Least-squares methods for identifying biochemical regulatory networks from noisy measurements

<b>Background</b>: We consider the problem of identifying the dynamic interactions in biochemical networks from noisy experimental data. Typically, approaches for solving this problem make use of an estimation algorithm such as the well-known linear Least-Squares (LS) estimation technique. We demonstrate that when time-series measurements are corrupted by white noise and/or drift noise, more accurate and reliable identification of network interactions can be achieved by employing an estimation algorithm known as Constrained Total Least Squares (CTLS). The Total Least Squares (TLS) technique is a generalised least squares method to solve an overdetermined set of equations whose coefficients are noisy. The CTLS is a natural extension of TLS to the case where the noise components of the coefficients are correlated, as is usually the case with time-series measurements of concentrations and expression profiles in gene networks. <b>Results</b>: The superior performance of the CTLS method in identifying network interactions is demonstrated on three examples: a genetic network containing four genes, a network describing p53 activity and <i>mdm2</i> messenger RNA interactions, and a recently proposed kinetic model for interleukin (IL)-6 and (IL)-12b messenger RNA expression as a function of ATF3 and NF-κB promoter binding. For the first example, the CTLS significantly reduces the errors in the estimation of the Jacobian for the gene network. For the second, the CTLS reduces the errors from the measurements that are corrupted by white noise and the effect of neglected kinetics. For the third, it allows the correct identification, from noisy data, of the negative regulation of (IL)-6 and (IL)-12b by ATF3. <b>Conclusion</b>: The significant improvements in performance demonstrated by the CTLS method under the wide range of conditions tested here, including different levels and types of measurement noise and different numbers of data points, suggests that its application will enable more accurate and reliable identification and modelling of biochemical networks

Stability of inflating branes in a texture

We investigate the stability of inflating branes embedded in an O(2) texture formed in one extra dimension. The model contains two 3-branes of nonzero tension, and the extra dimension is compact. When the gravitational perturbation is applied, the vacuum energy which is responsible for inflation on the branes stabilizes the branes if the symmetry-breaking scale of the texture is smaller than some critical value. This critical value is determined by the particle-hierarchy scale between the two branes, and is smaller than the 5D Planck-mass scale. The scale of the vacuum energy can be considerably low in providing the stability. This stability story is very different from the flat-brane case which always suffers from the instability due to the gravitational perturbation.Comment: 16 pages, 5 eps figures, revte

Development Of Third Harmonic Generation As A Short Pulse Probe Of Shock Heated Material

We are studying high-pressure laser produced shock waves in silicon (100). To examine the material dynamics, we are performing pump-probe style experiments utilizing 600 ps and 40 fs laser pulses from a Ti:sapphire laser. Two-dimensional interferometry reveals information about the shock breakout, while third harmonic light generated at the rear surface is used to infer the crystalline state of the material as a function of time. Sustained third harmonic generation (THG) during a similar to 100 kbar shock breakout indicate that the rear surface remains crystalline for at least 3 ns. However, a decrease in THG during a similar to 300 kbar shock breakout suggests a different behavior, which could include a change in crystalline structure.Mechanical Engineerin

Effective Lagrangian from Higher Curvature Terms: Absence of vDVZ Discontinuity in AdS Space

We argue that the van Dam-Veltman-Zakharov discontinuity arising in the $M^2 \to 0$ limit of the massive graviton through an explicit Pauli-Fierz mass term could be absent in anti de Sitter space. This is possible if the graviton can acquire mass spontaneously from the higher curvature terms or/and the massless limit $M^2\to 0$ is attained faster than the cosmological constant $\Lambda \to 0$. We discuss the effects of higher-curvature couplings and of an explicit cosmological term ($\Lambda$) on stability of such continuity and of massive excitations.Comment: 23 pages, Latex, the version to appear in Class. Quant. Gra

Quantum Mechanics on the h-deformed Quantum Plane

We find the covariant deformed Heisenberg algebra and the Laplace-Beltrami operator on the extended $h$-deformed quantum plane and solve the Schr\"odinger equations explicitly for some physical systems on the quantum plane. In the commutative limit the behaviour of a quantum particle on the quantum plane becomes that of the quantum particle on the Poincar\'e half-plane, a surface of constant negative Gaussian curvature. We show the bound state energy spectra for particles under specific potentials depend explicitly on the deformation parameter $h$. Moreover, it is shown that bound states can survive on the quantum plane in a limiting case where bound states on the Poincar\'e half-plane disappear.Comment: 16pages, Latex2e, Abstract and section 4 have been revise

Quasi-normal modes for doubly rotating black holes

Based on the work of Chen, L\"u and Pope, we derive expressions for the $D\geq 6$ dimensional metric for Kerr-(A)dS black holes with two independent rotation parameters and all others set equal to zero: $a_1\neq 0, a_2\neq0, a_3=a_4=...=0$. The Klein-Gordon equation is then explicitly separated on this background. For $D\geq 6$ this separation results in a radial equation coupled to two generalized spheroidal angular equations. We then develop a full numerical approach that utilizes the Asymptotic Iteration Method (AIM) to find radial Quasi-Normal Modes (QNMs) of doubly rotating flat Myers-Perry black holes for slow rotations. We also develop perturbative expansions for the angular quantum numbers in powers of the rotation parameters up to second order.Comment: RevTeX 4-1, various figure

Gravitational field of vacuumless defects

It has been recently shown that topological defects can arise in symmetry breaking models where the scalar field potential $V(\phi)$ has no minima and is a monotonically decreasing function of $|\phi|$. Here we study the gravitational fields produced by such vacuumless defects in the cases of both global and gauge symmetry breaking. We find that a global monopole has a strongly repulsive gravitational field, and its spacetime has an event horizon similar to that in de Sitter space. A gauge monopole spacetime is essentially that of a magnetically charged black hole. The gravitational field of a global string is repulsive and that of a gauge string is attractive at small distances and repulsive at large distances. Both gauge and global string spacetimes have singularities at a finite distance from the string core.Comment: 19 pages, REVTeX, 6 Postscript figure

Magnetic Moments of Heavy Baryons

First non-trivial chiral corrections to the magnetic moments of triplet (T) and sextet (S^(*)) heavy baryons are calculated using Heavy Hadron Chiral Perturbation Theory. Since magnetic moments of the T-hadrons vanish in the limit of infinite heavy quark mass (m_Q->infinity), these corrections occur at order O(1/(m_Q \Lambda_\chi^2)) for T-baryons while for S^(*)-baryons they are of order O(1/\Lambda_\chi^2). The renormalization of the chiral loops is discussed and relations among the magnetic moments of different hadrons are provided. Previous results for T-baryons are revised.Comment: 11 Latex pages, 2 figures, to be published in Phys.Rev.