Synthesis of Silver Colloids: Experiment and Computational Model

We summarize our recent results that model the formation of uniform spherical silver colloids prepared by mixing iso-ascorbic acid and silver-amine complex solutions in the absence of dispersants. We found that the experimental results can be modeled effectively by the two-stage formation mechanism used previously to model the preparation of colloidal gold spheres. The equilibrium concentration of silver atoms and the surface tension of silver precursor nanocrystals are both treated as free parameters, and the experimental reaction time scale is fit by a narrow region of this two-parameter space. The kinetic parameter required to match the final particle size is found to be very close to that used previously in modeling the formation of uniform gold particles, suggesting that similar kinetics governs the aggregation process. The model also reproduces semi quantitatively the effects of temperature and solvent viscosity on particle synthesis.Comment: 6 pages, 5 figure

Evolution into and out of the Andes: A Bayesian analysis of historical diversification in Thamnophilus antshrikes

The Andean uplift played important roles in the historical diversification of Neotropical organisms, both by producing new high-elevation habitats that could be colonized and by isolating organisms on either side of the mountains. Here, we present a molecular phylogeny of Thamnophlius antshrikes, a clade of 30 species whose collective distribution spans nearly the entirety of lowland habitats in tropical South America, the eastern slope foothills of the Andes, and the tepuis of northern South America. Our goal was to examine the role of the Andes in the diversification of lowland and foothill species. Using parsimony and Bayesian ancestral state reconstructions of a three-state distribution character (lowland-restricted, lowland-to-highland, highland-restricted), we found that the Andes were colonized twice independently and the tepuis once from lowland-restricted ancestors. Over the entire evolutionary history of Thamnophilus, the highest transition rates were between highland-restricted and lowland-to-highland distributions, with extremely low rates into and out of lowland-restricted distributions. This pattern suggests lowland-restricted distributions are limited not by physiological constraints, but by other forces, such as competition. These results highlight the need for additional comparative studies in elucidating processes associated with the colonization of high-elevation habitats and the differentiation of populations within them. © 2007 The Author(s)

Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae)

© 2014 The Author(s). Phylogenetic niche conservatism (PNC) and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model-based approaches offer the opportunity not only to distinguish between PNC and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group of sexually dimorphic small insectivorous forest birds that are relatively homogeneous in size and shape. Here, we integrate a comprehensive species-level molecular phylogeny of the Myrmotherula complex with morphometric and ecological data within a comparative framework to test whether phenotypic similarity is described by a pattern of PNC or convergence, and to identify evolutionary mechanisms underlying body size and shape evolution. We show that antwrens in the Myrmotherula complex represent distantly related clades that exhibit adaptive convergent evolution in body size and divergent evolution in body shape. Phenotypic similarity in the group is primarily driven by their tendency to converge toward smaller body sizes. Differences in body size and shape across lineages are associated to ecological and behavioral factors

Photochemical reaction paths of cis-dienes studied with RASSCF: the changing balance between ionic and covalent excited states

International audienc

Conjugate field and fluctuation-dissipation relation for the dynamic phase transition in the two-dimensional kinetic Ising model

The two-dimensional kinetic Ising model, when exposed to an oscillating applied magnetic field, has been shown to exhibit a nonequilibrium, second-order dynamic phase transition (DPT), whose order parameter Q is the period-averaged magnetization. It has been established that this DPT falls in the same universality class as the equilibrium phase transition in the two-dimensional Ising model in zero applied field. Here we study for the first time the scaling of the dynamic order parameter with respect to a nonzero, period-averaged, magnetic `bias' field, H_b, for a DPT produced by a square-wave applied field. We find evidence that the scaling exponent, \delta_d, of H_b at the critical period of the DPT is equal to the exponent for the critical isotherm, \delta_e, in the equilibrium Ising model. This implies that H_b is a significant component of the field conjugate to Q. A finite-size scaling analysis of the dynamic order parameter above the critical period provides further support for this result. We also demonstrate numerically that, for a range of periods and values of H_b in the critical region, a fluctuation-dissipation relation (FDR), with an effective temperature T_{eff}(T, P, H_0) depending on the period, and possibly the temperature and field amplitude, holds for the variables Q and H_b. This FDR justifies the use of the scaled variance of Q as a proxy for the nonequilibrium susceptibility, \partial / \partial H_b, in the critical region.Comment: revised version; 31 pages, 12 figures; accepted by Phys. Rev.

