Random Assembly Research Articles

High dispersal levels and lake warming are emergent drivers of cyanobacterial community assembly in peri-Alpine lakes

Disentangling the relative importance of deterministic and stochastic processes in shaping natural communities is central to ecology. Studies about community assembly over broad temporal and spatial scales in aquatic microorganisms are scarce. Here, we used 16S rDNA sequence data from lake sediments to test for community assembly patterns in cyanobacterial phylogenies across ten European peri-Alpine lakes and over a century of eutrophication and climate warming. We studied phylogenetic similarity in cyanobacterial assemblages over spatial and temporal distance, and over environmental gradients, comparing detected patterns with theoretical expectations from deterministic and stochastic processes. We found limited evidence for deviation of lake communities from a random assembly model and no significant effects of geographic distance on phylogenetic similarity, suggesting no dispersal limitation and high levels of stochastic assembly. We detected a weak influence of phosphorus, but no significant effect of nitrogen levels on deviation of community phylogenies from random. We found however a significant decay of phylogenetic similarity for non-random communities over a gradient of air temperature and water column stability. We show how phylogenetic data from sedimentary archives can improve our understanding of microbial community assembly processes, and support previous evidence that climate warming has been the strongest environmental driver of cyanobacterial community assembly over the past century.

The influence of spatial sampling scales on ant-plant interaction network architecture.

Despite great interest in metrics to quantify the structure of ecological networks, the effects of sampling and scale remain poorly understood. In fact, one of the most challenging issues in ecology is how to define suitable scales (i.e., temporal or spatial) to accurately describe and understand ecological systems. Here, we sampled a series of ant-plant interaction networks in the southern Brazilian Amazon rainforest in order to determine whether the spatial sampling scale, from local to regional, affects our understanding of the structure of these networks. To this end, we recorded ant-plant interactions in adjacent 25×30m subplots (local sampling scale) nested within twelve 250×30m plots (regional sampling scale). Moreover, we combined adjacent or random subplots and plots in order to increase the spatial sampling scales at the local and regional levels. We then calculated commonly used binary and quantitative network-level metrics for both sampling scales (i.e., number of species and interactions, nestedness, specialization and modularity), all of which encompass a wide array of structural patterns in interaction networks. We observed increasing species and interactions across sampling scales, and while most network descriptors remained relatively constant at the local level, there was more variation at the regional scale. Among all metrics, specialization was most constant across different spatial sampling scales. Furthermore, we observed that adjacent assembly did not generate more variation in network descriptor values compared to random assembly. This finding indicates that the spatially aggregated distribution of species/individuals and abiotic conditions does not affect the organization of these interacting assemblages. Our results have a direct impact on our empirical and theoretical understanding of the ecological dynamics of species interactions by demonstrating that small spatial sampling scales should suffice to record some patterns commonly found in ant-plant interaction networks in a highly diverse tropical rainforest.

Efficiency enhancements of a restricted stochastic search algorithm for locating local and global minima

Abstract Kick is a simple computational method that enables stochastic searches for stable structures of systems of up to ∼15 atoms. We propose two new filters to be applied with Kick to enforce minimum bond lengths between all pair of atoms and connectivity of all atoms in candidate structures. As this Restricted Kick method rejects a rapidly increasing number of structures with increasing system size, we furthermore devised the restricted Random Assembly Stochastic Search method, which randomly assembles structures that automatically satisfy these filters. Significant improvements in convergence rate over the original Kick method are obtained for several well-established examples.

A Pillow-Shaped 3D Hierarchical Piezoresistive Pressure Sensor Based on Conductive Silver Components-Coated Fabric and Random Fibers Assembly

Flexible pressure sensors are increasingly popular because of their extensive applications in smart textile and flexible robotics. Inspired by the composite hierarchical structure of conventional p...

