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

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

Capturing age-related changes in functional contrast sensitivity with decreasing light levels in monocular and binocular vision

Purpose: It is challenging to separate the effects of normal aging of the retina and visual pathways independently from optical factors, decreased retinal illuminance and early stage disease. This study determined limits to describe the effect of light level on normal, age-related changes in monocular and binocular functional contrast sensitivity. Methods: 95 participants aged 20 to 85 were recruited. Contrast thresholds for correct orientation discrimination of the gap in a Landolt C optotype were measured using a 4 four-alternative, forced-choice (4AFC) procedure at screen luminances from 34 to 0.12 cd/m2, at the fovea and parafovea (0° and ±4°). Pupil size was measured continuously. The Health of the Retina index (HRindex) was computed to capture the loss of contrast sensitivity with decreasing light level. Participants were excluded if they exhibited performance outside the normal limits of interocular differences or HRindex values, or signs of ocular disease. Results: Parafoveal contrast thresholds showed a steeper decline and higher correlation with age at the parafovea than the fovea. 83% of participants with clinical signs of ocular disease had HRindex values outside the normal limits. Binocular summation of contrast signals declined with age, independent of interocular differences. Conclusion: The HRindex worsens more rapidly with age at the parafovea, consistent with histological findings of rod loss and its link to age-related degenerative disease of the retina. The HRindex, and interocular differences could be used to screen for and separate the earliest stages of sub-clinical disease from changes caused by normal aging

Replicators in Fine-grained Environment: Adaptation and Polymorphism

Selection in a time-periodic environment is modeled via the two-player replicator dynamics. For sufficiently fast environmental changes, this is reduced to a multi-player replicator dynamics in a constant environment. The two-player terms correspond to the time-averaged payoffs, while the three and four-player terms arise from the adaptation of the morphs to their varying environment. Such multi-player (adaptive) terms can induce a stable polymorphism. The establishment of the polymorphism in partnership games [genetic selection] is accompanied by decreasing mean fitness of the population.Comment: 4 pages, 2 figure

Inverted Martian Craters in Lineated Glacial Valleys, Ismenius Lacus Region, Mars

We studied small, uniquely-shaped craters found on the surface of lineated terrain in the Ismenius Lacus region of Mars. By utilizing MOC and THEMIS satellite images, we located terrain including lineations (viscous flow features), smoothing of topography, and morphologic features such as polygons and gullies, which appear to be strong evidence of preexisting ice deposits

Noise spectroscopy of optical microcavity

The intensity noise spectrum of the light passed through an optical microcavity is calculated with allowance for thermal fluctuations of its thickness. The spectrum thus obtained reveals a peak at the frequency of acoustic mode localized inside the microcavity and depends on the size of the illuminated area. The estimates of the noise magnitude show that it can be detected using the up-to-date noise spectroscopy technique.Comment: 10 pages, 1 figur

Folding of small proteins: A matter of geometry?

We review some of our recent results obtained within the scope of simple lattice models and Monte Carlo simulations that illustrate the role of native geometry in the folding kinetics of two state folders.Comment: To appear in Molecular Physic