Swarm behaviour | EPFL Graph Search

Swarm behaviour, or swarming, is a collective behaviour exhibited by entities, particularly animals, of similar size which aggregate together, perhaps milling about the same spot or perhaps moving en masse or migrating in some direction. It is a highly interdisciplinary topic. As a term, swarming is applied particularly to insects, but can also be applied to any other entity or animal that exhibits swarm behaviour. The term flocking or murmuration can refer specifically to swarm behaviour in birds, herding to refer to swarm behaviour in tetrapods, and shoaling or schooling to refer to swarm behaviour in fish. Phytoplankton also gather in huge swarms called blooms, although these organisms are algae and are not self-propelled the way animals are. By extension, the term "swarm" is applied also to inanimate entities which exhibit parallel behaviours, as in a robot swarm, an earthquake swarm, or a swarm of stars. From a more abstract point of view, swarm behaviour is the collective mo

Microfluidic iMITOMI platform to study the architecture of low-affinity transcription factor binding site clusters

Ivan Istomin

Gene regulatory networks (GRNs) determine cellular behaviour, and ultimately the functioning of single- and multicellular organisms. Transcription factors regulate gene expression by binding to DNA or via remodelling chromatin. Recent advances in biotechnological methods have made it possible to precisely characterise the binding of transcription factors to single consensus binding sites. Advanced sequencing methods allow the efficient discovery of de novo binding consensus sequences, and thus provide insight into the evolution of GRNs. However, clusters of transcription factor binding sites have been poorly studied despite their prevalence in eukaryotic genomes. Widely-used methods of GRN interrogation lack the sensitivity for transient binding events with low-affinity binding sites. In my PhD, using the MITOMI platform I showed that two orthologs of the transcription factor Pho4 from S. cerevisiae and C. glabrata that have evolved distinct regulation have similar 3D structure and DNA binding preferences over a wide affinity range. I have developed the iMITOMI assay that preserves the unique advantages of the original MITOMI platform, and thus too has the ability to rapidly characterise transient binding events with high-throughput. In addition, iMITOMI enables the study of transcription factor binding site clusters. We have studied in detail the interactions of Pho4 and Zif268 with clusters of one to six binding sites. The individual binding sites had affinities one to two orders of magnitude below the affinity of the corresponding consensus sequence. We discovered that clusters of low-affinity binding sites could give rise to transcription factor occupancies comparable to or higher than those of single-consensus sequences. Our results demonstrate that low-affinity binding site clusters give rise to high occupancy levels. These have significant implications for the biophysical characterisation of transcription factor binding, the de novo evolution of enhancers and promoters, and the development of synthetic promoters.

EPFL2020

Modelling Global Behaviour in Object-Oriented Analysis: Scenarios, Use Cases and Interaction Diagrams

Most software development methods define notations for modelling global behaviour. Many of these notations use interaction diagrams to model possible sequences of interactions between a system and its environment, or between the objects of the system. Other methods use structured textual descriptions or regular expressions for specifying use cases or use scenarios. Although many methods use similar notations, there are often substantial differences in their underlying concepts and in the content expressed by the diagrams. On the other hand, completely different notations use sometime the same concepts and show the same aspects of the global behaviour of a system. In this document we investigate the characteristics of different notations. We show what their underlying concepts are and how they relate to each other. Finally, we give an overview of the techniques that are used by some of the current object-oriented analysis methods for modelling global behaviour.

1996

Ant-based Swarming with Positionless Micro Air Vehicles for Communication Relay

Dario Floreano, Sabine Hauert, Laurent Winkler, Jean-Christophe Zufferey

Swarming without positioning information is interesting in application- oriented systems because it alleviates the need for sensors which are dependent on the environment, expensive in terms of energy, cost, size and weight, or unusable at useful ranges for real-life scenarios. This principle is applied to the development of a swarm of micro air vehicles (SMAVs) for the deployment of ad hoc wireless communication networks (SMAVNETs) between ground users in disaster areas. Rather than relying on positioning information, MAVs rely on local communication with immediate neighbors and proprioceptive sensors which provide heading, speed and altitude. To solve the challenging task of designing agent controllers to achieve the swarm behavior of the SMAVNET, inspiration is taken from army ants which are capable of laying and maintaining pheromone paths leading from their nest to food sources in nature. This is analogous to the deployment of communication pathways between multiple ground users. However, instead of being physically deposited in the air or on a map, pheromone is virtually deposited on the MAVs using local communication. This approach is investigated in 3D simulation in a simplified scenario with two ground users.

2008

Microfluidic iMITOMI platform to study the architecture of low-affinity transcription factor binding site clusters

Ivan Istomin

EPFL2020