Modeling detergent applications using molecular dynamics

The molecular dynamics group at Fairmont State University models detergent systems with interdisciplinary applications. Simulations currently underway include octane interacting with sodium dodecyl sulfate (SDS) in aqueous solution as well as micelle formation in systems of cetyltrimethylammonium bromide and chloride (CTAB and CTAC, respectively). The simulation of octane and SDS in aqueous solution is designed to model the process of washing away grease with a detergent commonly found in dish soap. It is intended for use as a web-based educational tool to provide a dynamic visualization of micelle formation, e.g. in freshman chemistry classes. CTAB was chosen as a target because of literature evidence that low concentrations of the detergent cause a 100-fold increase in fluorescence of a small organic molecule. This organic molecule is a localized photosensitizer, which is useful in improving photodynamic light therapy that is currently being used as treatment for some cancers. Bromide ion parameters were adapted from the well parameterized chloride ion in the CHARMM forcefield; the comparison is interesting because CTAC and CTAB are known to have different aggregation numbers. Initial simulation results indicate that micelle formation from a random assembly of detergent molecules (n=20-130) occurs rapidly for both species. This research has been supported by the Fairmont State University College of Science and Technology as well as the NASA WV Space Grant Consortium.

Tailored Combinatorial Microcompartments through the Self‐Organization of Microobjects: Assembly, Characterization, and Cell Studies

AbstractA new concept enables the generation of cell microenvironments by microobject assembly at an water/air interface. As the orientation of 30 μm sized polymer cubes and their capillary force assembly are controlled by the surface wettability, which in turn can be modulated by coating the initially exposed surfaces with gold and self‐assembled monolayers, unique niches in closely packed arrays of cubes with vertex up orientation can be realized. The random assembly of distinctly different cubes, prefunctionalized or surface‐structured exclusively on their top surface, facilitates the parallel generation of different microenvironments in a combinatorial manner, which paves the way to future systematic structure–property relationship studies with cells.

Tailored Combinatorial Microcompartments through the Self-Organization of Microobjects: Assembly, Characterization, and Cell Studies.

A new concept enables the generation of cell microenvironments by microobject assembly at an water/air interface. As the orientation of 30 μm sized polymer cubes and their capillary force assembly are controlled by the surface wettability, which in turn can be modulated by coating the initially exposed surfaces with gold and self-assembled monolayers, unique niches in closely packed arrays of cubes with vertex up orientation can be realized. The random assembly of distinctly different cubes, prefunctionalized or surface-structured exclusively on their top surface, facilitates the parallel generation of different microenvironments in a combinatorial manner, which paves the way to future systematic structure-property relationship studies with cells.

Conversion of curved assemblies into two dimensional sheets.

The design and preparation of organic two dimensional (O2D) sheets and their conversion to curved nanostructures is in its infancy. To convert a flat structure into a curved structure, the molecule must have multiple interaction possibilities and an in-built twist. The conjugated small molecule iso-Indigo (i-Indigo) comprises two phenyl rings that are twisted (the dihedral angle is 15°) at the junction. The i-Indigo has been connected with moieties that impart hydrogen bonding and van der Waals interactions. Due to the presence of the π cloud in i-Indigo, π-π interactions are also present in the molecule. While all three interactions are in operation, rings and toroids are formed. Upon addition of hydrogen bonding competing solvents, the rings and toroids unravel to form O2D sheets. Control molecules that don't have hydrogen bonding moieties and π-π interactions form random assemblies. Please note that the rings, toroids and O2D sheets are formed in a single solvent by simple dissolution, unlike previous approaches that involve multiple steps and solvents.

Polyaniline nanorods random assembly on sugarcane bagasse pith-based carbon sheets with promising capacitive performance.

Polyaniline (PANI) nanorods were randomly deposited on oxidized 2D sugarcane pith-based porous carbon nanosheets by using dilute polymerization methods. The random stacked morphology of the PANI nanorods on the oxidized pith-based porous carbon nanosheets (SPCN) can be effectively controlled by simply changing the molar mass of aniline monomer. When the molar mass of the aniline monomer is increased to 0.02 M, the PANI nanorods can be randomly and uniformly stacked on the oxidized SPCN. Most of these stacked pores derived from random stack of the PANI nanorods on the oxidized SPCN are mesopore and macropore. These stacked pores not only facilitate the diffusion of ions in the stacked layer of the PANI nanorods, but also mitigate mechanical deformation of the PANI nanorods during the doping/dedoping process. Furthermore, the relationship between the properties of the oxidized SPCN/PANI-X (X represents the molar mass of aniline monomer) electrode materials and molar mass of aniline monomer is explored in detail. The oxidized SPCN/PANI-0.02 exhibits the best electrochemical performance in 1 M H2SO4. The largest specific electrode capacitance is up to 513 F g−1 at a current density of 0.25 A g−1. The oxidized SPCN/PANI-0.02 also exhibits excellent electrochemical cycling stability.

