Self-assembly of photonic crystals by controlling the nucleation and growth of DNA-coated colloids

DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but their applications have been limited by poor understanding and control over the crystallization dynamics. To address this challenge, we use microfluidics to quantify the kinetics of DNA-programmed self-assembly along the entire crystallization pathway, from thermally activated nucleation through reaction-limited and diffusion-limited phases of crystal growth. Our detailed measurements of the temperature and concentration dependence of the kinetics at all stages of crystallization provide a stringent test of classical theories of nucleation and growth. After accounting for the finite rolling and sliding rates of micrometer-sized DNA-coated colloids, we show that modified versions of these classical theories predict the absolute nucleation and growth rates with quantitative accuracy. We conclude by applying our model to design and demonstrate protocols for assembling large single crystals with pronounced structural coloration, an essential step in creating next-generation optical metamaterials from colloids.

By encoding specific short-range interactions, DNA molecules grafted to colloidal particles can be used to direct the self-assembly of complex, crystalline materials (1–3). This general approach to crystal engineering is a triumph of synthetic self-assembly and has yielded a vast diversity of crystal structures with programmable stoichiometries, composition, and crystallographic symmetries from both nanometer-(4–10) and micrometer-scale particles (11–17). Although the breadth of such structures has increased dramatically over time, experiments using optical-scale colloidal particles have produced relatively small, polycrystalline structures due to poorly understood crystallization kinetics. Realizing the ultimate goal of assembling colloidal metamaterials, such as photonic crystals, thus requires new experimental methodologies and theoretical models to understand and achieve control over the dynamics of self-assembly.Colloidal crystals are widely believed to self-assemble via classical nucleation and growth, following dynamical pathways analogous to those of atoms and simple molecules. According to classical nucleation theory (CNT), a crystalline nucleus spontaneously forms from a metastable fluid by surmounting a free-energy barrier (18). Subsequent growth then occurs by the addition of free particles to the nucleus. A central challenge in programmable self-assembly of colloids is to understand whether this framework quantitatively describes the crystallization dynamics of micrometer-sized colloidal particles. On the one hand, colloidal particles can be thought of as “model atoms” that interact via an effective interaction potential that is averaged over all of the molecular degrees of freedom (19). On the other hand, the effective interaction arises from the transient formation and rupture of very real DNA duplexes that link neighboring particles together, whose kinetics may dramatically influence the rates of local rearrangements within a colloidal assembly (13, 20, 21). Such dynamical considerations are crucially important, as numerous examples of colloidal self-assembly have shown that the thermodynamically stable phase that one would predict on the basis of the effective interactions alone is not always accessible, and that these systems are prone to becoming arrested as a colloidal gel instead (22, 23).Here we quantify the nucleation and growth dynamics of DNA-programmed crystallization in a binary mixture of colloidal particles. By monitoring the self-assembly of hundreds of isolated crystals simultaneously, we show that a modified version of CNT—which takes into account the finite rate at which bound particles roll or slide over one another at the crystal interface—quantitatively describes the observed temperature and concentration dependence of the nucleation barrier, as well as the absolute nucleation rate. Furthermore, our model of the friction-mediated attachment kinetics successfully captures the dynamics of the initial reaction-limited phase of crystal growth, which occurs before large crystals ultimately enter into a deterministic, diffusion-limited growth regime. With this understanding of the crystallization dynamics, we accurately predict the extremely narrow temperature window—less than 0.1 °C—in which large, faceted single crystals can be grown. We then use this knowledge to design and demonstrate a protocol for assembling millions of single crystals of DNA-coated particles that exhibit a pronounced photonic response, thereby overcoming a critical hurdle to using DNA-programmed assembly to build optical metamaterials (17, 24–26).     

Hierarchical self-assembly of polydisperse colloidal bananas into a two-dimensional vortex phase

Self-assembly of microscopic building blocks into highly ordered and functional structures is ubiquitous in nature and found at all length scales. Hierarchical structures formed by colloidal building blocks are typically assembled from monodisperse particles interacting via engineered directional interactions. Here, we show that polydisperse colloidal bananas self-assemble into a complex and hierarchical quasi–two-dimensional structure, called the vortex phase, only due to excluded volume interactions and polydispersity in the particle curvature. Using confocal microscopy, we uncover the remarkable formation mechanism of the vortex phase and characterize its exotic structure and dynamics at the single-particle level. These results demonstrate that hierarchical self-assembly of complex materials can be solely driven by entropy and shape polydispersity of the constituting particles.

Self-assembly of microscopic building blocks is a powerful route for preparing materials with predesigned structure and engineered properties (1–7). Nature provides a fascinating range of self-assembled architectures offering insight into how structural organization can emerge at different length scales (8–13). In the biological world, for instance, tobacco mosaic virus coat proteins self-organize into sophisticated capsids around viral RNA strands (11, 14). In molecular systems, lipid molecules, such as fatty acids, form a range of self-assembled structures as relevant as cell membranes and vesicles (15, 16). At the colloidal scale, a rich variety of crystals with remarkable optical properties, such as opal and other gemstones, also assembles from a range of colloidal constituents (12, 17–20). The structural complexity of self-assembled materials is typically dictated by the combination of the type of interactions between the constituent building blocks and their shape (2, 3, 5, 6). Colloids are ideal systems to independently study the role of these key parameters, as their shape and interactions can be systematically tuned and rationally designed (5, 18, 21–23).In colloidal systems interacting solely via excluded volume interactions, the shape of the particles can already lead to the assembly of complex structures (24–28). For instance, binary colloidal crystals (25) are obtained from spherical particles, complex dodecagonal quasicrystals are formed by tetrahedrons (26), and exotic banana-shaped liquid crystals are assembled from colloidal bananas (28). Introducing complex interactions between the colloidal building blocks—on the top of their shape—leads to their assembly into hierarchical materials with structural order at multiple length scales (3, 29–31). Examples include colloidal diamond structures assembled by patchy tetrahedrons functionalized with DNA strands (20) and superlattice structures formed by octapod-like particles functionalized with hydrophobic molecules (32). The successful hierarchical self-assembly of these structures relies not only on the directionality of the particle interactions but also, on the uniformity in size of the constituent building blocks, as polydispersity typically disrupts ordering via the formation of defects (33, 34).In this work, however, we show that a colloidal suspension of polydisperse banana-shaped particles interacting only via simple excluded volume interactions (28) self-assembles into remarkably ordered concentric structures, which we term colloidal vortices. At high packing fractions, these structures form a quasi–two-dimensional (quasi-2D) hierarchical material, which we term the vortex phase. Using confocal microscopy, we uncover the formation mechanism of this tightly packed phase and characterize its exotic structure and dynamics at the single-particle level.     

DNA self-organization controls valence in programmable colloid design

Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence—the number of interparticle bonds—is a prerequisite for the assembly of complex architectures. The assembly can be directed via solid “patchy” particles with prescribed geometries to make, for example, a colloidal diamond. We demonstrate here that the nanoscale ordering of individual molecular linkers can combine to program the structure of microscale assemblies. Specifically, we experimentally show that covering initially isotropic microdroplets with N mobile DNA linkers results in spontaneous and reversible self-organization of the DNA into Z(N) binding patches, selecting a predictable valence. We understand this valence thermodynamically, deriving a free energy functional for droplet–droplet adhesion that accurately predicts the equilibrium size of and molecular organization within patches, as well as the observed valence transitions with N. Thus, microscopic self-organization can be programmed by choosing the molecular properties and concentration of binders. These results are widely applicable to the assembly of any particle with mobile linkers, such as functionalized liposomes or protein interactions in cell–cell adhesion.

Building blocks encoded with assembly rules harness thermal energy to put themselves together in a process called self-assembly (1, 2). These elements can be proteins (3, 4), DNA (5–8), or colloids (8–12). Akin to atoms and molecules, colloidal particles with well-defined shapes and interactions self-organize into bulk crystalline phases that minimize the free energy (13–19). More-complex objects with nonrepeating structures, such as protein folds or aperiodic crystals, require a prescribed limit to particle valence (20, 21). A fundamental goal is to fabricate structures with important technological applications (22). For example, colloidal self-assembly into a diamond lattice (10) or a quasicrystal (23, 24) is expected to exhibit photonic band gaps due to the materials’ interaction with light (25, 26). At its most complex, self-assembly of biological cells is a crucial part of the development of a living organism (27).Experimentally, valence control can be achieved by designing anisotropic sticky particles with patches to create colloidal clusters (28–30) or DNA origami that specifies the bond orientation (31, 32). Mixing particles with a given size and number ratio can result in steric valence control (33). Other proposed methods include the self-organization of nematic shells on spheres (34, 35) or the arrested phase separation of lipids on droplet surfaces (36). These processes are complex to experimentally realize, feature slow assembly kinetics due to the necessity of patch-to-patch binding, and require extensive purification (28).Unlike solid particles, droplets (37–40), lipid vesicles (41–46), and biological cells (47–50) allow any sticky binders to freely diffuse at the interface and segregate into adhesions with their neighbors. If the particles are Brownian or mobile, they can rearrange even after binding to reach the most favorable valence and geometry, avoiding kinetic bottlenecks. Angioletti-Uberti et al. (51) theoretically proposed that mobile ligands coupled with an additional repulsive potential—such as a steric brush—could yield colloidal valence selection in the bulk. More generally, the mobility and reversibility of linker binding between particles allows the system to optimize its equilibrium structure according to the laws of statistical mechanics. Not only is this strategy more robust than directed irreversible assembly, but it enables colloidal design based on the properties of molecular binders.Here, we derive and experimentally validate the free energy functional for droplet–droplet adhesion and predict the consequent thermodynamically stable valence for given control parameters. Moreover, we show that droplets recover their equilibrium valence in a matter of minutes after their bonds are broken. Our results are applicable to any functionalized particles with mobile binders, showing that molecular properties and concentration are sufficient to predetermine valence. Emulsions serve as a template for programmable solid materials because the droplets can be readily polymerized at any stage of the self-assembly process (52, 53).     

