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 $w_{nm}$ that form a symmetric matrix. The long time evolution of the system is characterized by a diffusion coefficient $D$. In one dimension it is well known that $D$ can display an abrupt percolation-like transition from diffusion ($D>0$) to sub-diffusion (D=0). A question arises whether such a transition happens in higher dimensions. Numerically $D$ 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 $D$ 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

pp-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 $p$-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 $p$-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 $A_n$ 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