Geometric effects in random assemblies of ellipses.

Assemblies of anisotropic particles commonly appear in studies of active many-body systems. However, in two dimensions, the geometric ramifications of the finite density of such objects are not entirely understood. To fully characterize these effects, we perform an in-depth study of random assemblies generated by a slow compression of frictionless elliptical particles. The obtained configurations are then analysed using the Set Voronoi tessellation, which takes the particle shape into account. Not only do we analyse most scalar and vectorial morphological measures, which are commonly discussed in the literature or which have recently been addressed in experiments, but we also systematically explore the correlations between them. While in a limited range of parameters similarities with findings in 3D assemblies could be identified, important differences are found when a broad range of aspect ratios and packing fractions are considered. The data discussed in this study should thus provide a unique reference set such that geometric effects and differences from random assemblies could be clearly identified in more complex systems, including ones with soft and active particles that are typically found in biological systems.

Lattice Boltzmann simulation of gas-solid heat transfer in random assemblies of spheres: The effect of solids volume fraction on the average Nusselt number for Re ≤ 100

A thermal lattice Boltzmann method has been applied to simulate gas-solid heat transfer in a random assembly of spheres using an immersed moving boundary approach. The numerical data was correlated to propose an expression for the Nusselt number as a function of the Reynolds number and solid volume fraction over a wide range of solid volume fractions (ϕ=[0,0.5]) for Reynolds numbers up to 100. It is hoped that the new Nusselt number correlation for gas-solid systems improves the accuracy of Euler-Euler and Euler-Lagrangian simulations of gas-solid heat transfer in packed and fluidized beds.

Using functional trait diversity to infer community assembly mechanisms: an exclosure experiment as an example

The Qinghai-Tibetan Plateau has a mean altitude exceeding 4000 m and covers about 2.5 million km². More than 60% of this area is alpine grassland. Exclosures have been widely used in this region to study the sustainable use of grassland resources. We used patterns of functional trait diversity to infer the effects of exclosures on community assembly in alpine meadows. We studied functional diversity using five traits under grazing and three enclosed (exclosure) plots (3, 8, and 18 years old) in an alpine meadow on the Qinghai-Tibetan Plateau. We quantified the strength of the community assembly processes by comparing the observed functional trait diversity with a null model that assumes random community assembly. We found evidence for deterministic assembly processes for plant communities in exclosures. The changes in CWM of the five traits from grazing land to 18-year exclosure indicated that environmental filtering occurred due to the exclosures. Multivariate functional diversity (MFDis and MPDₛₑₛ), and functional diversity of individual traits, including that of leaf area, leaf weight and aboveground biomass (FDis of leaf area, leaf weight, and aboveground biomass), increased gradually from grazing land to the 18-year exclosure, and the values of the 18-year exclosure were significantly greater than null expectation. This can be interpreted to indicate that exclosures resulted in greater competitive interaction between species. These results suggest that the effect of exclosures on community assembly is more deterministic than stochastic in this meadow.

Random Assemblies for Lawmaking? Prospects and Limits

A randomly selected microcosm of the people can usefully play an official role in the lawmaking process. However, there are serious issues to be confronted if such a random sample were to take on the role of a full-scale, full-time second chamber. Some skeptical considerations are detailed. There are also advantages to short convenings of such a sample to take on some of the roles of a second chamber. This article provides a response to the skeptical considerations. Precedents from ancient Athens show how such short-term convenings of a deliberating microcosm can be positioned before, during, or after other elements of the lawmaking process. The article draws on experience from Deliberative Polling to show how this is both practical and productive for the lawmaking process.