An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers

Human culture, biology, and health were shaped dramatically by the onset of agriculture ∼12,000 y B.P. This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared “predicted” genetic contributions to height from paleogenomic data and “achieved” adult osteological height estimated from long bone measurements for 167 individuals across Europe spanning the Upper Paleolithic to Iron Age (∼38,000 to 2,400 B.P.). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of −3.82 cm relative to individuals from the Upper Paleolithic and Mesolithic (P = 0.040) and −2.21 cm shorter relative to post-Neolithic individuals (P = 0.068), with osteological vs. expected stature steadily increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when we additionally accounted for genome-wide genetic ancestry variation: for example, with Neolithic individuals −2.82 cm shorter than expected on average relative to pre-Neolithic individuals (P = 0.120). We also incorporated observations of paleopathological indicators of nonspecific stress that can persist from childhood to adulthood in skeletal remains into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.

The agricultural revolution—beginning ∼12,000 B.P. in the Fertile Crescent zone (1, 2) and then spreading (3–5) or occurring independently (6, 7) across much of the inhabited planet—precipitated profound changes to human subsistence, social systems, and health. Seemingly paradoxically, the agricultural transition may have presented conflicting biological benefits and costs for early farming communities (8, 9). Specifically, demographic reconstructions from archaeological and population genetic records suggest that the agricultural transition led to increased individual fitness and population growth (6, 10–12), likely due in part to new food production and storage capabilities. Yet, bioarchaeological analyses of human skeletal remains from this cultural period suggest simultaneous declines in individual physiological well-being and health, putatively from 1) nutritional deficiency and/or 2) increased pathogen loads as a function of greater human population densities, sedentary lifestyles, and proximity to livestock (9, 13–18).To date, anthropologists have used two principal approaches to study health across the foraging-to-farming transition in diverse global regions (13, 19, 20). The first approach involves identifying paleopathological indicators of childhood stress that persist into adult skeletal remains. For example, porotic hyperostosis (porous lesions on the cranial vault) and cribra orbitalia (porosity on the orbital roof) reflect a history of bone marrow hypertrophy or hyperplasia resulting from one or more periods of infection, metabolic deficiencies, malnutrition, and/or chronic disease (21–26). Meanwhile, linear enamel hypoplasia (transverse areas of reduced enamel thickness on teeth) occurs in response to similar childhood physiological stressors (e.g., disease, metabolic deficiencies, malnutrition, weaning) that disrupt enamel formation in the developing permanent dentition (27–30). Broadly, these paleopathological indicators of childhood stress tend to be observed at higher rates among individuals from initial farming communities relative to earlier periods, potentially reflecting their overall “poorer” health (14, 31–36).A second approach uses skeleton-based estimates of achieved adult stature as a proxy for health during childhood growth and development (37–39). Since stature is responsive to the influences of nutrition and disease burden alongside other factors, relatively short “height-for-age” (or “stunting”) has been used as an indicator of poorer health in both living and bioarchaeological contexts (39–43). When studying the past, individual stature can be estimated from long bone measurements and regression equations (44–47). Using these methods, multiple prior studies have reported a general profile of relatively reduced stature for individuals from early agricultural societies in Europe (15, 48–50), North America (51–53), the Levant (16, 32), and Asia (54, 55). For example, estimated average adult mean statures for early farmers are ∼10 cm shorter relative to those for preceding hunter-gatherers in both western Europe (females, −8 cm; males, −14 cm) (49, 50) and the eastern Mediterranean (females, −11 cm; males, −8 cm) (56). This pattern is not universal, as a few studies do not report such changes (57, 58); the variation could be informative with respect to identifying potential underlying factors (59).However, in addition to environmental effects like childhood nutrition and disease, inherited genetic variation can have an outsized impact on terminal stature, with ∼80% of the considerable degree of height variation within many modern populations explainable by heritable genetic variation (60–63). Moreover, migration and gene flow likely accompanied many subsistence shifts in human prehistory. For example, there is now substantial paleogenomic evidence of extensive population turnover across prehistoric Europe (64–69). Therefore, from osteological studies alone, we are unable to quantify the extent to which temporal changes in height reflect variation in childhood health vs. changes/differences in the frequencies of alleles associated with height variation.In this study, we have performed a combined analysis of ancient human paleogenomic and osteological data where both are available from the same n = 167 prehistoric European individuals representing cultural periods from the Upper Paleolithic (∼38,000 B.P.) to the Iron Age (∼2,400 B.P.). This approach allows us to explore whether “health,” as inferred from the per-individual difference between predicted genetic contributions to height and osteological estimates of achieved adult height, changed over the Neolithic cultural shift to agriculture in Europe. When craniodental elements were preserved and available for analysis (n = 98 of the 167 individuals), we also collected porotic hyperostosis, cribra orbitalia, and linear enamel hypoplasia paleopathological data in order to examine whether patterns of variation between osteological height and genetic contributions to height are explained in part by the presence/absence of these indicators of childhood or childhood-inclusive stress.     

Biotropic liquid crystal phase transformations in cellulose-producing bacterial communities

Biological functionality is often enabled by a fascinating variety of physical phenomena that emerge from orientational order of building blocks, a defining property of nematic liquid crystals that is also pervasive in nature. Out-of-equilibrium, “living” analogs of these technological materials are found in biological embodiments ranging from myelin sheath of neurons to extracellular matrices of bacterial biofilms and cuticles of beetles. However, physical underpinnings behind manifestations of orientational order in biological systems often remain unexplored. For example, while nematiclike birefringent domains of biofilms are found in many bacterial systems, the physics behind their formation is rarely known. Here, using cellulose-synthesizing Acetobacter xylinum bacteria, we reveal how biological activity leads to orientational ordering in fluid and gel analogs of these soft matter systems, both in water and on solid agar, with a topological defect found between the domains. Furthermore, the nutrient feeding direction plays a role like that of rubbing of confining surfaces in conventional liquid crystals, turning polydomain organization within the biofilms into a birefringent monocrystal-like order of both the extracellular matrix and the rod-like bacteria within it. We probe evolution of scalar orientational order parameters of cellulose nanofibers and bacteria associated with fluid-gel and isotropic-nematic transformations, showing how highly ordered active nematic fluids and gels evolve with time during biological-activity-driven, disorder-order transformation. With fluid and soft-gel nematics observed in a certain range of biological activity, this mesophase-exhibiting system is dubbed “biotropic,” analogously to thermotropic nematics that exhibit solely orientational order within a temperature range, promising technological and fundamental-science applications.

Many biological substances, like cholesterol, lipids, proteins, nucleic acids, microtubules, and viruses are known for their liquid crystalline (LC) phase behavior in either pure form or when in aqueous solutions and suspensions (1). The very first documented observations of LCs from well over a century ago utilized substances like derivatives of cholesterol extracted from living organisms (2, 3). Moreover, created within natural processes, LC-like structural organizations in tissues and key components of biological systems, like membranes, tend to endow complex functionality that remains superior to that of man-made materials (4, 5). Recognizing these important roles of LC-like organization, a biologist, D. Dervichian, once wrote “Liquid crystals stand between the isotropic liquid phase and the strongly organized state. Life stands between complete disorder, which is death and complete rigidity which is death again” (6). Understanding and recreating these LC-like nature’s elegant designs can revolutionize our ability of cost-effective mass-production of “living” materials and devices with attractive properties like low-cost, green manufacturing, self-healing and regeneration. However, how nature creates LC-like structures within out-of-equilibrium processes remains poorly understood despite of their diverse and ubiquitous observations (1–6).A particularly interesting form of a natural LC-like organization relates to bacterial biofilms, where birefringent domains of extracellular matrix and orientationally ordered bacteria have been reported for many microbiological systems (7–21). For example, Acetobacter xylinum (A. xylinum) bacteria biosynthesize cellulose filaments which can be organized in an orderly manner at the micrometer scales while exhibiting randomly aligned domains on larger scales within the three-dimensional (3D) reticulated biofilm (22–26). Limitations in controlling morphology and order within such biofilms hinder potential applications of bacterial cellulose-based materials (15–19). Here, we elucidate how a natural biological process leads to a spontaneous LC order of both cellulose nanofibers, which form an anisotropic extracellular matrix with strongly pronounced birefringence, and rod-like A. xylinum bacteria within a mesostructured active nematic system that can take both polydomain and monodomain structural forms. We probe orientationally ordered active nematic states in both aqueous environment and atop of solid agar surfaces. Using video-microscopy within different optical imaging modalities, we document the spontaneous emergence of nematic ordering in the course of biological activity. We find that directional feedings (and separately synthesized nematic hosts of colloidal nanocellulose used in our test experiments) break symmetry and lead to monodomain-like active nematic organizations, which we then use to quantitatively probe how orientational order of cellulose nanofibers and bacteria evolves with time. Holographic laser tweezers reveal onsets and details of formation of hydrogels with anisotropic networks of nanofibers. Characterization of distinct types of motions associated with A. xylinum’s nanocellulose production, as well as the estimation of order parameters (27, 28) in nematic and isotropic fluids and gels, reveals an active nematic system with disorder-to-order transformations driven by biological activity. Further, we show that such bacteria-made hydrogels can be readily converted to anisotropic aerogels and discuss how they may find diverse technological uses ranging from thermal insulation to scaffolding of biological tissue within LC-like matrices.     

