A format for phylogenetic placements

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements, and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.Comment: Documents version 3 of the forma

Strong-Segregation Theory of Bicontinuous Phases in Block Copolymers

We compute phase diagrams for $A_nB_m$ starblock copolymers in the strong-segregation regime as a function of volume fraction $\phi$, including bicontinuous phases related to minimal surfaces (G, D, and P surfaces) as candidate structures. We present the details of a general method to compute free energies in the strong segregation limit, and demonstrate that the gyroid G phase is the most nearly stable among the bicontinuous phases considered. We explore some effects of conformational asymmetry on the topology of the phase diagram.Comment: 14 pages, latex, 21 figures, to appear in Macromolecule

Interfaces in Diblocks: A Study of Miktoarm Star Copolymers

We study AB$_n$ miktoarm star block copolymers in the strong segregation limit, focussing on the role that the AB interface plays in determining the phase behavior. We develop an extension of the kinked-path approach which allows us to explore the energetic dependence on interfacial shape. We consider a one-parameter family of interfaces to study the columnar to lamellar transition in asymmetric stars. We compare with recent experimental results. We discuss the stability of the A15 lattice of sphere-like micelles in the context of interfacial energy minimization. We corroborate our theory by implementing a numerically exact self-consistent field theory to probe the phase diagram and the shape of the AB interface.Comment: 12 pages, 11 included figure

The non-centrosymmetric lamellar phase in blends of ABC triblock and ac diblock copolymers

The phase behaviour of blends of ABC triblock and ac diblock copolymers is examined using self-consistent field theory. Several equilibrium lamellar structures are observed, depending on the volume fraction of the diblocks, phi_2, the monomer interactions, and the degrees of polymerization of the copolymers. For segregations just above the order-disorder transition the triblocks and diblocks mix together to form centrosymmetric lamellae. As the segregation is increased the triblocks and diblocks spatially separate either by macrophase-separating, or by forming a non-centrosymmetric (NCS) phase of alternating layers of triblock and diblock (...ABCcaABCca...). The NCS phase is stable over a narrow region near phi_2=0.4. This region is widest near the critical point on the phase coexistence curve and narrows to terminate at a triple point at higher segregation. Above the triple point there is two-phase coexistence between almost pure triblock and diblock phases. The theoretical phase diagram is consistent with experiments.Comment: 9 pages, 8 figures, submitted to Macromolecule

A Geometric Theory of Diblock Copolymer Phases

We analyze the energetics of sphere-like micellar phases in diblock copolymers in terms of well-studied, geometric quantities for their lattices. We argue that the A15 lattice with Pm3n symmetry should be favored as the blocks become more symmetric and corroborate this through a self-consistent field theory. Because phases with columnar or bicontinuous topologies intervene, the A15 phase, though metastable, is not an equilibrium phase of symmetric diblocks. We investigate the phase diagram of branched diblocks and find thatthe A15 phase is stable.Comment: 4 pages, RevTeX, 3 eps figures include

New Method for Phase transitions in diblock copolymers: The Lamellar case

A new mean-field type theory is proposed to study order-disorder transitions (ODT) in block copolymers. The theory applies to both the weak segregation (WS) and the strong segregation (SS) regimes. A new energy functional is proposed without appealing to the random phase approximation (RPA). We find new terms unaccounted for within RPA. We work out in detail transitions to the lamellar state and compare the method to other existing theories of ODT and numerical simulations. We find good agreements with recent experimental results and predict that the intermediate segregation regime may have more than one scaling behavior.Comment: 23 pages, 8 figure

Phase diagram for diblock copolymer melts under cylindrical confinement

We extensively study the phase diagram of a diblock copolymer melt confined in a cylindrical nanopore using real-space self-consistent mean-field theory. We discover a rich variety of new two-dimensional equilibrium structures that have no analog in the unconfined system. These include non-hexagonally coordinated cylinder phases and structures intermediate between lamellae and cylinders. We map the stability regions and phase boundaries for all the structures we find. As the pore radius is decreased, the pore accommodates fewer cylindrical domains and structural transitions occur as cylinders are eliminated. Our results are consistent with experiments, but we also predict phases yet to be observed.Comment: 12 pages, 3 figures. submitted to Physical Review Letter

Domains in Melts of Comb-Coil Diblock Copolymers: Superstrong Segregation Regime

Conditions for the crossover from the strong to the superstrong segregation regime are analyzed for the case of comb-coil diblock copolymers. It is shown that the critical interaction energy between the components required to induce the crossover to the superstrong segregation regime is inversely proportional to mb = 1 + n/m, where n is the degree of polymerization of the side chain and m is the distance between successive grafting points. As a result, the superstrong segregation regime, being rather rare in the case of ordinary block copolymers, has a much better chance to be realized in the case of diblock copolymers with combs grafted to one of the blocks.