Cellular automata modelling of slime mould actin network signalling

© 2016, The Author(s). Actin is a cytoskeletal protein which forms dense, highly interconnected networks within eukaryotic cells. A growing body of evidence suggests that actin-mediated intra- and extracellular signalling is instrumental in facilitating organism-level emergent behaviour patterns which, crucially, may be characterised as natural expressions of computation. We use excitable cellular automata modelling to simulate signal transmission through cell arrays whose topology was extracted from images of Watershed transformation-derived actin network reconstructions; the actin networks sampled were from laboratory experimental observations of a model organism, slime mould Physarum polycephalum. Our results indicate that actin networks support directional transmission of generalised energetic phenomena, the amplification and trans-network speed of which of which is proportional to network density (whose primary determinant is the anatomical location of the network sampled). Furthermore, this model also suggests the ability of such networks for supporting signal-signal interactions which may be characterised as Boolean logical operations, thus indicating that a cell’s actin network may function as a nanoscale data transmission and processing network. We conclude by discussing the role of the cytoskeleton in facilitating intracellular computing, how computation can be implemented in such a network and practical considerations for designing ‘useful’ actin circuitry

Robust constrained model predictive control based on parameter-dependent Lyapunov functions

The problem of robust constrained model predictive control (MPC) of systems with polytopic uncertainties is considered in this paper. New sufficient conditions for the existence of parameter-dependent Lyapunov functions are proposed in terms of linear matrix inequalities (LMIs), which will reduce the conservativeness resulting from using a single Lyapunov function. At each sampling instant, the corresponding parameter-dependent Lyapunov function is an upper bound for a worst-case objective function, which can be minimized using the LMI convex optimization approach. Based on the solution of optimization at each sampling instant, the corresponding state feedback controller is designed, which can guarantee that the resulting closed-loop system is robustly asymptotically stable. In addition, the feedback controller will meet the specifications for systems with input or output constraints, for all admissible time-varying parameter uncertainties. Numerical examples are presented to demonstrate the effectiveness of the proposed techniques

The mineral clouds on HD209 458b and HD189 733b

This is the final version of the article. Available from the publisher via the DOI in this record.3D atmosphere model results are used to comparatively study the kinetic, nonequilibrium cloud formation in the atmospheres of two example planets guided by the giant gas planets HD 209 458b and HD 189 733b. Rather independently of hydrodynamic model differences, our cloud modelling suggests that both planets are covered in mineral clouds throughout the entire modelling domain. Both planets harbour chemically complex clouds that are made of mineral particles that have a height-dependent material composition and size. The remaining gas-phase element abundances strongly effects the molecular abundances of the atmosphere in the cloud forming regions. Hydrocarbon and cyanopolyyne molecules can be rather abundant in the inner, dense part of the atmospheres of HD 189 733b and HD 209 458b. No one value for metallicity and the C/O ratio can be used to describe an extrasolar planet. Our results concerning the presence and location of water in relation to the clouds explain some of the observed differences between the two planets. In HD 189 733b, strong water features have been reported while such features are less strong for HD 209 458b. By considering the location of the clouds in the two atmospheres, we see that obscuring clouds exist high in the atmosphere of HD 209 458b, but much deeper in HD 189 733b. We further conclude that the (self-imposed) degeneracy of cloud parameters in retrieval methods can only be lifted if the cloud formation processes are accurately modelled in contrast to prescribing them by independent parametersWe highlight financial support of the European Community under the FP7 by the ERC starting grant 257431 and by an ERC advanced grant 247060. JK acknowledges the Rosen fellowship from the Brooklyn College New York, US. Some of the calculations for this paper were performed on the DIRAC Facility jointly funded by STFC, the Large Facilities Capital Fund of BIS, and the University of Exeter

Supratentorial and spinal pediatric ependymomas display a hypermethylated phenotype which includes the loss of tumor suppressor genes involved in the control of cell growth and death

Epigenetic alterations, including methylation, have been shown to be an important mechanism of gene silencing in cancer. Ependymoma has been well characterized at the DNA copy number and mRNA expression levels. However little is known about DNA methylation changes. To gain a more global view of the methylation profile of ependymoma we conducted an array-based analysis. Our data demonstrated tumors to segregate according to their location in the CNS, which was associated with a difference in the global level of methylation. Supratentorial and spinal tumors displayed significantly more hypermethylated genes than posterior fossa tumors, similar to the ‘CpG island methylator phenotype’ (CIMP) identified in glioma and colon carcinoma. This hypermethylated profile was associated with an increase in expression of genes encoding for proteins involved in methylating DNA, suggesting an underlying mechanism. An integrated analysis of methylation and mRNA expression array data allowed us to identify methylation-induced expression changes. Most notably genes involved in the control of cell growth and death and the immune system were identified, including members of the JNK pathway and PPARG. In conclusion, we have generated a global view of the methylation profile of ependymoma. The data suggests epigenetic silencing of tumor suppressor genes is an important mechanism in the pathogenesis of supratentorial and spinal, but not posterior fossa ependymomas. Hypermethylation correlated with a decrease in expression of a number of tumor suppressor genes and pathways that could be playing an important role in tumor pathogenesis

