Gravitational Collapse of a Shell of Quantized Matter

The semi-classical collapse, including lowest order back-reaction, of a thin shell of self-gravitating quantized matter is illustrated. The conditions for which self-gravitating matter forms a thin shell are first discussed and an effective Lagrangian for such matter is obtained. The matter-gravity system is then quantized, the semi-classical limit for gravitation is taken and the method of adiabatic invariants is applied to the resulting time dependent matter Hamiltonian. The governing equations are integrated numerically, for suitable initial conditions, in order to illustrate the effect of back-reaction, due to the creation of matter, in slowing down the collapse near the horizon.Comment: 20 pages, 1 eps figure. Problem with figure fixe

The Rainbow Prim Algorithm for Selecting Putative Orthologous Protein Sequences

We present a selection method designed for eliminating species redundancy in clusters of putative orthologous sequences, to be applied as a post-processing procedure to pre-clustered data obtained from other methods. The algorithm can always zero-out the cluster redundancy while preserving the number of species of the original cluster

Theoretical survey of tidal-charged black holes at the LHC

We analyse a family of brane-world black holes which solve the effective four-dimensional Einstein equations for a wide range of parameters related to the unknown bulk/brane physics. We first constrain the parameters using known experimental bounds and, for the allowed cases, perform a numerical analysis of their time evolution, which includes accretion through the Earth. The study is aimed at predicting the typical behavior one can expect if such black holes were produced at the LHC. Most notably, we find that, under no circumstances, would the black holes reach the (hazardous) regime of Bondi accretion. Nonetheless, the possibility remains that black holes live long enough to escape from the accelerator (and even from the Earth's gravitational field) and result in missing energy from the detectors.Comment: RevTeX4, 12 pages, 4 figures, 5 tables, minor changes to match the accepted version in JHE

Gravitational Collapse of a Radiating Shell

We study the collapse of a self-gravitating and radiating shell. Matter constituting the shell is quantized and the construction is viewed as a semiclassical model of possible black hole formation. It is shown that the shell internal degrees of freedom are excited by the quantum non-adiabaticity of the collapse and, consequently, on coupling them to a massless scalar field, the collapsing matter emits a burst of coherent (thermal) radiation.Comment: LaTeX, 34 pages, 21 EPS figures include

Brane-world black holes and the scale of gravity

A particle in four dimensions should behave like a classical black hole if the horizon radius is larger than the Compton wavelength or, equivalently, if its degeneracy (measured by entropy in units of the Planck scale) is large. For spherically symmetric black holes in 4 + d dimensions, both arguments again lead to a mass threshold MC and degeneracy scale Mdeg of the order of the fundamental scale of gravity MG. In the brane-world, deviations from the Schwarzschild metric induced by bulk effects alter the horizon radius and effective four-dimensional Euclidean action in such a way that MC \simeq Mdeg might be either larger or smaller than MG. This opens up the possibility that black holes exist with a mass smaller than MG and might be produced at the LHC even if M>10 TeV, whereas effects due to bulk graviton exchanges remain undetectable because suppressed by inverse powers of MG. Conversely, even if black holes are not found at the LHC, it is still possible that MC>MG and MG \simeq 1TeV.Comment: 4 pages, no figur

Adiabatic Invariant Treatment of a Collapsing Sphere of Quantized Dust

The semiclassical collapse of a sphere of quantized dust is studied. A Born-Oppenheimer decomposition is performed for the wave function of the system and the semiclassical limit is considered for the gravitational part. The method of adiabatic invariants for time dependent Hamiltonians is then employed to find (approximate) solutions to the quantum dust equations of motions. This allows us to obtain corrections to the adiabatic approximation of the dust states associated with the time evolution of the metric. The diverse non-adiabatic corrections are generally associated with particle (dust) creation and related fluctuations. The back-reaction due to the dominant contribution to particle creation is estimated and seen to slow-down the collapse.Comment: LaTeX, 16 pages, no figures, final version to appear in Class. and Quantum Gravit

Minimum length effects in black hole physics

We review the main consequences of the possible existence of a minimum measurable length, of the order of the Planck scale, on quantum effects occurring in black hole physics. In particular, we focus on the ensuing minimum mass for black holes and how modified dispersion relations affect the Hawking decay, both in four space-time dimensions and in models with extra spatial dimensions. In the latter case, we briefly discuss possible phenomenological signatures.Comment: 29 pages, 12 figures. To be published in "Quantum Aspects of Black Holes", ed. X. Calmet (Springer, 2014

Quantum Black Holes from Cosmic Rays

We investigate the possibility for cosmic ray experiments to discover non-thermal small black holes with masses in the TeV range. Such black holes would result due to the impact between ultra high energy cosmic rays or neutrinos with nuclei from the upper atmosphere and decay instantaneously. They could be produced copiously if the Planck scale is in the few TeV region. As their masses are close to the Planck scale, these holes would typically decay into two particles emitted back-to-back. Depending on the angles between the emitted particles with respect to the center of mass direction of motion, it is possible for the simultaneous showers to be measured by the detectors.Comment: 6 pages, 3 figure

Finding functional motifs in protein sequences with deep learning and natural language models

Recently, prediction of structural/functional motifs in protein sequences takes advantage of powerful machine learning based approaches. Protein encoding adopts protein language models overpassing standard procedures. Different combinations of machine learning and encoding schemas are available for predicting different structural/functional motifs. Particularly interesting is the adoption of protein language models to encode proteins in addition to evolution information and physicochemical parameters. A thorough analysis of recent predictors developed for annotating transmembrane regions, sorting signals, lipidation and phosphorylation sites allows to investigate the state-of-the-art focusing on the relevance of protein language models for the different tasks. This highlights that more experimental data are necessary to exploit available powerful machine learning methods

Large-scale annotation of proteins with labelling methods

We revise a major important problem in bioinformatics: how to annotate protein sequences in the genomic era and all the solutions that have been described by implementing tools based on labelling methods. In this paper we mainly focus on our own work and the theoretical methods that are popular in the field of biosequence analysis in modern molecular biology. We will also review a recent application from our group that largely improves on the topology prediction of disulfide bonds in proteins from Eukaryotic organisms