On entropy and information in gene interaction networks.

Modern biological experiments often produce candidate lists of genes presumably related to the studied phenotype. One can ask if the gene list as a whole makes sense in the context of existing knowledge: Are the genes in the list reasonably related to each other or do they look like a random assembly? There are also situations when one wants to know if two or more gene sets are closely related. Gene enrichment tests based on counting the number of genes two sets have in common are adequate if we presume that two genes are related only when they are in fact identical. If by related we mean well connected in the interaction network space, we need a new measure of relatedness for gene sets. We derive entropy, interaction information and mutual information for gene sets on interaction networks, starting from a simple phenomenological model of a living cell. Formally, the model describes a set of interacting linear harmonic oscillators in thermal equilibrium. Because the energy function is a quadratic form of the degrees of freedom, entropy and all other derived information quantities can be calculated exactly. We apply these concepts to estimate the probability that genes from several independent genome-wide association studies are not mutually informative; to estimate the probability that two disjoint canonical metabolic pathways are not mutually informative; and to infer relationships among human diseases based on their gene signatures. We show that the present approach is able to predict observationally validated relationships not detectable by gene enrichment methods. The converse is also true; the two methods are therefore complementary. The functions defined in this paper are available in an R package, gsia, available for download at https://github.com/ucsd-ccbb/gsia.

Patterns of phylogenetic community structure of sand dune plant communities in the Yucatan Peninsula: the role of deterministic and stochastic processes in community assembly

ABSTRACTBackground: Tropical sand dunes are ideal systems for understanding drivers of community assembly as dunes are subject to both deterministic and stochastic processes. However, studies that evaluate the factors that mediate plant community assembly in these ecosystems are few.Aims: We evaluated phylogenetic community structure to elucidate the role of deterministic and stochastic processes in mediating the assembly of plant communities along the north of the Yucatan Peninsula, Mexico.Methods: We used plastid genetic markers to evaluate phylogenetic relationships in 16 sand-dune communities. To evaluate the role of climate in shaping plant community structure we carried out linear regressions between climatic variables and mean phylogenetic distance. We estimated the Net Relatedness Index and Nearest Taxon Index to identify ecological processes mediating community assembly.Results: Observed phylogenetic structure was not different from random, suggesting that stochastic processes are the major determinants of community assembly. Climate was slightly correlated with phylogenetic diversity suggesting that abiotic environment plays a minimal role in community assembly.Conclusions: Random assembly appears to be the primary factor structuring the studied sand dune plant communities. Environmental filters may represent a secondary factor contributing to the observed phylogenetic structure. Thus, both processes may act simultaneously to mediate the assembly of sand-dune plant communities.

Systems protobiology: origin of life in lipid catalytic networks.

Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems—hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.

Investigation of the Collective Properties in Monolayers of Exchange-Biased Fe3−δO4@CoO Core–Shell Nanoparticles

Owing to its potential to enhance the effective magnetic anisotropy energy of nanoparticles, exchange bias has been extensively studied during the last few years. Although most of studies have been conducted in the powder state, the effect of the dimensionality of nanoparticle assemblies has been scarcely investigated. In this context, we report on the study of the collective properties of monolayers of exchange-biased nanoparticles with different core–shell structures. Nanoparticles consist in a ferrimagnetic Fe3−δO4 core coated with an antiferromagnetic CoO shell. They were assembled in monolayers with local order by using the Langmuir–Blodgett technique. Exchange bias is significantly altered in 2D assemblies in comparison to powder samples which can be assimilated to 3D random assemblies. We show that exchange bias in Fe3−δO4@CoO nanoparticles is directly influenced by dipolar interactions between Fe3−δO4 cores, which are enhanced by shape anisotropy of 2D assemblies. Besides the dramatic influence of the core–shell structure, the systematic variation of the core size and the shell thickness showed that above a critical value, dipolar interactions compete exchange bias.

