1,336 research outputs found
Double and multiple knockout simulations for genome-scale metabolic network reconstructions
Constraint-based modeling of genome-scale metabolic network reconstructions
has become a widely used approach in computational biology. Flux coupling
analysis is a constraint-based method that analyses the impact of single
reaction knockouts on other reactions in the network. We present an extension
of flux coupling analysis for double and multiple gene or reaction knockouts,
and develop corresponding algorithms for an in silico simulation. To evaluate
our method, we perform a full single and double knockout analysis on a
selection of genome-scale metabolic network reconstructions and compare the
results
Diffusion in sparse networks: linear to semi-linear crossover
We consider random networks whose dynamics is described by a rate equation,
with transition rates that form a symmetric matrix. The long time
evolution of the system is characterized by a diffusion coefficient . In one
dimension it is well known that can display an abrupt percolation-like
transition from diffusion () to sub-diffusion (D=0). A question arises
whether such a transition happens in higher dimensions. Numerically can be
evaluated using a resistor network calculation, or optionally it can be deduced
from the spectral properties of the system. Contrary to a recent expectation
that is based on a renormalization-group analysis, we deduce that is
finite; suggest an "effective-range-hopping" procedure to evaluate it; and
contrast the results with the linear estimate. The same approach is useful for
the analysis of networks that are described by quasi-one-dimensional sparse
banded matrices.Comment: 13 pages, 4 figures, proofed as publishe
Response of discrete nonlinear systems with many degrees of freedom
We study the response of a large array of coupled nonlinear oscillators to
parametric excitation, motivated by the growing interest in the nonlinear
dynamics of microelectromechanical and nanoelectromechanical systems (MEMS and
NEMS). Using a multiscale analysis, we derive an amplitude equation that
captures the slow dynamics of the coupled oscillators just above the onset of
parametric oscillations. The amplitude equation that we derive here from first
principles exhibits a wavenumber dependent bifurcation similar in character to
the behavior known to exist in fluids undergoing the Faraday wave instability.
We confirm this behavior numerically and make suggestions for testing it
experimentally with MEMS and NEMS resonators.Comment: Version 2 is an expanded version of the article, containing detailed
steps of the derivation that were left out in version 1, but no additional
result
-adic Holography from the Hyperbolic Fracton Model
We reveal a low-temperature duality between the hyperbolic lattice model
featuring fractons and infinite decoupled copies of Zabrodin's -adic model
of AdS/CFT. The core of the duality is the subsystem symmetries of the
hyperbolic fracton model, which always act on both the boundary and the bulk.
These subsystem symmetries are associated with fractal trees embedded in the
hyperbolic lattice, which have the same geometry as Zabrodin's model. The
fracton model, rewritten as electrostatics theory on these trees, matches the
equation of motion of Zabrodin's model. The duality extends from the action to
lattice defects as -adic black holes.Comment: 6 pages, 5 figures, and appendi
An operational view of intercellular signaling pathways
Animal cells use a conserved repertoire of intercellular signaling pathways to communicate with one another. These pathways are well-studied from a molecular point of view. However, we often lack an “operational” understanding that would allow us to use these pathways to rationally control cellular behaviors. This requires knowing what dynamic input features each pathway perceives and how it processes those inputs to control downstream processes. To address these questions, researchers have begun to reconstitute signaling pathways in living cells, analyzing their dynamic responses to stimuli, and developing new functional representations of their behavior. Here we review important insights obtained through these new approaches, and discuss challenges and opportunities in understanding signaling pathways from an operational point of view
From Lagrangian Products to Toric Domains via the Toda Lattice
In this paper we use the periodic Toda lattice to show that certain
Lagrangian product configurations in the classical phase space are
symplectically equivalent to toric domains. In particular, we prove that the
Lagrangian product of a certain simplex and the Voronoi cell of the root
lattice is symplectically equivalent to a Euclidean ball. As a
consequence, we deduce that the Lagrangian product of an equilateral triangle
and a regular hexagon is symplectomorphic to a Euclidean ball in dimension 4.Comment: 22 pages, 5 figures, comments are welcome
Light with tunable non-Markovian phase imprint
We introduce a simple and flexible method to generate spatially non-Markovian
light with tunable coherence properties in one and two dimensions. The unusual
behavior of this light is demonstrated experimentally by probing the far field
and recording its diffraction pattern after a double slit: In both cases we
observe instead of a central intensity maximum a line or cross shaped dark
region, whose width and profile depend on the non-Markovian coherence
properties. Since these properties can be controlled and easily reproduced in
experiment, the presented approach lends itself to serve as a testbed to gain a
deeper understanding of non-Markovian processes
Relativistic Hydrodynamics with General Anomalous Charges
We consider the hydrodynamic regime of gauge theories with general triangle
anomalies, where the participating currents may be global or gauged, abelian or
non-abelian. We generalize the argument of arXiv:0906.5044, and construct at
the viscous order the stress-energy tensor, the charge currents and the entropy
current.Comment: 13 pages, Revte
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