415 research outputs found
Viral RNAs are unusually compact.
A majority of viruses are composed of long single-stranded genomic RNA molecules encapsulated by protein shells with diameters of just a few tens of nanometers. We examine the extent to which these viral RNAs have evolved to be physically compact molecules to facilitate encapsulation. Measurements of equal-length viral, non-viral, coding and non-coding RNAs show viral RNAs to have among the smallest sizes in solution, i.e., the highest gel-electrophoretic mobilities and the smallest hydrodynamic radii. Using graph-theoretical analyses we demonstrate that their sizes correlate with the compactness of branching patterns in predicted secondary structure ensembles. The density of branching is determined by the number and relative positions of 3-helix junctions, and is highly sensitive to the presence of rare higher-order junctions with 4 or more helices. Compact branching arises from a preponderance of base pairing between nucleotides close to each other in the primary sequence. The density of branching represents a degree of freedom optimized by viral RNA genomes in response to the evolutionary pressure to be packaged reliably. Several families of viruses are analyzed to delineate the effects of capsid geometry, size and charge stabilization on the selective pressure for RNA compactness. Compact branching has important implications for RNA folding and viral assembly
Folding Langmuir Monolayers
The maximum pressure a two-dimensional surfactant monolayer is able to
withstand is limited by the collapse instability towards formation of
three-dimensional material. We propose a new description for reversible
collapse based on a mathematical analogy between the formation of folds in
surfactant monolayers and the formation of Griffith Cracks in solid plates
under stress. The description, which is tested in a combined microscopy and
rheology study of the collapse of a single-phase Langmuir monolayer of
2-hydroxy-tetracosanoic acid (2-OH TCA), provides a connection between the
in-plane rheology of LM's and reversible folding
Avoided Critical Behavior in O(n) Systems
Long-range frustrating interactions, even if their strength is infinitesimal,
can give rise to a dramatic proliferations of ground or near-ground states. As
a consequence, the ordering temperature can exhibit a discontinuous drop as a
function of the frustration. A simple model of the doped Mott insulator, where
the short-range tendency of the holes to phase separate competes with
long-range Coulomb effects, exhibits this "avoided critical" behavior. This
model may serve as a paradigm for many other systems.Comment: 4 pages, 2 figure
The Critical Behaviour of Potts models with symmetry breaking fields
The -state Potts model in two dimensions in the presence of external
magnetic fields is studied. For general special choices of these
magnetic fields produce effective models with smaller symmetry . The phase diagram of these models and their critical behaviour are
explored by conventional finite-size scaling and conformal invariance. The
possibility of multicritical behavior, for finite values of the symmetry
breaking fields, in the cases where is also analysed. Our results
indicate that for effective models with symmetry the
multicritical point occurs at zero field. This last result is also corroborated
by Monte Carlo simulations.Comment: 15 pages (standart LaTex), 2 figure (PostScript) available by request
to [email protected]
A Phase-Field Model of Spiral Dendritic Growth
Domains of condensed-phase monolayers of chiral molecules exhibit a variety
of interesting nonequilibrium structures when formed via pressurization. To
model these domain patterns, we add a complex field describing the tilt degree
of freedom to an (anisotropic) complex-phase-field solidification model. The
resulting formalism allows for the inclusion of (in general, non-reflection
symmetric) interactions between the tilt, the solid-liquid interface, and the
bond orientation. Simulations demonstrate the ability of the model to exhibit
spiral dendritic growth.Comment: text plus Four postscript figure file
Static Scaling Behavior of High-Molecular-Weight Polymers in Dilute Solution: A Reexamination
Previous theories of dilute polymer solutions have failed to distinguish
clearly between two very different ways of taking the long-chain limit: (I) at fixed temperature , and (II) ,
with fixed. I argue that the modern
two-parameter theory (continuum Edwards model) applies to case II --- not case
I --- and in fact gives exactly the crossover scaling functions for
modulo two nonuniversal scale factors. A Wilson-type renormalization group
clarifies the connection between crossover scaling functions and continuum
field theories. [Also contains a general discussion of the connection between
the Wilson and field-theoretic renormalization groups. Comments solicited.]Comment: 10 pages including 1 figure, 181159 bytes Postscript
(NYU-TH-93/05/01
Polar Smectic Films
We report on a new experimental procedure for forming and studying polar
smectic liquid crystal films. A free standing smectic film is put in contact
with a liquid drop, so that the film has one liquid crystal/liquid interface
and one liquid crystal/air interface. This polar environment results in changes
in the textures observed in the film, including a boojum texture and a
previously unobserved spiral texture in which the winding direction of the
spiral reverses at a finite radius from its center. Some aspects of these
textures are explained by the presence of a Ksb term in the bulk elastic free
energy density that favors a combination of splay and bend deformations.Comment: 4 pages, REVTeX, 3 figures, submitted to PR
Hexatic Order and Surface Ripples in Spherical Geometries
In flat geometries, two dimensional hexatic order has only a minor effect on
capillary waves on a liquid substrate and on undulation modes in lipid
bilayers. However, extended bond orientational order alters the long wavelength
spectrum of these ripples in spherical geometries. We calculate this frequency
shift and suggest that it might be detectable in lipid bilayer vesicles, at the
surface of liquid metals and in multielectron bubbles in liquid helium at low
temperatures. Hexatic order also leads to a shift in the threshold for the
fission instability induced in the later two systems by an excess of electric
charge.Comment: 5 pages, 1 figure; revised version; to appear in Phys. Rev. Let
Towards a Tetravalent Chemistry of Colloids
We propose coating spherical particles or droplets with anisotropic
nano-sized objects to allow micron-scale colloids to link or functionalize with
a four-fold valence, similar to the sp3 hybridized chemical bonds associated
with, e.g., carbon, silicon and germanium. Candidates for such coatings include
triblock copolymers, gemini lipids, metallic or semiconducting nanorods and
conventional liquid crystal compounds. We estimate the size of the relevant
nematic Frank constants, discuss how to obtain other valences and analyze the
thermal distortions of ground state configurations of defects on the sphere.Comment: Replaced to improve figures. 4 figures Nano Letter
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