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Siekmann I.,Victorian Research Laboratory | Siekmann I.,University of Melbourne
Ecological Complexity

Individual-based models (IBMs) enable us to investigate the effects of inter-individual differences within a population much more easily than traditional modelling approaches based on differential equations. However, the greater flexibility of IBMs makes it difficult to systematically analyse the parameter dependency of the model behaviour so that an IBM may be hard to interpret. In this article, bifurcation analysis techniques for investigating models based on ordinary differential equations (ODE) are transferred to IBMs. For this purpose, we infer stationary solutions of the IBM from the asymptotic dynamics. The stability of these stationary solutions can then be studied depending on model parameters. As shown previously for ODE models (Siekmann et al., 2010; Siekmann, 2013), stationary solutions Si S can be used as bifurcation parameters which allows us to predict survival or extinction of populations by simple algebraic relationships. This is demonstrated with the example of a simple two-strain infection IBM. Moreover, analysing model behaviour based on stationary solutions provides a unified representation of different models that allows us to rigorously compare IBMs with other modelling frameworks like, for example, ODE models. A comparison of the IBM to a population-based ODE model of a two-strain infection leads to similar predictions although both models were built with very different modelling approaches. © 2014 Elsevier B.V. All rights reserved. Source

Siekmann I.,Victorian Research Laboratory | Siekmann I.,University of Melbourne | Sneyd J.,University of Auckland | Crampin E.J.,Victorian Research Laboratory | Crampin E.J.,University of Melbourne
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences

Ion channels regulate the concentrations of ions within cells. By stochastically opening and closing its pore, they enable or prevent ions from crossing the cell membrane. However, rather than opening with a constant probability, many ion channels switch between several different levels of activity even if the experimental conditions are unchanged. This phenomenon is known as modal gating: instead of directly adapting its activity, the channel seems to mix sojourns in active and inactive modes in order to exhibit intermediate open probabilities. Evidence is accumulating that modal gating rather than modulation of opening and closing at a faster time scale is the primary regulatory mechanism of ion channels. However, currently, no method is available for reliably calculating sojourns in different modes. In order to address this challenge, we develop a statistical framework for segmenting singlechannel datasets into segments that are characteristic for particular modes. The algorithm finds the number of mode changes, detects their locations and infers the open probabilities of the modes. We apply our approach to data from the inositoltrisphosphate receptor. Based upon these results, we propose that mode changes originate from alternative conformational states of the channel protein that determine a certain level of channel activity. © 2014 The Author(s) Published by the Royal Society. All rights reserved. Source

Al-Dirini F.,University of Melbourne | Al-Dirini F.,Victorian Research Laboratory | Hossain F.M.,University of Melbourne | Nirmalathas A.,University of Melbourne | Skafidas E.,University of Melbourne
IEEE Journal of the Electron Devices Society

In this work, we propose an atomically-thin all-graphene planar double barrier resonant tunneling diode that can be realized within a single graphene nanoribbon. The proposed device does not require any doping or external gating and can be fabricated using minimal process steps. The planar architecture of the device allows a simple in-plane connection of multiple devices in parallel without any extra processing steps during fabrication, enhancing the current driving capabilities of the device. Quantum mechanical simulation results, based on non-equilibrium Green's function formalism and the extended Huckel method, show promising device performance with a high reverse-to-forward current rectification ratio exceeding 50 000, and confirm the presence of negative differential resistance within the device's current-voltage characteristics. © 2014 IEEE. Source

Al-Dirini F.,University of Melbourne | Al-Dirini F.,Victorian Research Laboratory | Mohammed M.A.,Princess Sumaya University for Technology | Hossain F.M.,University of Melbourne | And 2 more authors.
IEEE Journal of the Electron Devices Society

This paper proposes a new class of resonant tunneling diodes (RTDs) that are planar and realizable with a single graphene nanoribbon. Unlike conventional RTDs, which incorporate vertical quantum well regions, the proposed devices incorporate two confined planar quantum dots within the single graphene nanoribbon, giving rise to a pronounced negative differential resistance (NDR) effect. The proposed devices, termed here as planar double-quantum-dot RTDs, and their transport properties are investigated using quantum simulations based on nonequilibrium Green's function formalism and the extended Huckel method. The proposed devices exhibit a unique current-voltage waveform consisting of a single pronounced current peak with an extremely high, in the order of 104, peak-to-valley ratio. The position of the current peak can be tuned between discrete voltage levels, allowing digitized tunability, which is exploited to realize multi-peak NDR devices. © 2013 IEEE. Source

Al-Dirini F.,University of Melbourne | Al-Dirini F.,Victorian Research Laboratory | Hossain F.M.,University of Melbourne | Mohammed M.A.,Princess Sumaya University for Technology | And 4 more authors.
Journal of Applied Physics

This paper presents a new molybdenum disulphide (MoS2) nanodevice that acts as a two-terminal field-effect rectifier. The device is an atomically-thin two-dimensional self-switching diode (SSD) that can be realized within a single MoS2 monolayer with very minimal process steps. Quantum simulation results are presented confirming the device's operation as a diode and showing strong non-linear I-V characteristics. Interestingly, the device shows p-type behavior, in which conduction is dominated by holes as majority charge carriers and the flow of reverse current is enhanced, while the flow of forward current is suppressed, in contrast to monolayer graphene SSDs, which behave as n-type devices. The presence of a large bandgap in monolayer MoS2 results in strong control over the channel, showing complete channel pinch-off in forward conduction, which was confirmed with transmission pathways plots. The device exhibited large leakage tunnelling current through the insulating trenches, which may have been due to the lack of passivation; nevertheless, reverse current remained to be 6 times higher than forward current, showing strong rectification. The effect of p-type substitutional channel doping of sulphur with phosphorus was investigated and showed that it greatly enhances the performance of the device, increasing the reverse-to-forward current rectification ratio more than an order of magnitude, up to a value of 70. © 2016 AIP Publishing LLC. Source

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