2,645 research outputs found
Joint Reconstruction of Multi-view Compressed Images
The distributed representation of correlated multi-view images is an
important problem that arise in vision sensor networks. This paper concentrates
on the joint reconstruction problem where the distributively compressed
correlated images are jointly decoded in order to improve the reconstruction
quality of all the compressed images. We consider a scenario where the images
captured at different viewpoints are encoded independently using common coding
solutions (e.g., JPEG, H.264 intra) with a balanced rate distribution among
different cameras. A central decoder first estimates the underlying correlation
model from the independently compressed images which will be used for the joint
signal recovery. The joint reconstruction is then cast as a constrained convex
optimization problem that reconstructs total-variation (TV) smooth images that
comply with the estimated correlation model. At the same time, we add
constraints that force the reconstructed images to be consistent with their
compressed versions. We show by experiments that the proposed joint
reconstruction scheme outperforms independent reconstruction in terms of image
quality, for a given target bit rate. In addition, the decoding performance of
our proposed algorithm compares advantageously to state-of-the-art distributed
coding schemes based on disparity learning and on the DISCOVER
A Criterion That Determines Fast Folding of Proteins: A Model Study
We consider the statistical mechanics of a full set of two-dimensional
protein-like heteropolymers, whose thermodynamics is characterized by the
coil-to-globular () and the folding () transition temperatures.
For our model, the typical time scale for reaching the unique native
conformation is shown to scale as , where
, is the number of residues, and scales
algebraically with . We argue that scales linearly with the inverse of
entropy of low energy non-native states, whereas is almost
independent of it. As , non-productive intermediates
decrease, and the initial rapid collapse of the protein leads to structures
resembling the native state. Based solely on {\it accessible} information,
can be used to predict sequences that fold rapidly.Comment: 10 pages, latex, figures upon reques
Cellular signaling networks function as generalized Wiener-Kolmogorov filters to suppress noise
Cellular signaling involves the transmission of environmental information
through cascades of stochastic biochemical reactions, inevitably introducing
noise that compromises signal fidelity. Each stage of the cascade often takes
the form of a kinase-phosphatase push-pull network, a basic unit of signaling
pathways whose malfunction is linked with a host of cancers. We show this
ubiquitous enzymatic network motif effectively behaves as a Wiener-Kolmogorov
(WK) optimal noise filter. Using concepts from umbral calculus, we generalize
the linear WK theory, originally introduced in the context of communication and
control engineering, to take nonlinear signal transduction and discrete
molecule populations into account. This allows us to derive rigorous
constraints for efficient noise reduction in this biochemical system. Our
mathematical formalism yields bounds on filter performance in cases important
to cellular function---like ultrasensitive response to stimuli. We highlight
features of the system relevant for optimizing filter efficiency, encoded in a
single, measurable, dimensionless parameter. Our theory, which describes noise
control in a large class of signal transduction networks, is also useful both
for the design of synthetic biochemical signaling pathways, and the
manipulation of pathways through experimental probes like oscillatory input.Comment: 15 pages, 5 figures; to appear in Phys. Rev.
Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model
Folding of Ubiquitin (Ub) is investigated at low and neutral pH at different
temperatures using simulations of the coarse-grained Self-Organized-Polymer
model with side chains. The calculated radius of gyration, showing dramatic
variations with pH, is in excellent agreement with scattering experiments. At
Ub folds in a two-state manner at low and neutral pH. Clustering analysis
of the conformations sampled in equilibrium folding trajectories at , with
multiple transitions between the folded and unfolded states, show a network of
metastable states connecting the native and unfolded states. At low and neutral
pH, Ub folds with high probability through a preferred set of conformations
resulting in a pH-dependent dominant folding pathway. Folding kinetics reveal
that Ub assembly at low pH occurs by multiple pathways involving a combination
of nucleation-collapse and diffusion collision mechanism. The mechanism by
which Ub folds is dictated by the stability of the key secondary structural
elements responsible for establishing long range contacts and collapse of Ub.
Nucleation collapse mechanism holds if the stability of these elements are
marginal, as would be the case at elevated temperatures. If the lifetimes
associated with these structured microdomains are on the order of hundreds of
then Ub folding follows the diffusion-collision mechanism with
intermediates many of which coincide with those found in equilibrium. Folding
at neutral pH is a sequential process with a populated intermediate resembling
that sampled at equilibrium. The transition state structures, obtained using a
analysis, are homogeneous and globular with most of the secondary
and tertiary structures being native-like. Many of our findings are not only in
agreement with experiments but also provide missing details not resolvable in
standard experiments
Multiple barriers in forced rupture of protein complexes
Curvatures in the most probable rupture force () versus log-loading rate
() observed in dynamic force spectroscopy (DFS) on biomolecular
complexes are interpreted using a one-dimensional free energy profile with
multiple barriers or a single barrier with force-dependent transition state.
Here, we provide a criterion to select one scenario over another. If the
rupture dynamics occurs by crossing a single barrier in a physical free energy
profile describing unbinding, the exponent , from with being a critical force in the
absence of force, is restricted to . For biotin-ligand
complexes and leukocyte-associated antigen-1 bound to intercellular adhesion
molecules, which display large curvature in the DFS data, fits to experimental
data yield , suggesting that ligand unbinding is associated with
multiple-barrier crossing.Comment: 8 pages, 5 figure
- …