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

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

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

Calculation of the Phase Behavior of Lipids

The self-assembly of monoacyl lipids in solution is studied employing a model in which the lipid's hydrocarbon tail is described within the Rotational Isomeric State framework and is attached to a simple hydrophilic head. Mean-field theory is employed, and the necessary partition function of a single lipid is obtained via a partial enumeration over a large sample of molecular conformations. The influence of the lipid architecture on the transition between the lamellar and inverted-hexagonal phases is calculated, and qualitative agreement with experiment is found.Comment: to appear in Phys.Rev.

Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.Comment: Version submitted to Algorithms for Molecular Biology. A number of fixes from previous versio

Block Copolymer at Nano-Patterned Surfaces

We present numerical calculations of lamellar phases of block copolymers at patterned surfaces. We model symmetric di-block copolymer films forming lamellar phases and the effect of geometrical and chemical surface patterning on the alignment and orientation of lamellar phases. The calculations are done within self-consistent field theory (SCFT), where the semi-implicit relaxation scheme is used to solve the diffusion equation. Two specific set-ups, motivated by recent experiments, are investigated. In the first, the film is placed on top of a surface imprinted with long chemical stripes. The stripes interact more favorably with one of the two blocks and induce a perpendicular orientation in a large range of system parameters. However, the system is found to be sensitive to its initial conditions, and sometimes gets trapped into a metastable mixed state composed of domains in parallel and perpendicular orientations. In a second set-up, we study the film structure and orientation when it is pressed against a hard grooved mold. The mold surface prefers one of the two components and this set-up is found to be superior for inducing a perfect perpendicular lamellar orientation for a wide range of system parameters

Partial integration and local mean-field approach for a vector lattice model of microemulsions

A vector model on the simple cubic lattice, describing a mixture of water, oil, and amphiphile, is considered. An integration over the amphiphile orientational degrees of freedom is performed exactly in order to obtain an effective Hamiltonian for the system. The resulting model is a three-state (spin-1) system and contains many-site interaction terms. The analysis of the ground state reveals the presence of the water-oil-rich phase as well as the amphiphile-rich and the cubic phases. The temperature phase diagram of the system is analyzed in a local mean-field approach, and a triple line of water-rich, oil-rich, and microemulsion coexistence is obtained. For some values of the model parameters, lamellar phases also appear in the system, but only at finite temperature. The Lifshitz line is determined in a semianalytical way in order to locate the microemulsion region of the disordered phase