An architecture for encoding sentence meaning in left mid-superior temporal cortex

Human brains flexibly combine the meanings of words to compose structured thoughts. For example, by combining the meanings of “bite,” “dog,” and “man,” we can think about a dog biting a man, or a man biting a dog. Here, in two functional magnetic resonance imaging (fMRI) experiments using multivoxel pattern analysis (MVPA), we identify a region of left mid-superior temporal cortex (lmSTC) that flexibly encodes “who did what to whom” in visually presented sentences. We find that lmSTC represents the current values of abstract semantic variables (“Who did it?” and “To whom was it done?”) in distinct subregions. Experiment 1 first identifies a broad region of lmSTC whose activity patterns (i) facilitate decoding of structure-dependent sentence meaning (“Who did what to whom?”) and (ii) predict affect-related amygdala responses that depend on this information (e.g., “the baby kicked the grandfather” vs. “the grandfather kicked the baby”). Experiment 2 then identifies distinct, but neighboring, subregions of lmSTC whose activity patterns carry information about the identity of the current “agent” (“Who did it?”) and the current “patient” (“To whom was it done?”). These neighboring subregions lie along the upper bank of the superior temporal sulcus and the lateral bank of the superior temporal gyrus, respectively. At a high level, these regions may function like topographically defined data registers, encoding the fluctuating values of abstract semantic variables. This functional architecture, which in key respects resembles that of a classical computer, may play a critical role in enabling humans to flexibly generate complex thoughts.Yesterday, the world’s tallest woman was serenaded by 30 pink elephants. The previous sentence is false, but perfectly comprehensible, despite the improbability of the situation it describes. It is comprehensible because the human mind can flexibly combine the meanings of individual words (“woman,” “serenade,” “elephants,” etc.) to compose structured thoughts, such as the meaning of the aforementioned sentence (1, 2). How the brain accomplishes this remarkable feat remains a central, but unanswered, question in cognitive science.Given the vast number of sentences we can understand and produce, it would be implausible for the brain to allocate individual neurons to represent each possible sentence meaning. Instead, it is likely that the brain employs a system for flexibly combining representations of simpler meanings to compose more complex meanings. By “flexibly,” we mean that the same meanings can be combined in many different ways to produce many distinct complex meanings. How the brain flexibly composes complex, structured meanings out of simpler ones is a matter of long-standing debate (3–10).At the cognitive level, theorists have held that the mind encodes sentence-level meaning by explicitly representing and updating the values of abstract semantic variables (3, 5) in a manner analogous to that of a classical computer. Such semantic variables correspond to basic, recurring questions of meaning such as “Who did it?” and “To whom was it done?” On such a view, the meaning of a simple sentence is partly represented by filling in these variables with representations of the appropriate semantic components. For example, “the dog bit the man” would be built out of the same semantic components as “the man bit the dog,” but with a reversal in the values of the “agent” variable (“Who did it?”) and the “patient” variable (“To whom was it done?”). Whether and how the human brain does this remains unknown.Previous research has implicated a network of cortical regions in high-level semantic processing. Many of these regions surround the left sylvian fissure (11–19), including regions of the inferior frontal cortex (13, 14), inferior parietal lobe (12, 20), much of the superior temporal sulcus and gyrus (12, 15, 21), and the anterior temporal lobes (17, 20, 22). Here, we describe two functional magnetic resonance imaging (fMRI) experiments aimed at understanding how the brain (in these regions or elsewhere) flexibly encodes the meanings of sentences involving an agent (“Who did it?”), an action (“What was done?”), and a patient (“To whom was it done?”).First, experiment 1 aims to identify regions that encode structure-dependent meaning. Here, we search for regions that differentiate between pairs of visually presented sentences, where these sentences convey different meanings using the same words (as in “man bites dog” and “dog bites man”). Experiment 1 identifies a region of left mid-superior temporal cortex (lmSTC) encoding structure-dependent meaning. Experiment 2 then asks how the lmSTC represents structure-dependent meaning. Specifically, we test the long-standing hypothesis that the brain represents and updates the values of abstract semantic variables (3, 5): here, the agent (“Who did it?”) and the patient (“To whom was it done?”). We search for distinct neural populations in lmSTC that encode these variables, analogous to the data registers of a computer (5).     

Decoupling of rotational and translational diffusion in supercooled colloidal fluids

We use confocal microscopy to directly observe 3D translational and rotational diffusion of tetrahedral clusters, which serve as tracers in colloidal supercooled fluids. We find that as the colloidal glass transition is approached, translational and rotational diffusion decouple from each other: Rotational diffusion remains inversely proportional to the growing viscosity whereas translational diffusion does not, decreasing by a much lesser extent. We quantify the rotational motion with two distinct methods, finding agreement between these methods, in contrast with recent simulation results. The decoupling coincides with the emergence of non-Gaussian displacement distributions for translation whereas rotational displacement distributions remain Gaussian. Ultimately, our work demonstrates that as the glass transition is approached, the sample can no longer be approximated as a continuum fluid when considering diffusion.Rapidly cooling a glass-forming liquid fundamentally changes the nature of fluid transport at a molecular scale (1–7). For a tracer in a continuum fluid, the translational and rotational diffusion coefficients D_T and D_R, respectively, depend on temperature T and viscosity η as D ∝ T/η. Therefore, the ratio D_T/D_R is a constant that is independent of both T and η. However, this relationship breaks down in the deeply supercooled regime near the glass transition, according to experiments with molecular glass formers and also molecular dynamics simulations (1–3, 8–14).Experiments with glass-forming materials find that rotational diffusion remains strongly coupled with viscosity, where D_R ∝ η⁻¹, whereas translational diffusion decouples, developing a fractional dependence on η where D_T ∝ η^−ξ with ξ < 1 (2, 8, 15). Near the glass transition, D_T can be enhanced by two orders of magnitude over what would be calculated from the material’s viscosity. The rotational diffusion coefficients from these experiments are inferred from measurements related to molecular rotations, and are evaluated using the “Debye model” due to an inability to directly observe molecular rearrangements in a material’s bulk (3, 8–10, 16, 17). This experimental limitation has inspired computational studies where diffusion can be calculated using the Debye model and also a complementary method, the “Einstein formulation,” which is more directly related to the trajectories of the diffusing objects. These simulations studied pure systems of water (9), ortho-terphenyl (10), and hard dumbbell particles (11). Intriguingly, the simulations found that decoupling depends qualitatively on the analysis method: They find rotational motion is enhanced over translational motion when quantified with the Einstein formulation, with the opposite being true in the Debye formulation. The results from these simulations raise the need for a critical reexamination of our current understanding of the relationship between translational and rotational diffusion, and only through direct observation can these differences be addressed (10). Unfortunately, there has been no direct experimental observation of diffusive decoupling in a 3D system which would allow for these findings to be tested.We use high-speed confocal microscopy to directly visualize the 3D translational and rotational motion of tetrahedral tracer colloidal clusters in a dense amorphous suspension of colloidal spheres. A glass transition occurs as the colloidal suspension’s volume fraction is increased above the value of ϕ_G ∼ 0.58 (18, 19). We observe that as the glass transition is approached from ϕ < ϕ_G, the long-time rotational diffusion of the tracers decreases proportionally with the bulk viscosity η, whereas long-time translational diffusion decreases by a much lesser extent, similar to observations made with molecular glasses (2, 8). Moreover, we quantify the rotational motion in several ways, and find that all rotational observations remain proportional to η⁻¹. Our results are in contrast with the aforementioned results from computer simulations (9–11), where the details depend on the analysis method, and rotational diffusion was either apparently enhanced or suppressed depending on the analysis. Our results persist regardless of the analysis used to characterize diffusion. Direct comparison between our results and those of computer simulations is problematic, given that they studied pure liquids whereas we study tracers; these differences are evaluated in the Discussion.Colloidal suspensions provide an insightful avenue for experimentally exploring the glass transition (18–22). The key control parameter is the volume fraction ϕ, rather than temperature. As ϕ increases, colloidal microspheres exhibit phase behavior that is in good agreement with the hard-sphere model (18, 19). Hard spheres are arguably the simplest system in which to study the most fundamental features of the glass transition. An important advantage of colloids is that individual particles can be followed in 3D using a confocal microscope, which permits direct observation of the complex dynamical processes of individual particles (22–25) that can be difficult to study with more conventional methods that average over many particles within the sample’s bulk (2, 16).Steric effects are key to understanding the colloidal glass transition: Particles cannot overlap one another, complicating their motion in a dense sample. For one sphere to move, its neighbors must move out of its way, and their neighbors must move out of their way, etc. This leads to large-scale rearrangements involving many particles (22, 25–27). In contrast, rotation of spheres is possible without colliding with neighboring particles. Rotation of optically anisotropic colloidal spheres has been studied (28–31). These rotations do slow near the colloidal glass transition, but due to hydrodynamic interactions rather than steric interactions. For this reason, in dense suspensions of spheres rotational diffusion is faster than translational diffusion (30); this is discussed further in Materials and Methods. The hydrodynamic slowing of rotational diffusion, while interesting in its own right, cannot speak to the question of slowing rotational diffusion in molecular glasses.Therefore, we use a dispersion of isolated nonspherical particles in a suspension of spherical particles. This is a simple physical model system in which to study rotational and translational diffusion near the glass transition. Our nonspherical tracer particles, developed through recent advances in colloidal science (32), are highly ordered clusters of colloidal particles (33). A confocal micrograph of one such cluster with corresponding 3D representations is shown in Fig. 1. The rotational motion of such clusters is hindered by collisions with neighboring spherical particles, and thus is a reasonable model of steric hindrances within molecular glass-forming systems. At short time scales, hydrodynamics are still expected to be important (30, 31); however, we focus on the long-time dynamics, for which the steric hindrance should be most significant (34–37).Open in a separate windowFig. 1.Visual representations of a colloidal tetrahedral cluster. Only the core of each particle is fluorescently labeled, surrounded by a blank undyed shell of PMMA, making each particle visually distinct from its clustered neighbors. (A) Composite, imaged using a confocal microscope and calculated by taking the mean of a 3D image. The composite images allow us to see through the cluster, where the overlap between multiple particles appears black. (B) Three-dimensional reconstruction. (C) Three-dimensional rendering of spheres at the centers of the particle coordinates, as determined by our tracking algorithms (38, 41). Sphere diameters are roughly equal to that of the fluorescent cores.With a recently developed means of tracking motion of such clusters (38), we are in a position to simultaneously study translational and rotational diffusion of anisotropic tracers in glassy and otherwise densely packed systems. Our system can be thought of as a 3D analog of samples used in very recent colloidal experiments, where rotational diffusion was studied in dense 2D samples of colloidal ellipsoids, with aspect ratios of ∼1.1 (39) and ∼6.0 (40). We follow the full 3D motion of our clusters, allowing us to observe rotations around any axis without any ambiguity, as discussed in Materials and Methods.     

