Condensed Matter Theory

Abstract:

We investigate how scale-free (SF) and Erdos-Rényi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006) we find that networks with SF(in) topologies, that is SF topology for incoming nodes and ER topology for outgoing nodes, are significantly more evolvable towards specific oscillatory targets than networks with ER topology for both incoming and outgoing nodes. Similar results are found for networks with SF(both) and SF(out) topologies. The functionality of the SF(out) topology, which most closely resembles the structure of biological gene networks (Babu et al., 2004), is compared to the ER topology in further detail through an extension to multiple target outputs, with either an oscillatory or a non-oscillatory nature. For multiple oscillatory targets of the same length, the differences between SF(out) and ER networks are enhanced, but for non-oscillatory targets both types of networks show fairly similar evolvability. We find that SF networks generate oscillations much more easily than ER networks do, and this may explain why SF networks are more evolvable than ER networks are for oscillatory phenotypes. In spite of their greater evolvability, we find that networks with SF(out) topologies are also more robust to mutations (mutational robustness) than ER networks. Furthermore, the SF(out) topologies are more robust to changes in initial conditions (environmental robustness). For both topologies, we find that once a population of networks has reached the target state, further neutral evolution can lead to an increase in both the mutational robustness and the environmental robustness to changes in initial conditions.

Abstract:

We consider the hydrodynamic interactions of low Reynolds number microswimmers, presenting a review of recent work based upon models of linked sphere swimmers. Particular attention is paid to those aspects that are generic, applicable to all microswimmers and not only to the simple models considered. The importance of the relative phase in swimmer-swimmer interactions is emphasised, as is the role of simple symmetry arguments in both understanding and constraining the hydrodynamic properties of microswimmers. © 2010 Society for Experimental Mechanics.

Abstract:

The 2 + 1 dimensional lattice models of Levin and Wen (2005) [1] provide the most general known microscopic construction of topological phases of matter. Based heavily on the mathematical structure of category theory, many of the special properties of these models are not obvious. In the current paper, we present a geometrical space-time picture of the partition function of the Levin-Wen models which can be described as doubles (two copies with opposite chiralities) of underlying anyon theories. Our space-time picture describes the partition function as a knot invariant of a complicated link, where both the lattice variables of the microscopic Levin-Wen model and the terms of the Hamiltonian are represented as labeled strings of this link. This complicated link, previously studied in the mathematical literature, and known as Chain-Mail, can be related directly to known topological invariants of 3-manifolds such as the so-called Turaev-Viro invariant and the Witten-Reshitikhin-Turaev invariant. We further consider quasi-particle excitations of the Levin-Wen models and we see how they can be understood by adding additional strings to the Chain-Mail link representing quasi-particle world-lines. Our construction gives particularly important new insight into how a doubled theory arises from these microscopic models. © 2010 Elsevier Inc.