Modularity Enhances the Rate of Evolution in a Rugged Fitness Landscape

Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show analytically how horizontal gene transfer couples to the modularity in the system and leads to more rapid rates of evolution at short times. The model, in general, analytically demonstrates a selective pressure for the prevalence of modularity in biology. We use this model to show how the evolution of the influenza virus is affected by the modularity of the proteins that are recognized by the human immune system. Approximately 25\% of the observed rate of fitness increase of the virus could be ascribed to a modular viral landscape.Comment: 45 pages; 7 figure

Field Theoretic Approach to Long Range Reactions

We analyze bimolecular reactions that proceed by a long-ranged reactive interaction, using a field theoretic approach that takes into account fluctuations. We consider both the one-species, $A+A \to \emptyset$ reaction and the two-species, $A+B \to \emptyset$ reaction. We consider both mobile and immobile reactants, both in the presence and in the absence of adsorption.Comment: 9 pages. 4 figures. Uses svjour macros. To appear in Europ. Phys. J.

Interactions between Membrane Inclusions on Fluctuating Membranes

We model membrane proteins as anisotropic objects characterized by symmetric-traceless tensors and determine the coupling between these order-parameters and membrane curvature. We consider the interactions between transmembrane proteins that respect up-down (reflection) symmetry of bilayer membranes and that have circular or non-circular cross-sectional areas in the tangent-plane of membranes. Using a field theoretic approach, we find non-entropic $1/R^{4}$ interactions between reflection-symmetry-breaking transmembrane proteins with circular cross-sectional area and entropic $1/R^{4}$ interactions between transmembrane proteins with circular cross-section that do not break up-down symmetry in agreement with previous calculations. We also find anisotropic $1/R^{4}$ interactions between reflection-symmetry-conserving transmembrane proteins with non-circular cross-section, anisotropic $1/R^{2}$ interactions between reflection-symmetry-breaking transmembrane proteins with non-circular cross-section, and non-entropic $1/R^{4}$ many-particle interactions among non-transmembrane proteins. For large $R$, these interactions might provide the dominant force inducing aggregation of the membrane proteins.Comment: REVTEX, 29 pages with 4 postscript figures compressed using uufiles. Introduction and Discussion sections revised. To appear in J. Phys. France I (September

Disclination Asymmetry in Deformable Hexatic Membranes and the Kosterlitz-Thouless Transitions

A disclination in a hexatic membrane favors the development of Gaussian curvature localized near its core. The resulting global structure of the membrane has mean curvature, which is disfavored by curvature energy. Thus a membrane with an isolated disclination undergoes a buckling transition from a flat to a buckled state as the ratio $\kappa/K_{A}$ of the bending rigidity $\kappa$ to the hexatic rigidity $K_{A}$ is decreased. In this paper we calculate the buckling transition and the energy of both a positive and a negative disclination. A negative disclination has a larger energy and a smaller critical value of $\kappa/K_{A}$ at buckling than does a positive disclination. We use our results to obtain a crude estimate of the Kosterlitz-Thouless transition temperature in a membrane. This estimate is higher than the transition temperature recently obtained by the authors in a renormalization calculation.Comment: REVTEX, 16 pages with 5 postscript figures compressed using uufiles. Accepted for publication in J. Phys. France

Quasispecies Theory for Evolution of Modularity

Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here develop a quasispecies theory for the dynamics of modularity in populations of these systems. We show how the steady-state fitness in a randomly changing environment can be computed. We derive a fluctuation dissipation relation for the rate of change of modularity and use it to derive a relationship between rate of environmental changes and rate of growth of modularity. We also find a principle of least action for the evolved modularity at steady state. Finally, we compare our predictions to simulations of protein evolution and find them to be consistent.Comment: 21 pages, 4 figures; presentation reordered; to appear in Phys. Rev.