Creativity and Autonomy in Swarm Intelligence Systems

This work introduces two swarm intelligence algorithms -- one mimicking the behaviour of one species of ants (\emph{Leptothorax acervorum}) foraging (a `Stochastic Diffusion Search', SDS) and the other algorithm mimicking the behaviour of birds flocking (a `Particle Swarm Optimiser', PSO) -- and outlines a novel integration strategy exploiting the local search properties of the PSO with global SDS behaviour. The resulting hybrid algorithm is used to sketch novel drawings of an input image, exploliting an artistic tension between the local behaviour of the `birds flocking' - as they seek to follow the input sketch - and the global behaviour of the `ants foraging' - as they seek to encourage the flock to explore novel regions of the canvas. The paper concludes by exploring the putative `creativity' of this hybrid swarm system in the philosophical light of the `rhizome' and Deleuze's well known `Orchid and Wasp' metaphor

Swarmic sketches and attention mechanism

This paper introduces a novel approach deploying the mechanism of ‘attention’ by adapting a swarm intelligence algorithm – Stochastic Diffusion Search – to selectively attend to detailed areas of a digital canvas. Once the attention of the swarm is drawn to a certain line within the canvas, the capability of another swarm intelligence algorithm – Particle Swarm Intelligence – is used to produce a ‘swarmic sketch’ of the attended line. The swarms move throughout the digital canvas in an attempt to satisfy their dynamic roles – attention to areas with more details – associated to them via their fitness function. Having associated the rendering process with the concepts of attention, the performance of the participating swarms creates a unique, non-identical sketch each time the ‘artist’ swarms embark on interpreting the input line drawings. The detailed investigation of the ‘creativity’ of such systems have been explored in our previous work; nonetheless, this papers provides a brief account of the ‘computational creativity’ of the work through two prerequisites of creativity within the swarm intelligence’s two infamous phases of exploration and exploitation; these phases are described herein through the attention and tracing mechanisms respectively

BLUF Domain Function Does Not Require a Metastable Radical Intermediate State

BLUF (blue light using flavin) domain proteins are an important family of blue light-sensing proteins which control a wide variety of functions in cells. The primary light-activated step in the BLUF domain is not yet established. A number of experimental and theoretical studies points to a role for photoinduced electron transfer (PET) between a highly conserved tyrosine and the flavin chromophore to form a radical intermediate state. Here we investigate the role of PET in three different BLUF proteins, using ultrafast broadband transient infrared spectroscopy. We characterize and identify infrared active marker modes for excited and ground state species and use them to record photochemical dynamics in the proteins. We also generate mutants which unambiguously show PET and, through isotope labeling of the protein and the chromophore, are able to assign modes characteristic of both flavin and protein radical states. We find that these radical intermediates are not observed in two of the three BLUF domains studied, casting doubt on the importance of the formation of a population of radical intermediates in the BLUF photocycle. Further, unnatural amino acid mutagenesis is used to replace the conserved tyrosine with fluorotyrosines, thus modifying the driving force for the proposed electron transfer reaction; the rate changes observed are also not consistent with a PET mechanism. Thus, while intermediates of PET reactions can be observed in BLUF proteins they are not correlated with photoactivity, suggesting that radical intermediates are not central to their operation. Alternative nonradical pathways including a keto–enol tautomerization induced by electronic excitation of the flavin ring are considered

Swarmic paintings and colour attention

Swarm-based multi-agent systems have been deployed in non-photorealistic rendering for many years. This paper introduces a novel approach in adapting a swarm intelligence algorithm – Stochastic Diffusion Search – for producing non-photorealistic images. The swarm-based system is presented with a digital image and the agents move throughout the digital canvas in an attempt to satisfy the dynamic roles – attention to different colours - associated to them via their fitness function. Having associated the rendering process with the concepts of ‘attention’ in general and colour attention in particular, this papers briefly discusses the ‘computational creativity’ of the work through two prerequisites of creativity (i.e. freedom and constraints) within the swarm intelligence’s two infamous phases of exploration and exploitation

On the Dynamic Stability of Cool Supergiant Atmospheres

We have developed a new formalism to compute the thermodynamic coefficient Gamma1 in the theory of stellar and atmospheric stability. We generalize the classical derivation of the first adiabatic index, which is based on the assumption of thermal ionization and equilibrium between gas and radiation temperature, towards an expression which incorporates photo-ionization due to radiation with a temperature T_rad different from the local kinetic gas temperature.Our formalism considers the important non-LTE conditions in the extended atmospheres of supergiant stars. An application to the Kurucz grid of cool supergiant atmospheres demonstrates that models with T_rad =~ T_eff between 6500 K and 7500 K become most unstable against dynamic perturbations, according to Ledoux' stability integral . This results from Gamma1 and acquiring very low values, below 4/3, throughout the entire stellar atmosphere, which causes very high gas compression ratios around these effective temperatures. Based on detailed NLTE-calculations, we discuss atmospheric instability of pulsating massive yellow supergiants, like the hypergiant rho Cas (Ia+), which exist in the extension of the Cepheid instability strip, near the Eddington luminosity limit.Comment: 54 pages including figures and the Appendix, 7 figures, Accepted for The Astrophysical Journal, Main Journal, 558, Sept. 200

