering is the science of designing, constructing and analyzing computational models of biological systems. It is inspired by concepts from software engineering and computing science. This paper illustrates a major theme in BioModel Engineering, namely that identifying a quantitative model of a dynamic system means building the structure, finding an initial state, and parameter fitting. In our approach, the structure is obtained by piecewise construction of models from modular parts, the initial state is obtained by analysis of the structure and parameter fitting comprises determining the rate parameters of the kinetic equations. We illustrate this with an example in the area of intracellular signalling pathways

Nonlinear thermoelectric response due to energy-dependent transport properties of a quantum dot

Quantum dots are useful model systems for studying quantum thermoelectric behavior because of their highly energy-dependent electron transport properties, which are tunable by electrostatic gating. As a result of this strong energy dependence, the thermoelectric response of quantum dots is expected to be nonlinear with respect to an applied thermal bias. However, until now this effect has been challenging to observe because, first, it is experimentally difficult to apply a sufficiently large thermal bias at the nanoscale and, second, it is difficult to distinguish thermal bias effects from purely temperature-dependent effects due to overall heating of a device. Here we take advantage of a novel thermal biasing technique and demonstrate a nonlinear thermoelectric response in a quantum dot which is defined in a heterostructured semiconductor nanowire. We also show that a theoretical model based on the Master equations fully explains the observed nonlinear thermoelectric response given the energy-dependent transport properties of the quantum dot.Comment: Cite as: A. Svilans, et al., Physica E (2015), http://dx.doi.org/10.1016/j.physe.2015.10.00

From Petri Nets to differential equations: An integrative approach for biochemical network analysis

We report on the results of an investigation into the integration of Petri nets and ordinary differential equations (ODEs) for the modelling and analysis of biochemical networks, and the application of our approach to the model of the influence of the Raf Kinase Inhibitor Protein (RKIP) on the Extracellular signal Regulated Kinase (ERK) signalling pathway. We show that analysis based on a discrete Petri net model of the system can be used to derive the sets of initial concentrations required by the corresponding continuous ordinary differential equation model, and no other initial concentrations produce meaningful steady states. Altogether, this paper represents a tutorial in step-wise modelling and analysis of larger models as well as in structured design of ODEs

Realization of a feedback controlled flashing ratchet

A flashing ratchet transports diffusive particles using a time-dependent, asymmetric potential. Particle speed is predicted to increase when a feedback algorithm based on particle positions is used. We have experimentally realized such a feedback ratchet using an optical line trap, and observed that use of feedback increases velocity by up to an order of magnitude. We compare two different feedback algorithms for small particle numbers, and find good agreement with simulations. We also find that existing algorithms can be improved to be more tolerant to feedback delay times

A dynamic 1/f noise protocol to assess visual attention without biasing perceptual processing

Psychophysical paradigms measure visual attention via localized test items to which observers must react or whose features have to be discriminated. These items, however, potentially interfere with the intended measurement, as they bias observers' spatial and temporal attention to their location and presentation time. Furthermore, visual sensitivity for conventional test items naturally decreases with retinal eccentricity, which prevents direct comparison of central and peripheral attention assessments. We developed a stimulus that overcomes these limitations. A brief oriented discrimination signal is seamlessly embedded into a continuously changing 1/f noise field, such that observers cannot anticipate potential test locations or times. Using our new protocol, we demonstrate that local orientation discrimination accuracy for 1/f filtered signals is largely independent of retinal eccentricity. Moreover, we show that items present in the visual field indeed shape the distribution of visual attention, suggesting that classical studies investigating the spatiotemporal dynamics of visual attention via localized test items may have obtained a biased measure. We recommend our protocol as an efficient method to evaluate the behavioral and neurophysiological correlates of attentional orienting across space and time

Using polymer electrolyte gates to set-and-freeze threshold voltage and local potential in nanowire-based devices and thermoelectrics

We use the strongly temperature-dependent ionic mobility in polymer electrolytes to 'freeze in' specific ionic charge environments around a nanowire using a local wrap-gate geometry. This enables us to set both the threshold voltage for a conventional doped substrate gate and the local disorder potential at temperatures below 200 Kelvin, which we characterize in detail by combining conductance and thermovoltage measurements with modeling. Our results demonstrate that local polymer electrolyte gates are compatible with nanowire thermoelectrics, where they offer the advantage of a very low thermal conductivity, and hold great potential towards setting the optimal operating point for solid-state cooling applications.Comment: Published in Advanced Functional Materials. Includes colour versions of figures and supplementary informatio

A quantum-dot heat engine operating close to the thermodynamic efficiency limits

Cyclical heat engines are a paradigm of classical thermodynamics, but are impractical for miniaturization because they rely on moving parts. A more recent concept is particle-exchange (PE) heat engines, which uses energy filtering to control a thermally driven particle flow between two heat reservoirs. As they do not require moving parts and can be realized in solid-state materials, they are suitable for low-power applications and miniaturization. It was predicted that PE engines could reach the same thermodynamically ideal efficiency limits as those accessible to cyclical engines, but this prediction has not been verified experimentally. Here, we demonstrate a PE heat engine based on a quantum dot (QD) embedded into a semiconductor nanowire. We directly measure the engine's steady-state electric power output and combine it with the calculated electronic heat flow to determine the electronic efficiency $\eta$. We find that at the maximum power conditions, $\eta$ is in agreement with the Curzon-Ahlborn efficiency and that the overall maximum $\eta$ is in excess of 70$\%$ of the Carnot efficiency while maintaining a finite power output. Our results demonstrate that thermoelectric power conversion can, in principle, be achieved close to the thermodynamic limits, with direct relevance for future hot-carrier photovoltaics, on-chip coolers or energy harvesters for quantum technologies

The Language Awareness of Finnish and German EFL Senior High School Learners and Student Teachers Regarding English Grammar and Its Teaching

The aim of this study is to examine and contrast the language awareness of Finnish and German EFL senior high school students and student teachers regarding aspects of English grammar and its teaching. Data was collected from Finland and Germany during the academic school years of 2015–16 and 2016–17. It consists of the responses to twosurvey questions of 1st year EFL senior high school students (n = 200 from Finland, n = 200 from Germany) andstudent teachers (n = 118 from Finland, n = 118 from Germany). The study utilizes both qualitative (content analysis) and quantitative (frequencies, percentages, cross tabulation [χ2-test]) research methods. The results show that the subjects’ awareness of English grammar and its teaching was mainly based on intuitive, implicit knowledge. It was difficult for both senior high school learners and student teachers to build a cognitive understanding that would increase their awareness of English grammar, and, as a result of this, its teaching, and respectively their grammar-related didactical competences.The aim of this study is to examine and contrast the language awareness of Finnish and German EFL senior high school students and student teachers regarding aspects of English grammar and its teaching. Data was collected from Finland and Germany during the academic school years of 2015–16 and 2016–17. It consists of the responses to two survey questions of 1st year EFL senior high school students (n = 200 from Finland, n = 200 from Germany) and student teachers (n = 118 from Finland, n = 118 from Germany). The study utilizes both qualitative (content analysis) and quantitative (frequencies, percentages, cross tabulation [χ2-test]) research methods. The results show that the subjects’ awareness of English grammar and its teaching was mainly based on intuitive, implicit knowledge. It was difficult for both senior high school learners and student teachers to build a cognitive understanding that would increase their awareness of English grammar, and, as a result of this, its teaching, and respectively their grammar-related didactical competences.Peer reviewe