331 research outputs found
Drift without flux: Brownian walker with a space dependent diffusion coefficient
Space dependent diffusion of micrometer sized particles has been directly
observed using digital video microscopy. The particles were trapped between two
nearly parallel walls making their confinement position dependent.
Consequently, not only did we measure a diffusion coefficient which depended on
the particles' position, but also report and explain a new effect: a drift of
the particles' individual positions in the direction of the diffusion
coefficient gradient, in the absence of any external force or concentration
gradient.Comment: 4 pages, 4 ps figures, include
The Mystery of Two Straight Lines in Bacterial Genome Statistics. Release 2007
In special coordinates (codon position--specific nucleotide frequencies)
bacterial genomes form two straight lines in 9-dimensional space: one line for
eubacterial genomes, another for archaeal genomes. All the 348 distinct
bacterial genomes available in Genbank in April 2007, belong to these lines
with high accuracy. The main challenge now is to explain the observed high
accuracy. The new phenomenon of complementary symmetry for codon
position--specific nucleotide frequencies is observed. The results of analysis
of several codon usage models are presented. We demonstrate that the
mean--field approximation, which is also known as context--free, or complete
independence model, or Segre variety, can serve as a reasonable approximation
to the real codon usage. The first two principal components of codon usage
correlate strongly with genomic G+C content and the optimal growth temperature
respectively. The variation of codon usage along the third component is related
to the curvature of the mean-field approximation. First three eigenvalues in
codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and
archaeal genomes codon usage is clearly distributed along two third order
curves with genomic G+C content as a parameter.Comment: Significantly extended version with new data for all the 348 distinct
bacterial genomes available in Genbank in April 200
Conspiracy in bacterial genomes
The rank ordered distribution of the codon usage frequencies for 123
bacteriae is best fitted by a three parameters function that is the sum of a
constant, an exponential and a linear term in the rank n. The parameters depend
(two parabolically) from the total GC content. The rank ordered distribution of
the amino acids is fitted by a straight line. The Shannon entropy computed over
all the codons is well fitted by a parabola in the GC content, while the
partial entropies computed over subsets of the codons show peculiar different
behavior, exhibiting therefore a first conspiracy effect. Moreover the sum of
the codon usage frequencies over particular sets, e.g. with C and A
(respectively G and U) as i-th nucleotide, shows a clear linear dependence from
the GC content, exhibiting another conspiracy effect.Comment: revised version: introduction and conclusion enhanced, references
added, figures added, some tables remove
DC-conductivity of a suspension of insulating particles with internal rotation
We analyse the consequences of Quincke rotation on the conductivity of a
suspension. Quincke rotation refers to the spontaneous rotation of insulating
particles dispersed in a slightly conducting liquid and subject to a high DC
electric field: above a critical field, each particle rotates continuously
around itself with an axis pointing in any direction perpendicular to the DC
field. When the suspension is subject to an electric field lower than the
threshold one, the presence of insulating particles in the host liquid
decreases the bulk conductivity since the particles form obstacles to ion
migration. But for electric fields higher than the critical one, the particles
rotate and facilitate ion migration: the effective conductivity of the
suspension is increased. We provide a theoretical analysis of the impact of
Quincke rotation on the apparent conductivity of a suspension and we present
experimental results obtained with a suspension of PMMA particles dispersed in
weakly conducting liquids
Relaxation of surface charge on rotating dielectric spheres: Implications on dynamic electrorheological effects
We have examined the effect of an oscillatory rotation of a polarized
dielectric particle. The rotational motion leads to a re-distribution of the
polarization charge on the surface of the particle. We show that the time
averaged steady-state dipole moment is along the field direction, but its
magnitude is reduced by a factor which depends on the angular velocity of
rotation. As a result, the rotational motion of the particle reduces the
electrorheological effect. We further assume that the relaxation of polarized
charge is arised from a finite conductivity of the particle or host medium. We
calculate the relaxation time based on the Maxwell-Wagner theory, suitably
generalized to include the rotational motion. Analytic expressions for the
reduction factor and the relaxation time are given and their dependence on the
angular velocity of rotation will be discussed.Comment: Accepted for publications by Phys. Rev.
