Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming

A fundamental question in systems biology is the construction and training to data of mathematical models. Logic formalisms have become very popular to model signaling networks because their simplicity allows us to model large systems encompassing hundreds of proteins. An approach to train (Boolean) logic models to high-throughput phospho-proteomics data was recently introduced and solved using optimization heuristics based on stochastic methods. Here we demonstrate how this problem can be solved using Answer Set Programming (ASP), a declarative problem solving paradigm, in which a problem is encoded as a logical program such that its answer sets represent solutions to the problem. ASP has significant improvements over heuristic methods in terms of efficiency and scalability, it guarantees global optimality of solutions as well as provides a complete set of solutions. We illustrate the application of ASP with in silico cases based on realistic networks and data

Energy-Momentum Tensor of Particles Created in an Expanding Universe

We present a general formulation of the time-dependent initial value problem for a quantum scalar field of arbitrary mass and curvature coupling in a FRW cosmological model. We introduce an adiabatic number basis which has the virtue that the divergent parts of the quantum expectation value of the energy-momentum tensor are isolated in the vacuum piece of , and may be removed using adiabatic subtraction. The resulting renormalized is conserved, independent of the cutoff, and has a physically transparent, quasiclassical form in terms of the average number of created adiabatic `particles'. By analyzing the evolution of the adiabatic particle number in de Sitter spacetime we exhibit the time structure of the particle creation process, which can be understood in terms of the time at which different momentum scales enter the horizon. A numerical scheme to compute as a function of time with arbitrary adiabatic initial states (not necessarily de Sitter invariant) is described. For minimally coupled, massless fields, at late times the renormalized goes asymptotically to the de Sitter invariant state previously found by Allen and Folacci, and not to the zero mass limit of the Bunch-Davies vacuum. If the mass m and the curvature coupling xi differ from zero, but satisfy m^2+xi R=0, the energy density and pressure of the scalar field grow linearly in cosmic time demonstrating that, at least in this case, backreaction effects become significant and cannot be neglected in de Sitter spacetime.Comment: 28 pages, Revtex, 11 embedded .ps figure

QFT, String Temperature and the String Phase of De Sitter Space-time

The density of mass levels \rho(m) and the critical temperature for strings in de Sitter space-time are found. QFT and string theory in de Sitter space are compared. A `Dual'-transform is introduced which relates classical to quantum string lengths, and more generally, QFT and string domains. Interestingly, the string temperature in De Sitter space turns out to be the Dual transform of the QFT-Hawking-Gibbons temperature. The back reaction problem for strings in de Sitter space is addressed selfconsistently in the framework of the `string analogue' model (or thermodynamical approach), which is well suited to combine QFT and string study.We find de Sitter space-time is a self-consistent solution of the semiclassical Einstein equations in this framework. Two branches for the scalar curvature R(\pm) show up: a classical, low curvature solution (-), and a quantum high curvature solution (+), enterely sustained by the strings. There is a maximal value for the curvature R_{\max} due to the string back reaction. Interestingly, our Dual relation manifests itself in the back reaction solutions: the (-) branch is a classical phase for the geometry with intrinsic temperature given by the QFT-Hawking-Gibbons temperature.The (+) is a stringy phase for the geometry with temperature given by the intrinsic string de Sitter temperature. 2 + 1 dimensions are considered, but conclusions hold generically in D dimensions.Comment: LaTex, 24 pages, no figure

The Dimensional-Reduction Anomaly in Spherically Symmetric Spacetimes

In D-dimensional spacetimes which can be foliated by n-dimensional homogeneous subspaces, a quantum field can be decomposed in terms of modes on the subspaces, reducing the system to a collection of (D-n)-dimensional fields. This allows one to write bare D-dimensional field quantities like the Green function and the effective action as sums of their (D-n)-dimensional counterparts in the dimensionally reduced theory. It has been shown, however, that renormalization breaks this relationship between the original and dimensionally reduced theories, an effect called the dimensional-reduction anomaly. We examine the dimensional-reduction anomaly for the important case of spherically symmetric spaces.Comment: LaTeX, 19 pages, 2 figures. v2: calculations simplified, references adde