Contribution analysis of a Bolivian innovation grant fund: mixing methods to verify relevance, efficiency and effectiveness

We used contribution analysis to verify the key assumption in the intervention logic of an innovation fund in Bolivia directed to economic farmer organisations to develop value-added activities. We focused the research on three sub-components of the intervention logic: relevance of the farmer groups for local economic development, effectiveness of the fund in strengthening these group, and efficiency of the grant allocation mechanism. We used a case-based comparative analysis to assess effectiveness: improved market access for members, strengthened organisational capacities and the capacity to pay organisational costs. We showed that the grants to already well-endowed organisations were particularly unsuccessful

Pseudospin rotation and valley mixing in electron scattering at graphene edges

In graphene, the pseudospin and the valley flavor arise as new types of quantum degrees of freedom due to the honeycomb lattice comprising two sublattices (A and B) and two inequivalent Dirac points (K and K') in the Brillouin zone, respectively. Unique electronic properties of graphene result in striking phenomena such as Klein tunnelling, Veselago lens, and valley-polarized currents. Here, we investigate the roles of the pseudospin and the valley in electron scattering at graphene edges and show that they are strongly correlated with charge density modulations of short-wavelength oscillations and slowly-decaying beat patterns. Theoretical analyses using nearest-neighbor tight-binding methods and first-principles density-functional theory calculations agree well with our experimental data from the scanning tunneling microscopy. We believe that this study will lead to useful application of graphene to "valleytronics" and "pseudospintronics".Comment: 13 pages, 4 figures, Supplementary Information available upon reques

Neuromorphic liquid marbles with aqueous carbon nanotube cores

Neuromorphic computing devices attempt to emulate features of biological nervous systems through mimicking the properties of synapses, towards implementing the emergent properties of their counterparts, such as learning. Inspired by recent advances in the utilisation of liquid marbles (microlitre quantities of fluid coated in hydrophobic powder) for the creation of unconventional computing devices, we describe the development of liquid marbles with neuromorphic properties through the use of copper coatings and l.0mgml-1 carbon nanotube-containing fluid cores. Experimentation was performed through sandwiching the marbles between two cup-style electrodes and stimulating them with repeated DC pulses at 3.0 V. Our results demonstrate that 'entrainment∗ of a carbon nanotube filled-copper liquid marble via periodic pulses can cause their electrical resistance to rapidly switch between high to low resistance profiles, upon inverting the polarity of stimulation: The reduction in resistance between high and low profiles was approximately 88% after two rounds of entrainment. This effect was found to be reversible through reversion to the original stimulus polarity and was strengthened by repeated experimentation, as evidenced by a mean reduction in time to switching onset of 43%. These effects were not replicated in nanotube solutions not bound inside liquid marbles. Our electrical characterisation also reveals that nanotube-filled liquid marbles exhibit pinched loop hysteresis IV profiles consistent with the description of memristors. We conclude by discussing the applications of this technology to the development of unconventional computing devices and the study of emergent characteristics in biological neural tissue

Fault-tolerant formation driving mechanism designed for heterogeneous MAVs-UGVs groups

A fault-tolerant method for stabilization and navigation of 3D heterogeneous formations is proposed in this paper. The presented Model Predictive Control (MPC) based approach enables to deploy compact formations of closely cooperating autonomous aerial and ground robots in surveillance scenarios without the necessity of a precise external localization. Instead, the proposed method relies on a top-view visual relative localization provided by the micro aerial vehicles flying above the ground robots and on a simple yet stable visual based navigation using images from an onboard monocular camera. The MPC based schema together with a fault detection and recovery mechanism provide a robust solution applicable in complex environments with static and dynamic obstacles. The core of the proposed leader-follower based formation driving method consists in a representation of the entire 3D formation as a convex hull projected along a desired path that has to be followed by the group. Such an approach provides non-collision solution and respects requirements of the direct visibility between the team members. The uninterrupted visibility is crucial for the employed top-view localization and therefore for the stabilization of the group. The proposed formation driving method and the fault recovery mechanisms are verified by simulations and hardware experiments presented in the paper

日本語学習者の会話における｢文末表現｣の研究

博士（学術）神戸大