Life cycle air quality impacts of conventional and alternative light-duty transportation in the United States

Commonly considered strategies for reducing the environmental impact of light-duty transportation include using alternative fuels and improving vehicle fuel economy. We evaluate the air quality-related human health impacts of 10 such options, including the use of liquid biofuels, diesel, and compressed natural gas (CNG) in internal combustion engines; the use of electricity from a range of conventional and renewable sources to power electric vehicles (EVs); and the use of hybrid EV technology. Our approach combines spatially, temporally, and chemically detailed life cycle emission inventories; comprehensive, fine-scale state-of-the-science chemical transport modeling; and exposure, concentration–response, and economic health impact modeling for ozone (O₃) and fine particulate matter (PM_2.5). We find that powering vehicles with corn ethanol or with coal-based or “grid average” electricity increases monetized environmental health impacts by 80% or more relative to using conventional gasoline. Conversely, EVs powered by low-emitting electricity from natural gas, wind, water, or solar power reduce environmental health impacts by 50% or more. Consideration of potential climate change impacts alongside the human health outcomes described here further reinforces the environmental preferability of EVs powered by low-emitting electricity relative to gasoline vehicles.Society is in the midst of a great effort to understand and mitigate anthropogenic greenhouse gas (GHG) emissions and their effects on the global climate (1–5). However, GHG damages are not the only environmental impact of human activities, and are often not even the largest. In transportation, for example, non-GHG air pollution damage externalities generally exceed those from climate change (6–8). Here, we explore the air quality impacts of several proposed transportation fuel interventions: liquid biofuels (9), electric vehicles (EVs) powered by conventional and alternative energy sources (3), biomass feedstocks to power EVs (10, 11), compressed natural gas (CNG) powered vehicles (5), and improved vehicle fuel economy.The air quality impacts of biofuels, transportation electrification, CNG vehicles, and improved fuel economy have been studied (refs. 7, 8, and 12–21; results are summarized in Table S1); our work advances prior research by combining estimates of life cycle emissions [i.e., emissions from production (“upstream”) and consumption (“tailpipe”) of the fuel] with an advanced air quality impact assessment. In addition, we incorporate greater spatial, temporal, and chemical detail than have prior research efforts. We also report non-GHG air quality life cycle impacts of biomass-powered EVs, which to our knowledge have not yet been described.We use a spatially and temporally explicit life cycle inventory model (22) to estimate total fuel supply chain air pollutant emissions for scenarios where 10% of US projected vehicle miles traveled in year 2020 are driven in 1 of 11 types of passenger cars: (i) conventional gasoline powered vehicles (abbreviation: “gasoline”); (ii) grid-independent hybrid EVs (“gasoline hybrid”); (iii) diesel powered light-duty vehicles (“diesel”); (iv) internal-combustion CNG vehicles (“CNG”); (v) vehicles powered by ethanol from corn grain through natural-gas–powered dry milling (“corn ethanol”); (vi) vehicles powered by cellulosic ethanol from corn stover (“stover ethanol”); and battery EVs (“EV”) powered by electricity from the following: (vii) the projected year 2020 US average electric generation mix (“EV grid average”); (viii) coal (“EV coal”); (ix) natural gas (“EV natural gas”); (x) the combustion of corn stover (“EV corn stover”); and (xi) wind turbines, dynamic water power, or solar power (“EV WWS”). Because year 2020 electric generation infrastructure is not predetermined, we explore a range of electricity technologies rather than attempting to predict future electrical generation and dispatch deterministically; our approach can inform transportation and electricity generation policies in tandem. Based on prior research, we assume that the difference among scenarios in emissions from manufacturing and disposal of vehicles and from upstream infrastructure is small relative to differences in vehicle operation emissions (8, 23, 24) with the exception of lithium ion EV battery production. To highlight battery-related impacts, we analyze them separately from fuel-related impacts.We use spatially and temporally explicit simulations, including a state-of-the-science mechanistic meteorology and chemical transport model, to estimate for each scenario the changes in annual-average concentrations of the regulated pollutants fine particulate matter (PM_2.5) and ground-level ozone (O₃). We use spatially explicit population data (25) and results from major epidemiological studies (26, 27) to estimate increases in mortalities attributable to each scenario. We estimate monetized externalities from mortalities using a value of statistical life (VSL) metric. Results are given next; methods are described thereafter.     