Information sharing impact of stochastic diffusion search on differential evolution algorithm

This work details the research aimed at applying the powerful resource allocation mechanism deployed in stochastic diffusion search (SDS) to the differential evolution (DE), effectively merging a nature inspired swarm intelligence algorithm with a biologically inspired evolutionary algorithm. The results reported herein suggest that the hybrid algorithm, exploiting information sharing between the population elements, has the potential to improve the optimisation capability of classical DE algorithms. This claim is verified by running several experiments using state-of-the-art benchmarks. Additionally, the significance of the frequency within which SDS introduces communication and information exchange is also investigated

Changes in Channel Trafficking and Protein Stability Caused by LQT2 Mutations in the PAS Domain of the HERG Channel

Inherited human long-QT2 syndrome (LQTS) results from mutations in the gene encoding the HERG channel. Several LQT2-associated mutations have been mapped to the amino terminal cytoplasmic Per-Arnt-Sim (PAS) domain of the HERG1a channel subunit. Here we have characterized the trafficking properties of some LQT2-associated PAS domain mutants and analyzed rescue of the trafficking mutants by low temperature (27°C) or by the pore blocker drug E4031. We show that the LQT2-associated mutations in the PAS domain of the HERG channel display molecular properties that are distinct from the properties of LQT2-associated mutations in the trans-membrane region. Unlike the latter, many of the tested PAS domain LQT2-associated mutations do not result in trafficking deficiency of the channel. Moreover, the majority of the PAS domain mutations that cause trafficking deficiencies are not rescued by a pore blocking drug. We have also explored the in vitro folding stability properties of isolated mutant PAS domain proteins using a thermal unfolding fluorescence assay and a chemical unfolding assay

The N–Terminal Tail of hERG Contains an Amphipathic α–Helix That Regulates Channel Deactivation

The cytoplasmic N–terminal domain of the human ether–a–go–go related gene (hERG) K+ channel is critical for the slow deactivation kinetics of the channel. However, the mechanism(s) by which the N–terminal domain regulates deactivation remains to be determined. Here we show that the solution NMR structure of the N–terminal 135 residues of hERG contains a previously described Per–Arnt–Sim (PAS) domain (residues 26–135) as well as an amphipathic α–helix (residues 13–23) and an initial unstructured segment (residues 2–9). Deletion of residues 2–25, only the unstructured segment (residues 2–9) or replacement of the α–helix with a flexible linker all result in enhanced rates of deactivation. Thus, both the initial flexible segment and the α–helix are required but neither is sufficient to confer slow deactivation kinetics. Alanine scanning mutagenesis identified R5 and G6 in the initial flexible segment as critical for slow deactivation. Alanine mutants in the helical region had less dramatic phenotypes. We propose that the PAS domain is bound close to the central core of the channel and that the N–terminal α–helix ensures that the flexible tail is correctly orientated for interaction with the activation gating machinery to stabilize the open state of the channel

Structural Basis for c-di-GMP-Mediated Inside-Out Signaling Controlling Periplasmic Proteolysis

X-ray crystallographic structural analyses of the bacterial transmembrane receptor LapD identify conserved molecular mechanisms that control biofilm formation in response to changes in the intracellular levels of the second messenger c-di-GMP

A LOV Protein Modulates the Physiological Attributes of Xanthomonas axonopodis pv. citri Relevant for Host Plant Colonization

Recent studies have demonstrated that an appropriate light environment is required for the establishment of efficient vegetal resistance responses in several plant-pathogen interactions. The photoreceptors implicated in such responses are mainly those belonging to the phytochrome family. Data obtained from bacterial genome sequences revealed the presence of photosensory proteins of the BLUF (Blue Light sensing Using FAD), LOV (Light, Oxygen, Voltage) and phytochrome families with no known functions. Xanthomonas axonopodis pv. citri is a Gram-negative bacterium responsible for citrus canker. The in silico analysis of the X. axonopodis pv. citri genome sequence revealed the presence of a gene encoding a putative LOV photoreceptor, in addition to two genes encoding BLUF proteins. This suggests that blue light sensing could play a role in X. axonopodis pv. citri physiology. We obtained the recombinant Xac-LOV protein by expression in Escherichia coli and performed a spectroscopic analysis of the purified protein, which demonstrated that it has a canonical LOV photochemistry. We also constructed a mutant strain of X. axonopodis pv. citri lacking the LOV protein and found that the loss of this protein altered bacterial motility, exopolysaccharide production and biofilm formation. Moreover, we observed that the adhesion of the mutant strain to abiotic and biotic surfaces was significantly diminished compared to the wild-type. Finally, inoculation of orange (Citrus sinensis) leaves with the mutant strain of X. axonopodis pv. citri resulted in marked differences in the development of symptoms in plant tissues relative to the wild-type, suggesting a role for the Xac-LOV protein in the pathogenic process. Altogether, these results suggest the novel involvement of a photosensory system in the regulation of physiological attributes of a phytopathogenic bacterium. A functional blue light receptor in Xanthomonas spp. has been described for the first time, showing an important role in virulence during citrus canker disease