The arrival of the frequent: how bias in genotype-phenotype maps can steer populations to local optima

Genotype-phenotype (GP) maps specify how the random mutations that change genotypes generate variation by altering phenotypes, which, in turn, can trigger selection. Many GP maps share the following general properties: 1) The number of genotypes $N_G$ is much larger than the number of selectable phenotypes; 2) Neutral exploration changes the variation that is accessible to the population; 3) The distribution of phenotype frequencies $F_p=N_p/N_G$, with $N_p$ the number of genotypes mapping onto phenotype $p$, is highly biased: the majority of genotypes map to only a small minority of the phenotypes. Here we explore how these properties affect the evolutionary dynamics of haploid Wright-Fisher models that are coupled to a simplified and general random GP map or to a more complex RNA sequence to secondary structure map. For both maps the probability of a mutation leading to a phenotype $p$ scales to first order as $F_p$, although for the RNA map there are further correlations as well. By using mean-field theory, supported by computer simulations, we show that the discovery time $T_p$ of a phenotype $p$ similarly scales to first order as $1/F_p$ for a wide range of population sizes and mutation rates in both the monomorphic and polymorphic regimes. These differences in the rate at which variation arises can vary over many orders of magnitude. Phenotypic variation with a larger $F_p$ is therefore be much more likely to arise than variation with a small $F_p$. We show, using the RNA model, that frequent phenotypes (with larger $F_p$) can fix in a population even when alternative, but less frequent, phenotypes with much higher fitness are potentially accessible. In other words, if the fittest never `arrive' on the timescales of evolutionary change, then they can't fix. We call this highly non-ergodic effect the `arrival of the frequent'.Comment: full paper plus supplementary material

Extended electrode technique

The extended electrode technique is a unique welding process which utilizes manual gas-metal-arc (GMAW) semi-automatic equipment and close, square butt joints to effectively produce a weld. The technique takes advantage of the resistance heating of the electode extension to effect the root pass. Weldments as large as 72-X30-X2-inch have been fabricated with this technique under normal shipyard welding conditions. Mechanical properties and explosion bulge tests indicate that satisfactory results are obtained with this process. Potential savings of approximately 50 percent can be achieved in flat welding and repair of heavy structural steel members

Nondestructive Evaluation (NDE) for Thermal-Spray Coatings

Thermal spray is the process of depositing metal, alloy, and ceramic coatings on properly prepared substrate materials so that they solidify on and bond mechanically, chemically, and metallurgically to the substrate materials. Thermal-spray coatings are applied to improve surface-wear characteristics, to provide resistance to heat, oxidation, and chemical environments; to restore dimension to the original equipment manufacturer\u27s (OEM) specifications; to reduce erosion wear; and to improve corrosion control

Wakefield-Induced Ionization injection in beam-driven plasma accelerators

We present a detailed analysis of the features and capabilities of Wakefield-Induced Ionization (WII) injection in the blowout regime of beam driven plasma accelerators. This mechanism exploits the electric wakefields to ionize electrons from a dopant gas and trap them in a well-defined region of the accelerating and focusing wake phase, leading to the formation of high-quality witness-bunches [Martinez de la Ossa et al., Phys. Rev. Lett. 111, 245003 (2013)]. The electron-beam drivers must feature high-peak currents ($I_b^0\gtrsim 8.5~\mathrm{kA}$) and a duration comparable to the plasma wavelength to excite plasma waves in the blowout regime and enable WII injection. In this regime, the disparity of the magnitude of the electric field in the driver region and the electric field in the rear of the ion cavity allows for the selective ionization and subsequent trapping from a narrow phase interval. The witness bunches generated in this manner feature a short duration and small values of the normalized transverse emittance ($k_p\sigma_z \sim k_p\epsilon_n \sim 0.1$). In addition, we show that the amount of injected charge can be adjusted by tuning the concentration of the dopant gas species, which allows for controlled beam loading and leads to a reduction of the total energy spread of the witness beams. Electron bunches, produced in this way, fulfil the requirements to drive blowout regime plasma wakes at a higher density and to trigger WII injection in a second stage. This suggests a promising new concept of self-similar staging of WII injection in steps with increasing plasma density, giving rise to the potential of producing electron beams with unprecedented energy and brilliance from plasma-wakefield accelerators

Epistasis can lead to fragmented neutral spaces and contingency in evolution

In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space - namely, that networks of genomes encoding the same phenotype may not be connected by single mutational moves. We use the folding of RNA sequences into secondary structures as a model genotype-phenotype map and explore the neutral spaces corresponding to networks of genotypes with the same phenotype. In most of these networks, we find that it is not possible to connect all genotypes to one another by single point mutations. Instead, a network for a phenotypic structure with $n$ bonds typically fragments into at least $2^n$ neutral components, often of similar size. While components of the same network generate the same phenotype, they show important variations in their properties, most strikingly in their evolvability and mutational robustness. This heterogeneity implies contingency in the evolutionary process.Comment: 21 pages, 21 figure

Impurity intrusion in radio-frequency micro-plasma jets operated in ambient air

Space and time resolved concentrations of helium metastable atoms in an atmospheric pressure radio-frequency micro-plasma jet were measured using tunable diode laser absorption spectroscopy. Spatial profiles as well as lifetime measurements show significant influences of air entering the discharge from the front nozzle and of impurities originating from the gas supply system. Quenching of metastables was used to deduce quantitative concentrations of intruding impurities. The impurity profile along the jet axis was determined from optical emission spectroscopy as well as their dependance on the feed gas flow through the jet.Comment: Journal of Physics D: Applied Physics (accepted), 6 page

In Vitro Formation of Urinary Stones : Generation of Spherulites of Calcium Phosphate in Gel and Overgrowth with Calcium Oxalate Using a New Flow Model of Crystallization

Calcium phosphate (CaP) has been detected in the majority of urinary stones containing predominantly calcium oxalate (CaOx). Therefore, crystal phases of CaP might play an important role with respect to the formation of urinary calcium stones in general. Very often, CaP found in stones or tissue of human kidney occurs in the shape of small spherulites. In this paper, we report on a new flow model of crystallization (FMCG), which has been used to generate spherulites of CaP in a gel matrix of 1% agar-agar at 37°C from a supersaturated, metastable solution continuously flowing over the gel surface. Scanning electron microscopy (SEM), X-ray diffraction and microscopic Fourier transformed infrared spectroscopy (FTIR) revealed that the particles formed (diameter: up to 200 μm) consisted of a poorly crystal-line core of carbonatoapatite which was partly surrounded by a well-crystallized shell of octacalcium phosphate (OCP) showing radially oriented sheet-like structures. Subsequently, CaOx was grown on these spherulites from a flow of a correspondingly supersaturated solution conducted over the gel matrix. It could be shown by SEM that growth of calcium oxalate monohydrate (COM) was characteristically induced by the OCP shell. Radial sheet-like forms of OCP were directly continued by COM showing a certain radial orientation. The model of crystallization in gel matrices applied here should be well-suited to simulate the process of urinary stone formation under in vitro conditions