Physical evidence of predatory behavior in Tyrannosaurus rex

Feeding strategies of the large theropod, Tyrannosaurus rex, either as a predator or a scavenger, have been a topic of debate previously compromised by lack of definitive physical evidence. Tooth drag and bone puncture marks have been documented on suggested prey items, but are often difficult to attribute to a specific theropod. Further, postmortem damage cannot be distinguished from intravital occurrences, unless evidence of healing is present. Here we report definitive evidence of predation by T. rex: a tooth crown embedded in a hadrosaurid caudal centrum, surrounded by healed bone growth. This indicates that the prey escaped and lived for some time after the injury, providing direct evidence of predatory behavior by T. rex. The two traumatically fused hadrosaur vertebrae partially enclosing a T. rex tooth were discovered in the Hell Creek Formation of South Dakota.One of the most daunting tasks of paleontology is inferring the behavior and feeding habits of extinct organisms. Accurate reconstruction of the lifestyle of extinct animals is dependent on the fossil evidence and its interpretation is most confidently predicated on analogy with modern counterparts (1–6). This challenge to understanding the lifestyle of extinct animals is exemplified by the controversy over the feeding behavior of the Late Cretaceous theropod Tyrannosaurus rex (3, 7–17). Although predation and scavenging have often been suggested as distinct feeding behavior alternatives (3, 7–9, 11–17), these terms merit semantic clarification. In this study, predation is considered a subset of feeding behavior, by which any species kills what it eats. Although the term “predator” is used to distinguish such animals from obligate scavengers, it does not imply that the animal did not also scavenge.Ancient diets can be readily reconstructed on the basis of the available evidence, although their derivation (e.g., predation or scavenging behavior) often remains elusive. Speculation as to dinosaur predation has ranged from inferences based on skeletal morphology, ichnofossils such as bite marks, coprolites, stomach contents, and trackways and, by more rarely, direct predator–prey skeletal associations (3, 4, 18–23).Direct evidence of predation in nonavian dinosaurs other than tyrannosaurids has been observed in rare instances, such as the Deinonychus–Tenontosaurus kill site of the Cloverly Formation where the remains of both were found in close association along with shed teeth (9, 24), and the “fighting dinosaurs” from the Gobi Desert, in which a Velociraptor and Protoceratops were found locked in mortal combat (9, 17). The evidence on tyrannosaurids is more limited. Putative stomach contents, such as partially digested juvenile hadrosaur bones, have been reported in association with tyrannosaurid remains (3, 12, 18). This latter instance only represents physical evidence of the last items consumed before the animal’s death, an indicator of diet but not behavior.Mass death assemblages of ornithischians frequently preserve shed theropod teeth (6, 22, 24). Lockley et al. (23) suggest such shed teeth are evidence of scavenging behavior. It is widely argued that T. rex procured food through obligate scavenging rather than hunting (11, 14, 25–27) despite the fact that there is currently no modern analog for such a large bodied obligate scavenger (26). Horner (25) argued that T. rex was too slow to pursue and capture prey items (14) and that large theropods procured food solely through scavenging, rather than hunting (11, 25). Horner also suggested that the enlarged olfactory lobes in T.rex were characteristic of scavengers (25). More recent studies (28, 29) determined the olfactory lobes of modern birds are “poorly developed,” inferring that enlarged olfactory lobes in T. rex are actually a secondary adaptation for predation navigation “to track mobile, dispersed prey” (30). T. rex has a calculated bite force stronger than that of any other terrestrial predator (7), between 35,000 and 57,000 Newtons (30, 31), and possible ambulatory speeds between 20 and 40 kph (7, 15, 16), documenting that it had the capability to pursue and kill prey items.Healed injuries on potential prey animals provide the most unequivocal evidence of survival of a traumatic event (e.g., predation attempt) (3, 32, 33), and several reports attribute such damage to T. rex (4, 17, 19, 20). These include broken and healed proximal caudal vertebral dorsal spines in Edmontosaurus (17) and healed cranial lesions in Triceratops (4, 19). Although the presence of healed injuries demonstrates that an animal lived long enough after the attack to create new bone at the site of the damage (a rare occurrence in the fossil record) (19), the healing usually obliterates any clear signature linking the injury to a specific predator. Bite traces (e.g., raking tooth marks on bone and puncture wounds in the bones of possible prey animals) attributed to T. rex (2, 4, 19) are ambiguous, because the damage inflicted upon an animal during and after a successful hunt mirrors feeding during scavenging. This makes distinction between the two modes of food acquisition virtually impossible with such evidence (3, 34–38).Tooth marks, reported from dinosaur bone-bearing strata worldwide (e.g., 2–4, 8, 19, 20, 39, 40), are further direct evidence of theropod feeding behavior, attributed by some to specific theropod groups (2, 4, 19, 20). Happ (19) and Carpenter (17) identified theropods to family and genus by matching spaces to parallel marks (traces) with intertooth distance. Happ (19) described opposing conical depressions on a left supraorbital Triceratops horn that was missing its distal third (tip), attributing them to a bite by either a T. rex or a crocodilian. Happ (19) stated that the spacing of the parallel marks present on the left squamosal of the same individual matched the intertooth distance of tyrannosaurids. The presence of periosteal reaction documents healing. This contrasts with the report by Farlow and Holtz (3) and again by Hone and Rauhut (20) of the same Hypacrosaurus fibula containing a superficially embedded theropod tooth. Absence of bone reaction precludes confident attribution to predation.Two coalesced hadrosaur (compare with Edmontosaurus annectens) caudal vertebrae were discovered in the Hell Creek Formation of Harding County, South Dakota (40). Archosaur fauna identified in this site include crocodiles, dinosaurs, and birds (41). Physical evidence of dental penetration and extensive infection (osteomylitis) of the fused vertebral centra and healing (bone overgrowth) document an unsuccessful attack by a large predator. A tooth crown was discovered within the wound, permitting identification of the predator as T. rex. This is unambiguous evidence that T. rex was an active predator, fulfilling the criteria that Farlow and Holtz (3) advanced. As T. rex comprises between 1% and 16% of the Upper Cretaceous dinosaurian fauna in Western North America (41–45), its status as a predator or obligate scavenger is nontrivial and could have significant implications for paleoecological reconstructions of that time period. The present contribution provides unique information demonstrating the ecological role for T. rex as that of an active predator. Despite this documentation of predatory behavior by T. rex, we do not make the argument that T. rex was an obligate predator. Like most modern large predators (27, 45) it almost certainly did also scavenge carcasses (9, 16).     

Obstacles to integrated pest management adoption in developing countries

Despite its theoretical prominence and sound principles, integrated pest management (IPM) continues to suffer from anemic adoption rates in developing countries. To shed light on the reasons, we surveyed the opinions of a large and diverse pool of IPM professionals and practitioners from 96 countries by using structured concept mapping. The first phase of this method elicited 413 open-ended responses on perceived obstacles to IPM. Analysis of responses revealed 51 unique statements on obstacles, the most frequent of which was “insufficient training and technical support to farmers.” Cluster analyses, based on participant opinions, grouped these unique statements into six themes: research weaknesses, outreach weaknesses, IPM weaknesses, farmer weaknesses, pesticide industry interference, and weak adoption incentives. Subsequently, 163 participants rated the obstacles expressed in the 51 unique statements according to importance and remediation difficulty. Respondents from developing countries and high-income countries rated the obstacles differently. As a group, developing-country respondents rated “IPM requires collective action within a farming community” as their top obstacle to IPM adoption. Respondents from high-income countries prioritized instead the “shortage of well-qualified IPM experts and extensionists.” Differential prioritization was also evident among developing-country regions, and when obstacle statements were grouped into themes. Results highlighted the need to improve the participation of stakeholders from developing countries in the IPM adoption debate, and also to situate the debate within specific regional contexts.Feeding the 9,000 million people expected to inhabit Earth by 2050 will present a constant and significant challenge in terms of agricultural pest management (1–3). Despite a 15- to 20-fold increase in pesticide use since the 1960s, global crop losses to pests—arthropods, diseases, and weeds—have remained unsustainably high, even increasing in some cases (4). These losses tend to be highest in developing countries, averaging 40–50%, compared with 25–30% in high-income countries (5). Alarmingly, crop pest problems are projected to increase because of agricultural intensification (4, 6), trade globalization (7), and, potentially, climate change (8).Since the 1960s, integrated pest management (IPM) has become the dominant crop protection paradigm, being endorsed globally by scientists, policymakers, and international development agencies (2, 9–15). The definitions of IPM are numerous, but all involve the coordinated integration of multiple complementary methods to suppress pests in a safe, cost-effective, and environmentally friendly manner (9, 11). These definitions also recognize IPM as a dynamic process in terms of design, implementation, and evaluation (11). In practice, however, there is a continuum of interpretations of IPM (e.g., refs. 14, 16, 17), but bounded by those that emphasize pesticide management (i.e., “tactical IPM”) and those that emphasize agroecosystem management (i.e., “strategic IPM,” also known as “ecologically based pest management”) (16, 18, 19). Despite apparently solid conceptual grounding and substantial promotion by the aforementioned groups, IPM has a discouragingly poor adoption record, particularly in developing-country settings (9, 10, 15–23), raising questions over its applicability as it is presently conceived (15, 16, 22, 24).The possible reasons behind the developing countries’ poor adoption of IPM have been the subject of considerable discussion since the 1980s (9, 15, 16, 22, 25–31), but this debate has been notable for the limited direct involvement from developing-country stakeholders. Most of the literature exploring poor adoption of IPM in the developing world has originated in the developed world (e.g., refs. 15, 16, 22). An international workshop, entitled “IPM in Developing Countries,” was held at the Pontificia Universidad Católica del Ecuador (PUCE) from October 31 to November 3, 2011. Poor IPM adoption spontaneously became a central discussion point, creating an opportunity to address the apparent participation bias in the IPM adoption debate.It was therefore decided to explore the topic further by eliciting and mapping the opinions of a large and diverse pool of IPM professionals and practitioners from around the world, including many based in developing countries. The objective was to generate and prioritize a broad list of hypotheses to explain poor IPM adoption in developing-country agriculture. We also wanted to explore differences as influenced by respondents’ characteristics, particularly their region of practice. To achieve these objectives, we used structured concept mapping (32), an empirical survey method often used to quantify and give thematic structure to open-ended opinions (33).We know of only one other similar study that characterizes obstacles to IPM. It was based on the structured responses of 153 experts, all from high-income countries (30). Our survey was designed to progress from unstructured to structured responses, and to reach a much larger and diverse pool of participants, particularly those from the “Global South.” Considering that the vast majority of farmers live in developing countries (34), it would seem imperative that the voices from this region be heard.     