High-throughput fabrication of vascularized spheroids for bioprinting

Overcoming the problem of vascularization remains the main challenge in the field of tissue engineering. As three-dimensional (3D) bioprinting is the rising technique for the fabrication of large tissue constructs, small prevascularized building blocks were generated that can be incorporated throughout a printed construct, answering the need for a microvasculature within the small micron range (<10 μm). Uniform spheroids with an ideal geometry and diameter for bioprinting were formed, using a high-throughput non-adhesive agarose microwell system. Since monoculture spheroids of endothelial cells were unable to remain stable, coculture spheroids combining endothelial cells with fibroblasts and/or adipose tissue derived mesenchymal stem cells (ADSC) as supporting cells, were created. When applying the favorable coculture ratio, viable spheroids were obtained and endothelial cells spontaneously formed a capillary-like network and lumina, as shown by immunohistochemistry and transmission electron microscopy. Especially the presence of ADSC led to a higher vascularization and extracellular matrix production of the microtissue. Moreover, spheroids were able to assemble at random in suspension and in a hydrogel, creating a macrotissue. During at random assembly, cells reorganized, creating a branched capillary-network throughout the entire fused construct by inoculating with capillaries of adjacent spheroids. Combining the advantage of this natural capacity of microtissues to self-assemble and the controlled organization by bioprinting technologies, these prevascularized spheroids can be useful as building blocks for the engineering of large vascularized 3D tissues.

Thermodynamic Model of Solvent Effects in Semiflexible Diblock and Random Copolymer Assembly

We present a field-theoretic model to predict the equilibrium thermodynamic behavior of semiflexible diblock copolymers and random copolymers in the presence of solvent. We find that in both systems polymer–solvent contacts dramatically influence the thermodynamic behavior with decreasing the copolymer segment length (i.e., molecular weight). When a copolymer has unequal monomer composition, both polymer length and solvent concentration have a strong influence on the phase transition spinodal and magnitude of the critical wave modes. Diblock copolymers exhibit an expanded region of the lamellar phase in the phase diagram with decreasing chain length and polymer concentration. Such effects suggest a breakdown of the dilute approximation for solutions of short diblock copolymers. Random copolymer solutions also exhibit changes in the phase-transition spinodal and critical wave mode at asymmetric chemical compositions. This effect is highly relevant to most random copolymer materials, since a monomer is typi...

Emergence of weak‐intransitive competition through adaptive diversification and eco‐evolutionary feedbacks

Abstract Indirect biotic interactions—such as intransitive competition—are increasingly recognized as being important in shaping ecological patterns in natural systems. Over long time‐scales, such indirect interactions may affect the evolution of species phenotypes, which in turn can modify these interactions, thereby begetting eco‐evolutionary feedbacks. If indirect intransitive interactions can emerge in situ during lineage diversification, they could profoundly affect species’ phenotypic diversity, temporal stability, and subsequent diversification rates. We address these questions by investigating the conditions under which indirect intransitive competition can emerge from a lineage diversifying in sympatry. We use an adaptive dynamics model to study the ecological and evolutionary properties of this lineage under different scenarios where competition for resources between phenotypes varies in strength and (a)symmetry. Results show that weak‐intransitive competition can emerge during the sympatric diversification of a single lineage. “Weak‐intransitivity” here refers to situations where species interactions are not perfectly transitive, that is, there is no strict hierarchy in species competitive abilities. The strength of such weak‐intransitivity increases when the competition between phenotypes increases in strength and asymmetry. The strength of intransitivity also correlates with other system properties. We notably found that the strength of intransitivity increases with the number of phenotypes, and that greater intransitivity correlates with the evolution of greater functional trait divergences between phenotypes, greater resistance to invasion by new phenotypes but lower resistance to disturbances as well as slower evolutionary rates. Synthesis. This theoretical exploration of the evolution of intransitive competition provides the first formal bridge between the ecological and evolutionary aspects of intransitive competition. We show that, when competitive interactions are strong enough, weak‐intransitive competition is more likely to emerge through adaptive diversification than from a random community assembly. Intransitive competition is, therefore, not only restricted to between‐species interactions but can also function as a regulator of diversification within species, thereby affecting lineage functional diversity, and ecological and evolutionary stability.