ASTEC -- the Aarhus STellar Evolution Code

The Aarhus code is the result of a long development, starting in 1974, and still ongoing. A novel feature is the integration of the computation of adiabatic oscillations for specified models as part of the code. It offers substantial flexibility in terms of microphysics and has been carefully tested for the computation of solar models. However, considerable development is still required in the treatment of nuclear reactions, diffusion and convective mixing.Comment: Astrophys. Space Sci, in the pres

Analytical approximation of the stress-energy tensor of a quantized scalar field in static spherically symmetric spacetimes

Analytical approximations for ${}$ and ${}$ of a quantized scalar field in static spherically symmetric spacetimes are obtained. The field is assumed to be both massive and massless, with an arbitrary coupling $\xi$ to the scalar curvature, and in a zero temperature vacuum state. The expressions for ${}$ and ${}$ are divided into low- and high-frequency parts. The contributions of the high-frequency modes to these quantities are calculated for an arbitrary quantum state. As an example, the low-frequency contributions to ${}$ and ${}$ are calculated in asymptotically flat spacetimes in a quantum state corresponding to the Minkowski vacuum (Boulware quantum state). The limits of the applicability of these approximations are discussed.Comment: revtex4, 17 pages; v2: three references adde

Method to compute the stress-energy tensor for the massless spin 1/2 field in a general static spherically symmetric spacetime

A method for computing the stress-energy tensor for the quantized, massless, spin 1/2 field in a general static spherically symmetric spacetime is presented. The field can be in a zero temperature state or a non-zero temperature thermal state. An expression for the full renormalized stress-energy tensor is derived. It consists of a sum of two tensors both of which are conserved. One tensor is written in terms of the modes of the quantized field and has zero trace. In most cases it must be computed numerically. The other tensor does not explicitly depend on the modes and has a trace equal to the trace anomaly. It can be used as an analytic approximation for the stress-energy tensor and is equivalent to other approximations that have been made for the stress-energy tensor of the massless spin 1/2 field in static spherically symmetric spacetimes.Comment: 34 pages, no figure

Stellar Inversion Techniques

Stellar seismic inversions have proved to be a powerful technique for probing the internal structure of stars, and paving the way for a better understanding of the underlying physics by revealing some of the shortcomings in current stellar models. In this lecture, we provide an introduction to this topic by explaining kernel-based inversion techniques. Specifically, we explain how various kernels are obtained from the pulsation equations, and describe inversion techniques such as the Regularised Least-Squares (RLS) and Optimally Localised Averages (OLA) methods.Comment: 20 pages, 8 figures. Lecture presented at the IVth Azores International Advanced School in Space Sciences on "Asteroseismology and Exoplanets: Listening to the Stars and Searching for New Worlds" (arXiv:1709.00645), which took place in Horta, Azores Islands, Portugal in July 201

Casimir Effect, Achucarro-Ortiz Black Hole and the Cosmological Constant

We treat the two-dimensional Achucarro-Ortiz black hole (also known as (1+1) dilatonic black hole) as a Casimir-type system. The stress tensor of a massless scalar field satisfying Dirichlet boundary conditions on two one-dimensional "walls" ("Dirichlet walls") is explicitly calculated in three different vacua. Without employing known regularization techniques, the expression in each vacuum for the stress tensor is reached by using the Wald's axioms. Finally, within this asymptotically non-flat gravitational background, it is shown that the equilibrium of the configurations, obtained by setting Casimir force to zero, is controlled by the cosmological constant.Comment: 20 pages, LaTeX, minor corrections, comments and clarifications added, version to appear in Phys. Rev.

Frame Theory for Signal Processing in Psychoacoustics

This review chapter aims to strengthen the link between frame theory and signal processing tasks in psychoacoustics. On the one side, the basic concepts of frame theory are presented and some proofs are provided to explain those concepts in some detail. The goal is to reveal to hearing scientists how this mathematical theory could be relevant for their research. In particular, we focus on frame theory in a filter bank approach, which is probably the most relevant view-point for audio signal processing. On the other side, basic psychoacoustic concepts are presented to stimulate mathematicians to apply their knowledge in this field