From the Cover: A holistic picture of Austronesian migrations revealed by phylogeography of Pacific paper mulberry

The peopling of Remote Oceanic islands by Austronesian speakers is a fascinating and yet contentious part of human prehistory. Linguistic, archaeological, and genetic studies have shown the complex nature of the process in which different components that helped to shape Lapita culture in Near Oceania each have their own unique history. Important evidence points to Taiwan as an Austronesian ancestral homeland with a more distant origin in South China, whereas alternative models favor South China to North Vietnam or a Southeast Asian origin. We test these propositions by studying phylogeography of paper mulberry, a common East Asian tree species introduced and clonally propagated since prehistoric times across the Pacific for making barkcloth, a practical and symbolic component of Austronesian cultures. Using the hypervariable chloroplast ndhF-rpl32 sequences of 604 samples collected from East Asia, Southeast Asia, and Oceanic islands (including 19 historical herbarium specimens from Near and Remote Oceania), 48 haplotypes are detected and haplotype cp-17 is predominant in both Near and Remote Oceania. Because cp-17 has an unambiguous Taiwanese origin and cp-17–carrying Oceanic paper mulberries are clonally propagated, our data concur with expectations of Taiwan as the Austronesian homeland, providing circumstantial support for the “out of Taiwan” hypothesis. Our data also provide insights into the dispersal of paper mulberry from South China “into North Taiwan,” the “out of South China–Indochina” expansion to New Guinea, and the geographic origins of post-European introductions of paper mulberry into Oceania.The peopling of Remote Oceania by Austronesian speakers (hereafter Austronesians) concludes the last stage of Neolithic human expansion (1–3). Understanding from where, when, and how ancestral Austronesians bridged the unprecedentedly broad water gaps of the Pacific is a fascinating and yet contentious subject in anthropology (1–8). Linguistic, archaeological, and genetic studies have demonstrated the complex nature of the process, where different components that helped to shape Lapita culture in Near Oceania each have their own unique history (1–3). Important evidence points to Taiwan as an Austronesian ancestral homeland with a more distant origin in South China (S China) (3, 4, 9–12), whereas alternative models suggest S China to North Vietnam (N Vietnam) (7) or a Southeast Asian (SE Asian) origin based mainly on human genetic data (5). The complexity of the subject is further manifested by models theorizing how different spheres of interaction with Near Oceanic indigenous populations during Austronesian migrations have contributed to the origin of Lapita culture (1–3), ranging from the “Express Train” model, assuming fast migrations from S China/Taiwan to Polynesia with limited interaction (4), to the models of “Slow Boat” (5) or “Voyaging Corridor Triple I,” in which “Intrusion” of slower Austronesian migrations plus the “Integration” with indigenous Near Oceanic cultures had resulted in the “Innovation” of the Lapita cultural complex (2, 13).Human migration entails complex skills of organization and cultural adaptations of migrants or colonizing groups (1, 3). Successful colonization to resource-poor islands in Remote Oceania involved conscious transport of a number of plant and animal species critical for both the physical survival of the settlers and their cultural transmission (14). In the process of Austronesian expansion into Oceania, a number of animals (e.g., chicken, pigs, rats, and dogs) and plant species (e.g., bananas, breadfruit, taro, yam, paper mulberry, etc.), either domesticated or managed, were introduced over time from different source regions (3, 8, 15). Although each of these species has been shown to have a different history (8), all these “commensal” species were totally dependent upon humans for dispersal across major water gaps (6, 8, 16). The continued presence of these species as living populations far outside their native ranges represents legacies of the highly skilled seafaring and navigational abilities of the Austronesian voyagers.Given their close association to and dependence on humans for their dispersal, phylogeographic analyses of these commensal species provide unique insights into the complexities of Austronesian expansion and migrations (6, 8, 17). This “commensal approach,” first used to investigate the transport of the Pacific rat Rattus exulans (6), has also been applied to other intentionally transported animals such as pigs, chickens, and the tree snail Partula hyalina, as well as to organisms transported accidentally, such as the moth skink Lipinia noctua and the bacterial pathogen Helicobacter pylori (see refs. 2, 8 for recent reviews).Ancestors of Polynesian settlers transported and introduced a suite of ∼70 useful plant species into the Pacific, but not all of these reached the most isolated islands (15). Most of the commensal plants, however, appear to have geographic origins on the Sahul Plate rather than being introduced from the Sunda Plate or East Asia (16). For example, Polynesian breadfruit (Artocarpus altilis) appears to have arisen over generations of vegetative propagation and selection from Artocarpus camansi that is found wild in New Guinea (18). Kava (Piper methysticum), cultivated for its sedative and anesthetic properties, is distributed entirely to Oceania, from New Guinea to Hawaii (16). On the other hand, ti (Cordyline fruticosa), also a multifunctional plant in Oceania, has no apparent “native” distribution of its own, although its high morphological diversity in New Guinea suggests its origin there (19). Other plants have a different history, such as sweet potato, which is of South American origin and was first introduced into Oceania in pre-Columbian times and secondarily transported across the Pacific by Portuguese and Spanish voyagers via historically documented routes from the Caribbean and Mexico (17).Of all commensal species introduced to Remote Oceania as part of the “transported landscapes” (1), paper mulberry (Broussonetia papyrifera; also called Wauke in Hawaii) is the only species that has a temperate to subtropical East Asian origin (15, 20, 21). As a wind-pollinated, dioecious tree species with globose syncarps of orange–red juicy drupes dispersed by birds and small mammals, paper mulberry is common in China, Taiwan, and Indochina, growing and often thriving in disturbed habitats (15, 20, 21). Because of its long fiber and ease of preparation, paper mulberry contributed to the invention of papermaking in China in A.D. 105 and continues as a prime source for high-quality paper (20, 21). In A.D. 610, this hardy tree species was introduced to Japan for papermaking (21). Subsequently it was also introduced to Europe and the United States (21). Paper mulberry was introduced to the Philippines for reforestation and fiber production in A.D. 1935 (22). In these introduced ranges, paper mulberry often becomes naturalized and invasive (20–22). In Oceania, linguistic evidence suggests strongly an ancient introduction of paper mulberry (15, 20); its propagation and importance across Remote Oceanic islands were well documented in Captain James Cook’s first voyage as the main material for making barkcloth (15, 20).Barkcloth, generally known as tapa (or kapa in Hawaii), is a nonwoven fabric used by prehistoric Austronesians (15, 21). Since the 19th century, daily uses of barkcloth have declined and were replaced by introduced woven textiles; however, tapa remains culturally important for ritual and ceremony in several Pacific islands such as Tonga, Fiji, Samoa, and the SE Asian island of Sulawesi (23). The symbolic status of barkcloth is also seen in recent revivals of traditional tapa making in several Austronesian cultures such as Taiwan (24) and Hawaii (25). To make tapa, the inner bark is peeled off and the bark pieces are expanded by pounding (20, 21, 23). Many pieces of the bark are assembled and felted together via additional poundings to create large textiles (23). The earliest stone beaters, a distinctive tool used for pounding bark fiber, were excavated in S China from a Late Paleolithic site at Guangxi dating back to ∼8,000 y B.P. (26) and from coastal Neolithic sites in the Pearl River Delta dating back to 7,000 y B.P. (27), providing the earliest known archaeological evidence for barkcloth making. Stone beaters dated to slightly later periods have also been excavated in Taiwan (24), Indochina, and SE Asia, suggesting the diffusion of barkcloth culture to these regions (24, 27). These archaeological findings suggest that barkcloth making was invented by Neolithic Austric-speaking peoples in S China long before Han-Chinese influences, which eventually replaced proto-Austronesian language as well as culture (27).In some regions (e.g., Philippines and Solomon Islands), tapa is made of other species of the mulberry family (Moraceae) such as breadfruit and/or wild fig (Ficus spp.); however, paper mulberry remains the primary source of raw material to produce the softest and finest cloth (20, 23). Before its eradication and extinction from many Pacific islands due to the decline of tapa culture, paper mulberry was widely grown across Pacific islands inhabited by Austronesians (15, 20). Both the literature (15, 20) and our own observations (28–30) indicate that extant paper mulberry populations in Oceania are only found in cultivation or as feral populations in abandoned gardens as on Rapa Nui (Easter Island), with naturalization only known from the Solomon Islands (20). For tapa making, its stems are cut and harvested before flowering, and as a majority of Polynesian-introduced crops (16), paper mulberry is propagated clonally by cuttings or root shoots (15, 20), reducing the possibility of fruiting and dispersal via seeds. The clonal nature of the Oceanic paper mulberry has been shown by the lack of genetic variability in nuclear internal transcribed spacer (ITS) DNA sequences (31). With a few exceptions (30), some authors suggest that only male trees of paper mulberry were introduced to Remote Oceania in prehistoric time (15, 20). Furthermore, because paper mulberry has no close relative in Near and Remote Oceania (20), the absence of sexual reproduction precludes the possibility of introgression and warrants paper mulberry as an ideal commensal species to track Austronesian migrations (6, 30).To increase our understanding of the prehistoric Austronesian expansion and migrations, we tracked geographic origins of Oceanic paper mulberry, the only Polynesian commensal plant likely originating in East Asia, using DNA sequence variation of the maternally inherited (32) and hypervariable (SI Text) chloroplast ndhF-rpl32 intergenic spacer (33). We sampled broadly in East Asia (Taiwan, S China, and Japan) and SE Asia (Indochina, the Philippines, and Sulawesi) as well as Oceanic islands where traditional tapa making is still practiced. Historical herbarium collections (A.D. 1899–1964) of Oceania were also sampled to strengthen inferences regarding geographic origins of Oceanic paper mulberry. The employment of ndhF-rpl32 sequences and expanded sampling greatly increased phylogeographic resolution not attainable in a recent study (31) using nuclear ITS sequences (also see SI Text and Fig. S1) and intersimple sequence repeat (ISSR) markers with much smaller sampling.Open in a separate windowFig. S1.ITS haplotype network (n = 17, A–Q) and haplotype distribution and frequency. The haplotype network was reconstructed using TCS (34), with alignment gaps treated as missing data. The sizes of the circles and pie charts are proportional to the frequency of the haplotype (shown in parentheses). Squares denote unique haplotypes (haplotype found only in one individual).     

