1,038 research outputs found
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 starblock copolymers in the
strong-segregation regime as a function of volume fraction , 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 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
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