Newick format tree of Gruidae

Branch lengths are in millions of years. Krajewski et al. (2010) calculated divergence dates in parallel analyses using a standard deviation of 0.5, 1.0, and 1.5 on the lognormal priors of the age calibration points based on crane fossil records. We used branch lengths derived from 0.5 standard deviation because it produced a highly resolved topology, however still with a polytomy comprising nodes 12.5 and 11. We used the median value of the 95% highest posterior density interval as our branch length for node 12.5 to resolve the tree

Universal Noble Metal Nanoparticle Seeds Realized Through Iterative Reductive Growth and Oxidative Dissolution Reactions

Control over nanoparticle shape and size is commonly achieved via a seed-mediated approach, where nanoparticle precursors, or seeds, are hypothesized to act as templates for the heterogeneous nucleation of anisotropic products. Despite the wide variety of shapes that have been produced via this approach, high yield and uniformity have been more difficult to achieve. These shortcomings are attributed to limited structural control and characterization of the initial distribution of seeds. Herein, we report how iterative reductive growth and oxidative dissolution reactions can be used to systematically control seed structural uniformity. Using these reactions, we verify that seed structure dictates anisotropic nanoparticle uniformity and show that iterative seed refinement leads to unprecedented noble metal nanoparticle uniformities and purities for eight different shapes produced from a single seed source. Because of this uniformity, the first nanoparticle optical extinction coefficients for these eight shapes were analytically determined

<i>In Situ</i> Electron Microscopy Imaging and Quantitative Structural Modulation of Nanoparticle Superlattices

We use liquid-phase transmission electron microscopy (LP-TEM) to characterize the structure and dynamics of a solution-phase superlattice assembled from gold nanoprisms at the single particle level. The lamellar structure of the superlattice, determined by a balance of interprism interactions, is maintained and resolved under low-dose imaging conditions typically reserved for biomolecular imaging. In this dose range, we capture dynamic structural changes in the superlattice in real time, where contraction and smaller steady-state lattice constants are observed at higher electron dose rates. Quantitative analysis of the contraction mechanism based on a combination of direct LP-TEM imaging, ensemble small-angle X-ray scattering, and theoretical modeling allows us to elucidate: (1) the superlattice contraction in LP-TEM results from the screening of electrostatic repulsion due to as much as a 6-fold increase in the effective ionic strength in the solution upon electron beam illumination; and (2) the lattice constant serves as a means to understand the mechanism of the <i>in situ</i> interaction modulation and precisely calibrate electron dose rates with the effective ionic strength of the system. These results demonstrate that low-dose LP-TEM is a powerful tool for obtaining structural and kinetic properties of nanoassemblies in liquid conditions that closely resemble real experiments. We anticipate that this technique will be especially advantageous for those structures with heterogeneity or disorder that cannot be easily probed by ensemble methods and will provide important insight that will aid in the rational design of sophisticated reconfigurable nanomaterials

Simulation data

The final generation (generation 1250) of each simulation run and replicate. Simulations are divided into no selection simulations ("Nsims"), gradient selection simulations ("Gsims"), and discrete selection simulations ("H1/H5/H9sims")

Uniform Circular Disks With Synthetically Tailorable Diameters: Two-Dimensional Nanoparticles for Plasmonics

Herein, we report the synthesis of structurally uniform gold circular disks as two-dimensional plasmonic nanostructures that complement the well-established one-dimensional rod and three-dimensional shell structures. We show that a Au conproportionation reaction can be used to etch a collection of nonuniform triangular prisms into a uniform circular disk product with thickness and diameter varying <10%. These new particles have broadly tunable plasmon resonances (650–1000 nm) with narrow bandwidths (0.23–0.28 eV) and can be described as “effectively two-dimensional” plasmonic structures, as they do not support a significant transverse mode

The Use of Graphene and Its Derivatives for Liquid-Phase Transmission Electron Microscopy of Radiation-Sensitive Specimens

