10,715 research outputs found
Parametric Inference for Biological Sequence Analysis
One of the major successes in computational biology has been the unification,
using the graphical model formalism, of a multitude of algorithms for
annotating and comparing biological sequences. Graphical models that have been
applied towards these problems include hidden Markov models for annotation,
tree models for phylogenetics, and pair hidden Markov models for alignment. A
single algorithm, the sum-product algorithm, solves many of the inference
problems associated with different statistical models. This paper introduces
the \emph{polytope propagation algorithm} for computing the Newton polytope of
an observation from a graphical model. This algorithm is a geometric version of
the sum-product algorithm and is used to analyze the parametric behavior of
maximum a posteriori inference calculations for graphical models.Comment: 15 pages, 4 figures. See also companion paper "Tropical Geometry of
Statistical Models" (q-bio.QM/0311009
Noninvasive Measurement of Dissipation in Colloidal Systems
According to Harada and Sasa [Phys. Rev. Lett. 95, 130602 (2005)], heat
production generated in a non-equilibrium steady state can be inferred from
measuring response and correlation functions. In many colloidal systems,
however, it is a nontrivial task to determine response functions, whereas
details about spatial steady state trajectories are easily accessible. Using a
simple conditional averaging procedure, we show how this fact can be exploited
to reliably evaluate average heat production. We test this method using
Brownian dynamics simulations, and apply it to experimental data of an
interacting driven colloidal system
Multi-k magnetic structures in USb_{0.9}Te_{0.1} and UAs_{0.8}Se_{0.2} observed via resonant x-ray scattering at the U M4 edge
Experiments with resonant photons at the U M4 edge have been performed on a
sample of USb_{0.9}Te_{0.1}, which has an incommensurate magnetic structure
with k = 0.596(2) reciprocal lattice units. The reflections of the form ,
as observed previously in a commensurate k = 1/2 system [N. Bernhoeft et al.,
Phys. Rev. B 69 174415 (2004)] are observed, removing any doubt that these
occur because of multiple scattering or high-order contamination of the
incident photon beam. They are clearly connected with the presence of a 3k
configuration. Measurements of the reflections from the sample
UAs_{0.8}Se_{0.2} in a magnetic field show that the transition at T* ~ 50 K is
between a low-temperature 2k and high-temperature 3k state and that this
transition is sensitive to an applied magnetic field. These experiments stress
the need for quantitative theory to explain the intensities of these
reflections.Comment: submitted to Phys. Rev.
Tagged particle in a sheared suspension: effective temperature determines density distribution in a slowly varying external potential beyond linear response
We consider a sheared colloidal suspension under the influence of an external
potential that varies slowly in space in the plane perpendicular to the flow
and acts on one selected (tagged) particle of the suspension. Using a
Chapman-Enskog type expansion we derive a steady state equation for the tagged
particle density distribution. We show that for potentials varying along one
direction only, the tagged particle distribution is the same as the equilibrium
distribution with the temperature equal to the effective temperature obtained
from the violation of the Einstein relation between the self-diffusion and
tagged particle mobility coefficients. We thus prove the usefulness of this
effective temperature for the description of the tagged particle behavior
beyond the realm of linear response. We illustrate our theoretical predictions
with Brownian dynamics computer simulations.Comment: Accepted for publication in Europhys. Let
When it Pays to Rush: Interpreting Morphogen Gradients Prior to Steady-State
During development, morphogen gradients precisely determine the position of
gene expression boundaries despite the inevitable presence of fluctuations.
Recent experiments suggest that some morphogen gradients may be interpreted
prior to reaching steady-state. Theoretical work has predicted that such
systems will be more robust to embryo-to-embryo fluctuations. By analysing two
experimentally motivated models of morphogen gradient formation, we investigate
the positional precision of gene expression boundaries determined by
pre-steady-state morphogen gradients in the presence of embryo-to-embryo
fluctuations, internal biochemical noise and variations in the timing of
morphogen measurement. Morphogens that are direct transcription factors are
found to be particularly sensitive to internal noise when interpreted prior to
steady-state, disadvantaging early measurement, even in the presence of large
embryo-to-embryo fluctuations. Morphogens interpreted by cell-surface receptors
can be measured prior to steady-state without significant decrease in
positional precision provided fluctuations in the timing of measurement are
small. Applying our results to experiment, we predict that Bicoid, a
transcription factor morphogen in Drosophila, is unlikely to be interpreted
prior to reaching steady-state. We also predict that Activin in Xenopus and
Nodal in zebrafish, morphogens interpreted by cell-surface receptors, can be
decoded in pre-steady-state.Comment: 18 pages, 3 figure
Mobility and Diffusion of a Tagged Particle in a Driven Colloidal Suspension
We study numerically the influence of density and strain rate on the
diffusion and mobility of a single tagged particle in a sheared colloidal
suspension. We determine independently the time-dependent velocity
autocorrelation functions and, through a novel method, the response functions
with respect to a small force. While both the diffusion coefficient and the
mobility depend on the strain rate the latter exhibits a rather weak
dependency. Somewhat surprisingly, we find that the initial decay of response
and correlation functions coincide, allowing for an interpretation in terms of
an 'effective temperature'. Such a phenomenological effective temperature
recovers the Einstein relation in nonequilibrium. We show that our data is well
described by two expansions to lowest order in the strain rate.Comment: submitted to EP
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