The effects of resource limitation and consensual incentives on cooperation

Exploring the evolution of cooperation has been one of the most challenging topics and attracted increasing attention in various realms. Hereby, we institute an analytic model where the relationship between the common benefits and contributions is the typical saturation nonlinearity. We investigate the evolutionary dynamics of cooperation with and without consensual incentives respectively. The population always evolves to full defection when the incentives are absent. Cooperation, however, can be promoted by consensual incentives when the degree of cooperators' preferences for incentives is great. There exists an intermediate amount of resources at which the positive effect of consensual incentives on cooperation is minimized. Furthermore, there is a U-shape relationship between the degree of cooperators' preference for an incentive and the evolution of cooperation. A greater basin of full cooperation can be induced when the cooperators' preference for reward is more pronounced than that for punishment.     

Second Order Nonlinear Evolution Inclusions Ⅰ： Existence and Relaxation Results

This is the first part of a work on second order nonlinear, nonmonotone evolution inclusions defined in the framework of an evolution triple of spaces and with a multivalued nonlinearity depending on both x（t） and x（t）. In this first part we prove existence and relaxation theorems. We consider the case of an usc, convex valued nonlinearity and we show that for this problem the solution set is nonempty and compact in C^1 （T, H）. Also we examine the Isc, nonconvex case and again we prove the existence of solutions. In addition we establish the existence of extremal solutions and by strengthening our hypotheses, we show that the extremal solutions are dense in C^1 （T, H） to the solutions of the original convex problem （strong relaxation）. An example of a nonlinear hyperbolic optimal control problem is also discussed.     

Hele-Shaw type problems with dynamical boundary conditions

In this paper, we study the nonlinear evolution equation of Hele-Shaw type with dynamical boundary conditions. That is, the equation ut=Δw+f where u∈H(w) and H is the Heaviside function, with boundary condition μ(x,w)t_∂w+k∇w⋅ν=g, where ν denotes the outward normal vector of the fixed boundary of the domain. We prove existence, uniqueness and some qualitative properties of the solution.     

Directed triangles in directed graphs

We show that each directed graph (with no parallel arcs) on n vertices, each with indegree and outdegree at least n/twhere t=2.888997… contains a directed circuit of length at most 3.     

Novel scaling behavior of directed polymers: Disorder distribution with long tails

We study the problem of directed polymers (DP) on a square lattice. The distribution of disorder is assumed to be independent but non-Gaussian. We show that for distributions with a power-law tailP() 1/||¹⁺ , where>2, so that the mean and variance are well defined, the scaling exponentv of the DP model depends on in a continuous fashion.     

Directed polymers in Hartree-Fock approximation

A replica trick is used to map the problem of directed polymers into a quantum mechanics problem ofn-body bound states. This bound-state problem is then treated using a self-consistent method of Hartree-Fock. Ford=2, the exact result of the DP exponents is reproduced; and for complex DP, the ground-state energyE _n n² is found, confirming previous numerical results.     

Evolutionary rate variation and RNA secondary structure prediction

Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions. In addition we obtained an alignment of the 5' HIV-1 region that is more consistent with the structure than that currently in the database. We added randomized noise to the original values of the rates to investigate the stability of predictions to rate matrix deviations. We find that changes within a fairly large range still produce reliable predictions and conclude that using rates from a limited set of RNA sequences is valid over a broader range of sequences.     

A genetic algorithm for the automated generation of molecules within constraints

Summary A genetic algorithm has been designed which generates molecular structures within constraints. The constraints may be any useful function, for example an enzyme active site, a pharmacophore or molecular properties from pattern recognition or rule-induction analyses. The starting point may be random or may utilise known molecules. These are modified to grow into families of structures which, using the evolutionary operators of selection, crossover and mutation evolve to better fit the constraints. The basis of the algorithm is described together with some applications in lead generation, 3D database construction and drug design. Genetic algorithms of this type may have wider applications in chemistry, for example in the design and optimisation of new polymers, materials (e.g. superconducting materials) or synthetic enzymes.     

Nonuniversality and analytical continuation in moments of directed polymers on hierarchical lattices

We prove the moments of the directed polymer partition function GZ, using an exact position space renormalization group scheme on a hierarchical lattice. After sufficient iteration the characteristic functionf(n)=lnGZⁿ of the probability (Z) converges to a stable limitf ^*(n). For smalln the limiting behavior is independent of the initial distribution, while for largen,f ^*(n) is completely determined by it and is thus nonuniversal. There is a smooth crossover between the two regimes for small effective dimensions, and the nonlinear behavior of the small moments can be used to extract information on the universal scaling properties of the distribution. For large effective dimensions there is a sharp transition between the two regimes, and analytical continuation from integer moments ton0 is not possible. Replica arguments can account for most features of the observed results.