Decoding the information structure underlying the neural representation of concepts

The nature of the representational code underlying conceptual knowledge remains a major unsolved problem in cognitive neuroscience. We assessed the extent to which different representational systems contribute to the instantiation of lexical concepts in high-level, heteromodal cortical areas previously associated with semantic cognition. We found that lexical semantic information can be reliably decoded from a wide range of heteromodal cortical areas in the frontal, parietal, and temporal cortex. In most of these areas, we found a striking advantage for experience-based representational structures (i.e., encoding information about sensory-motor, affective, and other features of phenomenal experience), with little evidence for independent taxonomic or distributional organization. These results were found independently for object and event concepts. Our findings indicate that concept representations in the heteromodal cortex are based, at least in part, on experiential information. They also reveal that, in most heteromodal areas, event concepts have more heterogeneous representations (i.e., they are more easily decodable) than object concepts and that other areas beyond the traditional “semantic hubs” contribute to semantic cognition, particularly the posterior cingulate gyrus and the precuneus.

The capacity for conceptual knowledge is arguably one of the most defining properties of human cognition, and yet it is still unclear how concepts are represented in the brain. Recent developments in functional neuroimaging and computational linguistics have sparked renewed interest in elucidating the information structures and neural circuits underlying concept representation (1–5). Attempts to characterize the representational code for concepts typically involve information structures based on three qualitatively distinct types of information, namely, taxonomic, experiential, and distributional information. As the term implies, a taxonomic information system relies on category membership and intercategory relations. Our tendency to organize objects, events, and experiences into discrete categories has led most authors—dating back at least to Plato (6)—to take taxonomic structure as the central property of conceptual knowledge (7). The taxonomy for concepts is traditionally seen as a hierarchically structured network, with basic-level categories (e.g., “apple,” “orange”) grouped into superordinate categories (e.g., “fruit,” “food”) and subdivided into subordinate categories (e.g., “Gala apple,” “tangerine”) (8). A prominent account in cognitive science maintains that such categories are represented in the mind/brain as purely symbolic entities, whose semantic content and usefulness derive primarily from how they relate to each other (9, 10). Such representations are seen as qualitatively distinct from the sensory-motor processes through which we interact with the world, much like the distinction between software and hardware in digital computers.An experiential representational system, on the other hand, encodes information about the experiences that led to the formation of particular concepts. It is motivated by a view, often referred to as embodied, grounded, or situated semantics, in which concepts arise primarily from generalization over particular experiences, as information originating from the various modality-specific systems (e.g., visual, auditory, tactile, motor, affective) is combined and re-encoded into progressively more schematic representations that are stored in memory. Since, in this view, there is a degree of continuity between conceptual and modality-specific systems, concept representations are thought to reflect the structure of the perceptual, affective, and motor processes involved in those experiences (11–14).Finally, distributional information pertains to statistical patterns of co-occurrence between lexical concepts (i.e., concepts that are widely shared within a population and denoted by a single word) in natural language usage. As is now widely appreciated, these co-occurrence patterns encode a substantial amount of information about word meaning (15–17). Although word co-occurrence patterns primarily encode contextual associations, such as those connecting the words “cow,” “barn,” and “farmer,” semantic similarity information is indirectly encoded since words with similar meanings tend to appear in similar contexts (e.g., “cow” and “horse,” “pencil” and “pen”). This has led some authors to propose that concepts may be represented in the brain, at least in part, in terms of distributional information (15, 18).Whether, and to what extent, each of these types of information plays a role in the neural representation of conceptual knowledge is a topic of intense research and debate. A large body of evidence has emerged from behavioral studies, functional neuroimaging experiments, and neuropsychological assessments of patients with semantic deficits, with results typically interpreted in terms of taxonomic (19–24), experiential (13, 25–34), or distributional (2, 3, 5, 35, 36) accounts. However, the extent to which each of these representational systems plays a role in the neural representation of conceptual knowledge remains controversial (23, 37, 38), in part, because their representations of common lexical concepts are strongly intercorrelated. Patterns of word co-occurrence in natural language are driven in part by taxonomic and experiential similarities between the concepts to which they refer, and the taxonomy of natural categories is systematically related to the experiential attributes of the exemplars (39–41). Consequently, the empirical evidence currently available is unable to discriminate between these representational systems.Several computational models of concept representation have been proposed based on these structures. While earlier models relied heavily on hierarchical taxonomic structure (42, 43), more recent proposals have emphasized the role of experiential and/or distributional information (34, 44–46). The model by Chen and colleagues (45), for example, showed that graded taxonomic structure can emerge from the statistical coherent covariation found across experiences and exemplars without explicitly coding such taxonomic information per se. Other models propose that concepts may be formed through the combination of experiential and distributional information (44, 46), suggesting a dual representational code akin to Paivio’s dual coding theory (47).We investigated the relative contribution of each representational system by deriving quantitative predictions from each system for the similarity structure of a large set of concepts and then using representational similarity analysis (RSA) with high-resolution functional MRI (fMRI) to evaluate those predictions. Unlike the more typical cognitive subtraction technique, RSA focuses on the information structure of the pattern of neural responses to a set of stimuli (48). For a given stimulus set (e.g., words), RSA assesses how well the representational similarity structure predicted by a model matches the neural similarity structure observed from fMRI activation patterns (Fig. 1). This allowed us to directly compare, in quantitative terms, predictions derived from the three representational systems.Open in a separate windowFig. 1.Representational similarity analysis. (A) An fMRI activation map was generated for each concept presented in the study, and the activation across voxels was reshaped as a vector. (B) The neural RDM for the stimulus set was generated by computing the dissimilarity between these vectors (1 − correlation) for every pair of concepts. (C) A model-based RDM was computed from each model, and the similarity between each model’s RDM and the neural RDM was evaluated via Spearman correlation. (D) Anatomically defined ROIs. The dashed line indicates the boundary where temporal lobe ROIs were split into anterior and posterior portions (see main text for acronyms). (E) Cortical areas included in the functionally defined semantic network ROI (49).     