Estimating species trees using multiple-allele DNA sequence data

Several techniques, such as concatenation and consensus methods, are available for combining data from multiple loci to produce a single statement of phylogenetic relationships. However, when multiple alleles are sampled from individual species, it becomes more challenging to estimate relationships at the level of species, either because concatenation becomes inappropriate due to conflicts among individual gene trees, or because the species from which multiple alleles have been sampled may not form monophyletic groups in the estimated tree. We propose a Bayesian hierarchical model to reconstruct species trees from multiple-allele, multilocus sequence data, building on a recently proposed method for estimating species trees from single allele multilocus data. A two-step Markov Chain Monte Carlo (MCMC) algorithm is adopted to estimate the posterior distribution of the species tree. The model is applied to estimate the posterior distribution of species trees for two multiple-allele datasets - yeast (Saccharomyces) and birds (Manacus - manakins). The estimates of the species trees using our method are consistent with those inferred from other methods and genetic markers, but in contrast to other species tree methods, it provides credible regions for the species tree. The Bayesian approach described here provides a powerful framework for statistical testing and integration of population genetics and phylogenetics. © 2008 The Author(s)

The utility of single nucleotide polymorphisms in inferences of population history

Single nucleotide polymorphisms (SNPs) represent the most widespread type of sequence variation in genomes, yet they have only emerged recently as valuable genetic markers for revealing the evolutionary history of populations. Their occurrence throughout the genome also makes them ideal for analyses of speciation and historical demography, especially in light of recent theory suggesting that many unlinked nuclear loci are needed to estimate population genetic parameters with statistical confidence. In spite of having lower variation compared with microsatellites, SNPs should make the comparison of genomic diversities and histories of different species (the core goal of comparative biogeography) more straightforward than has been possible with microsatellites. The most pervasive, but correctable, complication to SNP analysis is a bias towards analyzing only the most variable loci, an artifact that is usually introduced by the limited number of individuals used to screen initially for polymorphisms. Although the use of SNPs as markers in population studies is still new, innovative methods for SNP identification, automated screening, haplotype inference and statistical analysis might quickly make SNPs the marker of choice

High dispersal ability inhibits speciation in a continental radiation of passerine birds

Dispersal can stimulate speciation byfacilitating geographical expansion across barriers or inhibit speciation by maintaining gene flow among populations. Therefore, the relationship between dispersal ability and speciation rates can be positive or negative. Furthermore, an \u27intermediate dispersal\u27 model that combines positive and negative effects predicts a unimodal relationship between dispersal and diversification. Because both dispersal ability and speciation rates are difficult to quantify, empirical evidence for the relationship between dispersal and diversification remains scarce. Using a surrogate for flight performance and a species-level DNA-based phylogeny of a large South American bird radiation (the Furnariidae), we found that lineages with higher dispersal ability experienced lower speciation rates. We propose that the degree of fragmentation or permeability of the geographical setting together with the intermediate dispersal model are crucial in reconciling previous, often contradictory findings regarding the relationship between dispersal and diversification. © 2011 The Royal Society

When New Life Meets Death: Three Hermeneutic Case Studies From Switzerland.

Pregnant women in Switzerland expect safe and healthy birth outcomes for themselves and their babies. However, in 2018, 691 died in infancy with gaps identified in the provision of services to parents in such circumstances. Our study aims to illustrate these gaps and how, from participants' perspectives, they were addressed. A hermeneutic method was employed to analyze three cases: one from each major language region was via primary health-care providers. A thematic analysis was carried out with individual participants followed by a cross-case comparison which showed a hermeneutic of rupture, the juxtaposition of time and reshaping the family. This article shows the unique journeys experienced by parents whose baby dies before or shortly after birth in one country where neither the language nor experience is shared. The derivation of three hermeneutic themes may resonate with other parents or health professionals

Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595

Fluorescent proteins have been widely used as genetically encodable fusion tags for biological imaging. Recently, a new class of fluorescent proteins was discovered that can be reversibly light-switched between a fluorescent and a non-fluorescent state. Such proteins can not only provide nanoscale resolution in far-field fluorescence optical microscopy much below the diffraction limit, but also hold promise for other nanotechnological applications, such as optical data storage. To systematically exploit the potential of such photoswitchable proteins and to enable rational improvements to their properties requires a detailed understanding of the molecular switching mechanism, which is currently unknown. Here, we have studied the photoswitching mechanism of the reversibly switchable fluoroprotein asFP595 at the atomic level by multiconfigurational ab initio (CASSCF) calculations and QM/MM excited state molecular dynamics simulations with explicit surface hopping. Our simulations explain measured quantum yields and excited state lifetimes, and also predict the structures of the hitherto unknown intermediates and of the irreversibly fluorescent state. Further, we find that the proton distribution in the active site of the asFP595 controls the photochemical conversion pathways of the chromophore in the protein matrix. Accordingly, changes in the protonation state of the chromophore and some proximal amino acids lead to different photochemical states, which all turn out to be essential for the photoswitching mechanism. These photochemical states are (i) a neutral chromophore, which can trans-cis photoisomerize, (ii) an anionic chromophore, which rapidly undergoes radiationless decay after excitation, and (iii) a putative fluorescent zwitterionic chromophore. The overall stability of the different protonation states is controlled by the isomeric state of the chromophore. We finally propose that radiation-induced decarboxylation of the glutamic acid Glu215 blocks the proton transfer pathways that enable the deactivation of the zwitterionic chromophore and thus leads to irreversible fluorescence. We have identified the tight coupling of trans-cis isomerization and proton transfers in photoswitchable proteins to be essential for their function and propose a detailed underlying mechanism, which provides a comprehensive picture that explains the available experimental data. The structural similarity between asFP595 and other fluoroproteins of interest for imaging suggests that this coupling is a quite general mechanism for photoswitchable proteins. These insights can guide the rational design and optimization of photoswitchable proteins