Molecular Clock on a Neutral Network

The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network of high-fitness genotypes, we establish a formalism for computing all cumulants of the full probability distribution of accumulated mutations in terms of graph properties of the neutral network, and use the formalism to prove overdispersion of the molecular clock. We further show that significant overdispersion arises naturally in evolution when the neutral network is highly sparse, exhibits large global fluctuations in neutrality, and small local fluctuations in neutrality. The results are also relevant for elucidating the topological structure of a neutral network from empirical measurements of the substitution process.Comment: 10 page

Evaluating the effects of turf-replacement programs in Los Angeles

Water utilities incentivize turf replacement to promote water conservation, but the effects of such programs have received limited evaluations. In 2014, the Metropolitan Water District of Southern California (MWD) undertook an unprecedented investment to incentive turf replacement throughout Southern California in response to a serious Statewide drought. MWD devoted $350 million to the program, resulting in more than 46,000 rebate payments (25,000 in Los Angeles County) to remove 15.3 million square meters of turf. The program implementation provided a unique opportunity to address research gaps on turf replacement implementation. We analyzed socioeconomic and spatial trends of program participants and assessed landscape changes from turf replacement using a random sample of properties (4% of LA County participants in 2014–16). Specifically, we used a novel and cost-effective approach Google Earth Street View to characterize landscapes in front yards and created a typology of land cover types. Results showed: post-replacement landscapes had a diversity of land cover types – diverse yards with several land cover types, as well as more homogenous yards with a single land cover such as woodchips, bare soil, gravel, and artificial turf. Analysis also indicated some evidence of “neighborhood adoption” effects. We describe the need for longitudinal studies to understand long-term effects of turf replacement and associated water use, and suggest that water utilities should also evaluate results in backyards, which requires site visits. This study provides a novel contribution that can be replicated over space and time to further knowledge of turf replacement program implementations and evaluation

Hyperon production in near threshold nucleon-nucleon collisions

We study the mechanism of the associated Lambda-kaon and Sigma-kaon production in nucleon-nucleon collisions over an extended range of near threshold beam energies within an effective Lagrangian model, to understand of the new data on pp --> p Lambda K+ and pp --> p Sigma0 K+ reactions published recently by the COSY-11 collaboration. In this theory, the hyperon production proceeds via the excitation of N*(1650), N*(1710), and N*(1720) baryonic resonances. Interplay of the relative contributions of various resonances to the cross sections, is discussed as a function of the beam energy over a larger near threshold energy domain. Predictions of our model are given for the total cross sections of pp --> p Sigma+K0, pp --> n Sigma+K+, and pn --> n Lambda K+ reactions.Comment: 16 pages, 4 figures, one new table added and dicussions are updated, version accepted for publication by Physical Review

Neighbour transitivity on codes in Hamming graphs

We consider a \emph{code} to be a subset of the vertex set of a \emph{Hamming graph}. In this setting a \emph{neighbour} of the code is a vertex which differs in exactly one entry from some codeword. This paper examines codes with the property that some group of automorphisms acts transitively on the \emph{set of neighbours} of the code. We call these codes \emph{neighbour transitive}. We obtain sufficient conditions for a neighbour transitive group to fix the code setwise. Moreover, we construct an infinite family of neighbour transitive codes, with \emph{minimum distance} $\delta=4$, where this is not the case. That is to say, knowledge of even the complete set of code neighbours does not determine the code

Inelastic final-state interaction

The final-state interaction in multichannel decay processes is sytematically studied with application to B decay in mind. Since the final-state inteaction is intrinsically interwoven with the decay interaction in this case, no simple phase theorem like "Watson's theorem" holds for experimentally observed final states. We first examine in detail the two-channel problem as a toy-model to clarify the issues and to remedy common mistakes made in earlier literature. Realistic multichannel problems are too challenging for quantitative analysis. To cope with mathematical complexity, we introduce a method of approximation that is applicable to the case where one prominant inelastic channel dominates over all others. We illustrate this approximation method in the amplitude of the decay B to pi K fed by the intermediate states of a charmed meson pair. Even with our approximation we need more accurate information of strong interactions than we have now. Nonethless we are able to obtain some insight in the issue and draw useful conclusions on general fearyres on the strong phases.Comment: The published version. One figure correcte

Lack of self-averaging in neutral evolution of proteins

We simulate neutral evolution of proteins imposing conservation of the thermodynamic stability of the native state in the framework of an effective model of folding thermodynamics. This procedure generates evolutionary trajectories in sequence space which share two universal features for all of the examined proteins. First, the number of neutral mutations fluctuates broadly from one sequence to another, leading to a non-Poissonian substitution process. Second, the number of neutral mutations displays strong correlations along the trajectory, thus causing the breakdown of self-averaging of the resulting evolutionary substitution process.Comment: 4 pages, 2 figure

Counterion Condensation on Spheres in the Salt-free Limit

A highly-charged spherical colloid in a salt-free environment exerts such a powerful attraction on its counterions that a certain fraction condenses onto the surface of a particle. The degree of condensation depends on the curvature of the surface. So, for instance, condensation is triggered on a highly-charged sphere only if the radius exceeds a certain critical radius \collrad^{*}. \collrad^{*} is expected to be a simple function of the volume fraction of particles. To test these predictions, we prepare spherical particles which contain a covalently-bound ionic liquid, which is engineered to dissociate efficiently in a low-dielectric medium. By varying the proportion of ionic liquid to monomer we synthesise nonpolar dispersions of highly-charged spheres which contain essentially no free co-ions. The only ions in the system are counterions generated by the dissociation of surface-bound groups. We study the electrophoretic mobility of this salt-free system as a function of the colloid volume fraction, the particle radius, and the bare charge density and find evidence for extensive counterion condensation. At low electric fields, we observe excellent agreement with Poisson-Boltzmann predictions for counterion condensation on spheres. At high electric fields however, where ion advection is dominant, the electrophoretic mobility is enhanced significantly which we attribute to hydrodynamic stripping of the condensed layer of counterions from the surface of the particle.Comment: 13 pages, 9 figures and two table