One of the key challenges facing liquid-phase transmission electron microscopy (TEM) of biological specimens has been the damaging effects of electron beam irradiation. The strongly ionizing electron beam is known to induce radiolysis of surrounding water molecules, leading to the formation of reactive radical species. In this study, we employ DNA-assembled Au nanoparticle superlattices (DNA-AuNP superlattices) as a model system to demonstrate that graphene and its derivatives can be used to mitigate electron beam-induced damage. We can image DNA-AuNP superlattices in their native saline environment when the liquid cell window material is graphene, but not when it is silicon nitride. In the latter case, initial dissociation of assembled AuNPs was followed by their random aggregation and etching. Using graphene-coated silicon nitride windows, we were able to replicate the observation of stable DNA-AuNP superlattices achieved with graphene liquid cells. We then carried out a correlative Raman spectroscopy and TEM study to compare the effect of electron beam irradiation on graphene with and without the presence of water and found that graphene reacts with the products of water radiolysis. We attribute the protective effect of graphene to its ability to efficiently scavenge reactive radical species, especially the hydroxyl radicals which are known to cause DNA strand breaks. We confirmed this by showing that stable DNA-AuNP assemblies can be imaged in silicon nitride liquid cells when graphene oxide and graphene quantum dots, which have also recently been reported as efficient radical scavengers, are added directly to the solution. We anticipate that our study will open up more opportunities for studying biological specimens using liquid-phase TEM with the use of graphene and its derivatives as biocompatible radical scavengers to alleviate the effects of radiation damage

Selection surfaces and sampling file

One of the gradient selection files ("gradient1024x1024_N0_S1.txt") and a full set of habitat configuration rasters (H1/H5/H9 with 10 replicates each). The 500 randomly sampled individuals are provided in "sample500.csv"

Hybrid Lithographic and DNA-Directed Assembly of a Configurable Plasmonic Metamaterial That Exhibits Electromagnetically Induced Transparency

Metamaterials are architectures that interact with light in novel ways by virtue of symmetry manipulation, and have opened a window into studying unprecedented light-matter interactions. However, they are commonly fabricated via lithographic methods, are usually static structures, and are limited in how they can react to external stimuli. Here we show that by combining lithographic techniques with DNA-based self-assembly methods, we can construct responsive plasmonic metamaterials that exhibit the plasmonic analog of an effect known as electromagnetically induced transparency (EIT), which can dramatically change their spectra upon motion of their constituent parts. Correlative scanning electron microscopy measurements, scattering dark-field microscopy, and computational simulations are performed on single assemblies to determine the relationship between their structures and spectral responses to a variety of external stimuli. The strength of the EIT-like effect in these assemblies can be tuned by precisely controlling the positioning of the plasmonic nanoparticles in these structures. For example, changing the ionic environment or dehydrating the sample will change the conformation of the DNA linkers and therefore the distance between the nanoparticles. Dark-field spectra of individual assemblies show peak shifts of up to many tens of nanometers upon DNA perturbations. This dynamic metamaterial represents a stepping stone toward state-of-the-art plasmonic sensing platforms and next-generation dynamic metamaterials

What Controls the Hybridization Thermodynamics of Spherical Nucleic Acids?

The hybridization of free oligonucleotides to densely packed, oriented arrays of DNA modifying the surfaces of spherical nucleic acid (SNA)–gold nanoparticle conjugates occurs with negative cooperativity; i.e., each binding event destabilizes subsequent binding events. DNA hybridization is thus an ever-changing function of the number of strands already hybridized to the particle. Thermodynamic quantification of this behavior reveals a 3 orders of magnitude decrease in the binding constant for the capture of a free oligonucleotide by an SNA conjugate as the fraction of pre-hybridized strands increases from 0 to ∼30%. Increasing the number of pre-hybridized strands imparts an increasing enthalpic penalty to hybridization that makes binding more difficult, while simultaneously decreasing the entropic penalty to hybridization, which makes binding more favorable. Hybridization of free DNA to an SNA is thus governed by both an electrostatic barrier as the SNA accumulates charge with additional binding events and an effect consistent with allostery, where hybridization at certain sites on an SNA modify the binding affinity at a distal site through conformational changes to the remaining single strands. Leveraging these insights allows for the design of conjugates that hybridize free strands with significantly higher efficiencies, some of which approach 100%