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Self propelled particle (SPP) models are often compared with animal swarms. However, the collective behaviour observed in experiments usually leaves considerable unconstrained freedom in the structure of these models. To tackle this degeneracy, and better distinguish between candidate models, we study swarms of SPPs circulating in channels (like spins) where we permit information to pass through windows between neighbouring channels. Co-alignment between particles then couples the channels (antiferromagnetically) so that they tend to counter-rotate. We study channels arranged to mimic a geometrically frustrated antiferromagnet and show how the effects of this frustration allow us to better distinguish between SPP models. Similar experiments could therefore improve our understanding of collective motion in animals. Finally we discuss how the spin analogy can be exploited to construct universal logic gates and therefore swarming systems that can function as Turing machines.
Regulatory T cells (Tregs) play a crucial role in mediating immune response. Yet an algorithmic understanding of the role of Tregs in adaptive immunity remains lacking. Here, we present a biophysically realistic model of Treg mediated self-tolerance
Social hierarchy is central to decision-making in the coordinated movement of many swarming species. Here we propose a hierarchical swarm model in the spirit of the Vicsek model of self-propelled particles. We show that, as the hierarchy becomes impo
We propose an improved prediction method of the tertiary structures of $alpha$-helical membrane proteins based on the replica-exchange method by taking into account helix deformations. Our method allows wide applications because transmembrane helices
Biopolymer self-assembly pathways are central to biological activity, but are complicated by the ability of the monomeric subunits of biopolymers to adopt different conformational states. As a result, biopolymer nucleation often involves a two-step m
One of the causes of high fidelity of copying in biological systems is kinetic discrimination. In this mechanism larger dissipation and copying velocity result in improved copying accuracy. We consider a model of a polymerase which simultaneously cop