On local linearization of control systems
We consider the problem of topological linearization of smooth (C infinity or
real analytic) control systems, i.e. of their local equivalence to a linear
controllable system via point-wise transformations on the state and the control
(static feedback transformations) that are topological but not necessarily
differentiable. We prove that local topological linearization implies local
smooth linearization, at generic points. At arbitrary points, it implies local
conjugation to a linear system via a homeomorphism that induces a smooth
diffeomorphism on the state variables, and, except at "strongly" singular
points, this homeomorphism can be chosen to be a smooth mapping (the inverse
map needs not be smooth). Deciding whether the same is true at "strongly"
singular points is tantamount to solve an intriguing open question in
differential topology
Hydrodynamic Coupling of Two Brownian Spheres to a Planar Surface
We describe direct imaging measurements of the collective and relative
diffusion of two colloidal spheres near a flat plate. The bounding surface
modifies the spheres' dynamics, even at separations of tens of radii. This
behavior is captured by a stokeslet analysis of fluid flow driven by the
spheres' and wall's no-slip boundary conditions. In particular, this analysis
reveals surprising asymmetry in the normal modes for pair diffusion near a flat
surface.Comment: 4 pages, 4 figure
Controllability on infinite-dimensional manifolds
Following the unified approach of A. Kriegl and P.W. Michor (1997) for a
treatment of global analysis on a class of locally convex spaces known as
convenient, we give a generalization of Rashevsky-Chow's theorem for control
systems in regular connected manifolds modelled on convenient
(infinite-dimensional) locally convex spaces which are not necessarily
normable.Comment: 19 pages, 1 figur
Higher order glass-transition singularities in colloidal systems with attractive interactions
The transition from a liquid to a glass in colloidal suspensions of particles
interacting through a hard core plus an attractive square-well potential is
studied within the mode-coupling-theory framework. When the width of the
attractive potential is much shorter than the hard-core diameter, a reentrant
behavior of the liquid-glass line, and a glass-glass-transition line are found
in the temperature-density plane of the model. For small well-width values, the
glass-glass-transition line terminates in a third order bifurcation point, i.e.
in a A_3 (cusp) singularity. On increasing the square-well width, the
glass-glass line disappears, giving rise to a fourth order A_4 (swallow-tail)
singularity at a critical well width. Close to the A_3 and A_4 singularities
the decay of the density correlators shows stretching of huge dynamical
windows, in particular logarithmic time dependence.Comment: 19 pages, 12 figures, Phys. Rev. E, in prin
Conflict between Translation Initiation and Elongation in Vertebrate Mitochondrial Genomes
The strand-biased mutation spectrum in vertebrate mitochondrial genomes results in an AC-rich L-strand and a GT-rich H-strand. Because the L-strand is the sense strand of 12 protein-coding genes out of the 13, the third codon position is overall strongly AC-biased. The wobble site of the anticodon of the 22 mitochondrial tRNAs is either U or G to pair with the most abundant synonymous codon, with only one exception. The wobble site of Met-tRNA is C instead of U, forming the Watson-Crick match with AUG instead of AUA, the latter being much more frequent than the former. This has been attributed to a compromise between translation initiation and elongation; i.e., AUG is not only a methionine codon, but also an initiation codon, and an anticodon matching AUG will increase the initiation rate. However, such an anticodon would impose selection against the use of AUA codons because AUA needs to be wobble-translated. According to this translation conflict hypothesis, AUA should be used relatively less frequently compared to UUA in the UUR codon family. A comprehensive analysis of mitochondrial genomes from a variety of vertebrate species revealed a general deficiency of AUA codons relative to UUA codons. In contrast, urochordate mitochondrial genomes with two tRNA(Met) genes with CAU and UAU anticodons exhibit increased AUA codon usage. Furthermore, six bivalve mitochondrial genomes with both of their tRNA-Met genes with a CAU anticodon have reduced AUA usage relative to three other bivalve mitochondrial genomes with one of their two tRNA-Met genes having a CAU anticodon and the other having a UAU anticodon. We conclude that the translation conflict hypothesis is empirically supported, and our results highlight the fine details of selection in shaping molecular evolution
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