99 research outputs found
Protein-DNA computation by stochastic assembly cascade
The assembly of RecA on single-stranded DNA is measured and interpreted as a
stochastic finite-state machine that is able to discriminate fine differences
between sequences, a basic computational operation. RecA filaments efficiently
scan DNA sequence through a cascade of random nucleation and disassembly events
that is mechanistically similar to the dynamic instability of microtubules.
This iterative cascade is a multistage kinetic proofreading process that
amplifies minute differences, even a single base change. Our measurements
suggest that this stochastic Turing-like machine can compute certain integral
transforms.Comment: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129313/
http://www.pnas.org/content/99/18/11589.abstrac
Diffusion of a Deformable Body in a random Flow
We consider a deformable body immersed in an incompressible liquid that is
randomly stirred. Sticking to physical situations in which the body departs
only slightly from its spherical shape, we calculate the diffusion constant of
the body. We give explicitly the dependence of the diffusion constant on the
velocity correlations in the liquid and on the size of the body. We emphasize
the particular case in which the random velocity field follows from thermal
agitation.Comment: 9 pages, 2 figures, late
Power-Law Behavior of Power Spectra in Low Prandtl Number Rayleigh-Benard Convection
The origin of the power-law decay measured in the power spectra of low
Prandtl number Rayleigh-Benard convection near the onset of chaos is addressed
using long time numerical simulations of the three-dimensional Boussinesq
equations in cylindrical domains. The power-law is found to arise from
quasi-discontinuous changes in the slope of the time series of the heat
transport associated with the nucleation of dislocation pairs and roll
pinch-off events. For larger frequencies, the power spectra decay exponentially
as expected for time continuous deterministic dynamics.Comment: (10 pages, 6 figures
Discerning Aggregation in Homogeneous Ensembles: A General Description of Photon Counting Spectroscopy in Diffusing Systems
In order to discern aggregation in solutions, we present a quantum mechanical
analog of the photon statistics from fluorescent molecules diffusing through a
focused beam. A generating functional is developed to fully describe the
experimental physical system as well as the statistics. Histograms of the
measured time delay between photon counts are fit by an analytical solution
describing the static as well as diffusing regimes. To determine empirical
fitting parameters, fluorescence correlation spectroscopy is used in parallel
to the photon counting. For expedient analysis, we find that the distribution's
deviation from a single Poisson shows a difference between two single fluor
moments or a double fluor aggregate of the same total intensities. Initial
studies were performed on fixed-state aggregates limited to dimerization.
However preliminary results on reactive species suggest that the method can be
used to characterize any aggregating system.Comment: 30 pages, 5 figure
Spiral Defects in Motility Assays: A Measure of Motor Protein Force
In a commonly used motility assay, cytoskeletal filaments are observed as they glide over a surface coated with motor proteins. Defects in the motion frequently interrupt the flow of filaments. Examination of one such defect, in which a filament adopts a spiral form and rotates about a fixed point, provides a simple measure of the force exerted by the motor proteins. We demonstrate the universality of this approach by estimating the elementary forces of both myosin and kinesin
Multiple-length-scale elastic instability mimics parametric resonance of nonlinear oscillators
Spatially confined rigid membranes reorganize their morphology in response to
the imposed constraints. A crumpled elastic sheet presents a complex pattern of
random folds focusing the deformation energy while compressing a membrane
resting on a soft foundation creates a regular pattern of sinusoidal wrinkles
with a broad distribution of energy. Here, we study the energy distribution for
highly confined membranes and show the emergence of a new morphological
instability triggered by a period-doubling bifurcation. A periodic
self-organized focalization of the deformation energy is observed provided an
up-down symmetry breaking, induced by the intrinsic nonlinearity of the
elasticity equations, occurs. The physical model, exhibiting an analogy with
parametric resonance in nonlinear oscillator, is a new theoretical toolkit to
understand the morphology of various confined systems, such as coated materials
or living tissues, e.g., wrinkled skin, internal structure of lungs, internal
elastica of an artery, brain convolutions or formation of fingerprints.
Moreover, it opens the way to new kind of microfabrication design of
multiperiodic or chaotic (aperiodic) surface topography via self-organization.Comment: Submitted for publicatio
I. HÉLIUM SUPERFLUIDEPROPRIÉTÉS DE TRANSPORT ET COHÉRENCE DE PHASE DANS L'HÉLIUM SUPERFLUIDE
Nous étudions les propriétés de transport de l'hélium superfluide, propriétés de l'écoulement sous et sur critique. Les équations du mouvement du superfluide sont données à partir de deux modèles, l'un hydrodynamique, l'autre à partir de la notion de paramètre d'ordre. La deuxième partie consiste en une revue des expériences cruciales sur les courants permanents suivie d'une étude des superfuites et du transport dans les films d'hélium. Nous terminons par une analyse expérimentale des effets Josephson-Anderson.Transport properties of superfluid helium, critical and sub-critical flow, are presented. Experiments on permanent flow and Josephson-Anderson effects are described
- …