Quasicrystalline tilings with nematic colloidal platelets

Complex nematic fluids have the remarkable capability for self-assembling regular colloidal structures of various symmetries and dimensionality according to their micromolecular orientational order. Colloidal chains, clusters, and crystals were demonstrated recently, exhibiting soft-matter functionalities of robust binding, spontaneous chiral symmetry breaking, entanglement, shape-driven and topological driven assembly, and even memory imprinting. However, no quasicrystalline structures were found. Here, we show with numerical modeling that quasicrystalline colloidal lattices can be achieved in the form of original Penrose P1 tiling by using pentagonal colloidal platelets in layers of nematic liquid crystals. The tilings are energetically stabilized with binding energies up to 2500 k_BT for micrometer-sized platelets and further allow for hierarchical substitution tiling, i.e., hierarchical pentagulation. Quasicrystalline structures are constructed bottom-up by assembling the boat, rhombus, and star maximum density clusters, thus avoiding other (nonquasicrystalline) stable or metastable configurations of platelets. Central to our design of the quasicrystalline tilings is the symmetry breaking imposed by the platelet shape and the surface anchoring conditions at the colloidal platelets, which are misaligning and asymmetric over two perpendicular mirror planes. Finally, the design of the quasicrystalline tilings as platelets in nematic liquid crystals is inherently capable of a continuous variety of length scales of the tiling, ranging over three orders of magnitude in the typical length (from to ), which could allow for the design of quasicrystalline photonics at multiple frequency ranges.Quasicrystals are aperiodic crystalline materials, distinguished by noncrystallographic rotational symmetry of fivefold, sevenfold, eightfold, and higher rotational symmetry axes (1–3). These symmetries are typically found in atomic lattices of distinct metallic alloys (1, 4). However, more recently, a unique class of soft-matter quasicrystals is emerging (5–8), where the basic building blocks are not single atoms but rather macromolecules (9, 10), copolymers (11), molecular liquid crystalline fields (12, 13), or colloidal particles (14, 15). Two-dimensional realizations of materials with quasicrystalline symmetries are quasicrystalline tilings (2, 16, 17). In tilings, the structures of polygons or platelets—tiles—cover an area in complex patterns, typically following geometric rules. Tilings with fivefold (18, 19), sevenfold (20), eightfold (21), ninefold (22), tenfold (23), twelvefold (24), and other (25) quasicrystalline symmetries were realized, demonstrating analogous ordering mechanisms as in quasicrystals (26, 27). These ordering mechanisms and the formation dynamics were particularly explored in quasicrystalline colloidal monolayers stabilized by interfering laser beams (28, 29).Nematic liquid crystals are fluids with molecular orientational order, called the director field, and it is by designing the profiles of this field that colloidal structures of various functionalities can be self-assembled. The self-assembly is based on effective structural forces emerging between the particles (typically ∼1−10 pN for micrometer-sized particles), caused by the inhomogeneous and anisotropic director profiles imposed by the particle surfaces or general shapes (30). Already simple spherical colloidal particles were shown to self-assemble into chains (31), clusters (32), 2D (33), and 3D colloidal crystals (34, 35). A specifically strong way to affect the self-assembly is by shape-controlled colloidal interactions (36–38) and faceted colloidal particles (39), where the shape of the particles determines the interparticle potentials and the symmetry of the structures (40) as well as their rotational dynamics (41). However, despite using particles with geometrically quasicrystalline symmetry, e.g., pentagonal or heptagonal platelets, generically, structures with strictly crystalline symmetry are found (36, 40, 42). It was shown that such platelets effectively lose their faceted nature and behave as dipoles and quadrupoles in the distortion field of the fluid (36), exactly as already known for spherical particles. More generally, therefore, finding relations between the inherent symmetry of the building blocks and the actual symmetry of the structures made from these building blocks presents a far-reaching challenge in the design of advanced quasicrystalline and crystalline materials.In this paper, we combine the energy-based concept of structural forces in complex nematic fluids and geometry of building blocks to self-assemble quasicrystalline Penrose P1 tiling of pentagonal colloidal platelets. More specifically, we consider submicrometer-sized platelets whose top and bottom surfaces are treated to impose different alignment directions on the director field (Fig. 1), which generates interparticle potentials compatible with the quasicrystalline fivefold symmetry. The platelets are pre-positioned according to the symmetry of the Penrose lattice in thin nematic cells, typically ∼5 times platelet thickness, whose surfaces are taken to yield strong uniform planar anchoring along a common direction (denoted as the rubbing direction), and then relaxed to equilibrium. Such an approach creates strongly bound equilibrium platelet structures, which, however, do not necessarily correspond to the global ground states of the system. The quasicrystalline assembly is robust over multiple length scales of the tiling pattern, and allows a hierarchy of scales, i.e., quasicrystalline tilings at one scale, with smaller-scale (quasicrystalline) substitutions. Our main methodological approach is phenomenological numerical modeling based on the minimization of the Landau-de Gennes free energy (see SI Text and Theory and Method), which proves particularly efficient exactly in strongly confined systems with multiple particles, like tilings, and which can give full quantitative or qualitative agreement with experiments (36, 40). Finally, experimental strategies for the self-assembly of Penrose nematic colloidal tilings are proposed, suggesting optical fields or quasicrystalline seed colloidal particles as possible approaches.Open in a separate windowFig. 1.Colloidal pentagonal platelets as prototiles. Uniform planar anchoring imposed (A) at an angle 36° on the top surface and (B) at an angle 126° on the bottom surface. (C) Faceted surface generates surface topological defects (dark green) in the director field along the edges of the platelets. Molecular orientational profile—the director—is shown in black; defects are visualized as isosurfaces of nematic degree of order . (D) Rotation potential as function of the platelet angle with respect to the rubbing direction exhibits a minimum at 0° and 72°. (E) Pair interaction potential F of two pentagonal prototiles. Note free energy minimum regions 1, 2, and 3, which lead to the formation of equilibirum pair structures. Rubbing direction at cell walls is at an angle of 72° with respect to X (see inset). (F−H) The three equilibrium platelet pair structures, as corresponding to the free energy minima. Blue double-headed arrows in F−H indicate the imposed anchoring direction on top surface of both considered platelets.     

Definition of a saxitoxin (STX) binding code enables discovery and characterization of the anuran saxiphilin family

American bullfrog (Rana castesbeiana) saxiphilin (RcSxph) is a high-affinity “toxin sponge” protein thought to prevent intoxication by saxitoxin (STX), a lethal bis-guanidinium neurotoxin that causes paralytic shellfish poisoning (PSP) by blocking voltage-gated sodium channels (Na_Vs). How specific RcSxph interactions contribute to STX binding has not been defined and whether other organisms have similar proteins is unclear. Here, we use mutagenesis, ligand binding, and structural studies to define the energetic basis of Sxph:STX recognition. The resultant STX “recognition code” enabled engineering of RcSxph to improve its ability to rescue Na_Vs from STX and facilitated discovery of 10 new frog and toad Sxphs. Definition of the STX binding code and Sxph family expansion among diverse anurans separated by ∼140 My of evolution provides a molecular basis for understanding the roles of toxin sponge proteins in toxin resistance and for developing novel proteins to sense or neutralize STX and related PSP toxins.

Saxitoxin (STX), one of the most potent nonpeptidyl neurotoxins, blocks the bioelectrical signals in nerve and muscle required for life by inhibiting select voltage-gated sodium channel (Na_V) isoforms (1–3). Cyanobacteria and dinoflagellate species associated with oceanic red tides produce this bis-guanidinium small molecule and its congeners, whose accumulation in seafood can cause paralytic shellfish poisoning (PSP), a commercial fishing and public health hazard of growing importance due to climate change (1, 3–5). Its lethality has also earned STX the unusual distinction of being the only marine toxin declared a chemical weapon (1, 3). Select vertebrates, particularly frogs, resist STX poisoning (6–9), a property that is thought to rely on the ability of the soluble “toxin sponge” protein saxiphilin (Sxph) to sequester STX (8, 9). Recent structural studies (10) defined the molecular architecture of the American bullfrog [Rana (Lithobates) castesbeiana] Sxph (RcSxph) (8, 11–14) showing that this 91-kDa soluble, transferrin-related protein from frog heart and plasma has a single, high-affinity STX binding site on its C lobe. Remarkably, even though RcSxph and Na_Vs are unrelated, both engage STX through similar types of interactions (10). This structural convergence raises the possibility that determination of the factors that underlie the high-affinity Sxph:STX interaction could provide a generalizable molecular recognition code for STX that would enable the identification or engineering of STX binding sites in natural and designed proteins.To characterize RcSxph:STX interactions in detail, we developed a suite of assays comprising thermofluor (TF) measurements of ligand-induced changes in RcSxph stability, fluorescence polarization (FP) binding to a fluorescein-labeled STX, and isothermal titration calorimetry (ITC). We paired these assays with a scanning mutagenesis strategy (15, 16) to dissect the energetic contributions of RcSxph STX binding pocket residues. These studies show that the core RcSxph STX recognition code comprises two “hot spot” triads. One engages the STX tricyclic bis-guanidinium core through a pair of carboxylate groups and a cation–π interaction (17) in a manner that underscores the convergent STX recognition strategies shared by RcSxph and Na_Vs (17–22). The second triad largely interacts with the C13 carbamate group of STX and is the site of interactions that can enhance STX binding affinity and the ability of RcSxph to act as a “toxin sponge” that can reverse the effects of STX inhibition of Na_Vs (8, 9).Although Sxph-like STX binding activity has been reported in extracts from diverse organisms including arthropods (13), amphibians (11, 13, 23), fish (13), and reptiles (13), the molecular origins of this activity have remained obscure. Definition of the RcSxph STX recognition code enabled identification of 10 new Sxphs from diverse frogs and toads. This substantial enlargement of the Sxph family beyond RcSxph and the previously identified High Himalaya frog (Nanorana parkeri) Sxph (NpSxph) (10) reveals a varied STX binding pocket that surrounds a conserved core of “hot spot” positions. Comparison of the new Sxph family members further identifies dramatic differences in the number of thyroglobulin (Thy1) domains inserted into the modified transferrin fold upon which the Sxph family is built. Biochemical characterization of NpSxph, Oophaga sylvatica Sxph (OsSxph) (24), Mantella aurantiaca Sxph (MaSxph), and Ranitomeya imitator Sxph (RiSxph), together with structural determination of NpSxph, alone and as STX complexes, shows that the different Sxphs share the capacity to form high-affinity STX complexes and that binding site preorganization (10) is a critical factor for tight STX association. Together, these studies establish an STX molecular recognition code that provides a template for understanding how diverse STX binding proteins engage the toxin and its congeners and uncover that Sxph family members are abundantly found in the most varied and widespread group of amphibians, the anurans. This knowledge and suite of diverse Sxphs, conserved among anuran families separated by at least 140 My of evolution (25), provide a starting point for defining the physiological roles of Sxph in toxin resistance (9, 24, 26), should facilitate identification or design of other STX binding proteins, and may enable the development of new biologics to detect or neutralize STX and related PSPs.