arXiv subjects

Raul Rabadan

Publications and source records attributed to Raul Rabadan.

33 records · Page 2Linked to original sources

arXiv2011

Identifying Hosts of Families of Viruses: A Machine Learning Approach

Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely host of a virus, can be ambiguous when studying species very distant to known species and when there is very little reliable sequence information available in the early stages of the pandemic. Motivated by an existing framework for representing biological sequence information, we learn sparse, tree-structured models, built from decision rules based on subsequences, to predict viral hosts from protein sequence data using popular discriminative machine learning tools. Furthermore, the predictive motifs robustly selected by the learning algorithm are found to show strong host-specificity and occur in highly conserved regions of the viral proteome.

q-bio.QM↗

arXiv2011

Understanding the Origins of a Pandemic Virus

Understanding the origin of infectious diseases provides scientifically based rationales for implementing public health measures that may help to avoid or mitigate future epidemics. The recent ancestors of a pandemic virus provide invaluable information about the set of minimal genomic alterations that transformed a zoonotic agent into a full human pandemic. Since the first confirmed cases of the H1N1 pandemic virus in the spring of 2009, several hypotheses about the strain's origins have been proposed. However, how, where, and when it first infected humans is still far from clear. The only way to piece together this epidemiological puzzle relies on the collective effort of the international scientific community to increase genomic sequencing of influenza isolates, especially ones collected in the months prior to the origin of the pandemic.

q-bio.PE↗

arXiv2010

Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data

Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing, expression profiles, proteomics, and electronic health records are some examples of such technologies. Extracting meaningful information from those technologies requires careful analysis of the large volumes of data they produce. In this note, we present a set of distributions that commonly appear in the analysis of such data. These distributions present some interesting features: they are discontinuous in the rational numbers, but continuous in the irrational numbers, and possess a certain self-similar (fractal-like) structure. The first set of examples which we present here are drawn from a high-throughput sequencing experiment. Here, the self-similar distributions appear as part of the evaluation of the error rate of the sequencing technology and the identification of tumorogenic genomic alterations. The other examples are obtained from risk factor evaluation and analysis of relative disease prevalence and co-mordbidity as these appear in electronic clinical data. The distributions are also relevant to identification of subclonal populations in tumors and the study of the evolution of infectious diseases, and more precisely the study of quasi-species and intrahost diversity of viral populations.

q-bio.QM↗

arXiv2008

Spectroscopic Constraints on (pseudo-)Scalar Particles from Compact Astrophysical Objects

We propose a new method to search for light (pseudo-)scalar particles in the spectra of compact astrophysical objects such as magnetars, pulsars, and quasars. On accounts of compact astrophysical objects having intense magnetic fields extending over large volumes, they provide good conditions for efficient photon-particle oscillations via the Primakoff process. In particular, we show that if the coupling constant for light (<1e-2 eV) axions, g>1e-13 [1/GeV] then it is likely that absorption-like features would be detectable in the spectrum of compact astrophysical sources.

astro-ph↗

arXiv2008

Spectral Signatures of Photon-Particle Oscillations from Celestial Objects

We give detailed predictions for the spectral signatures arising from photon-particle oscillations in astrophysical objects. The calculations include quantum electrodynamic effects as well as those due to active relativistic plasma. We show that, by studying the spectra of compact sources, it may be possible to directly detect (pseudo-)scalar particles, such as the axion, with much greater sensitivity, by roughly three orders of magnitude, than is currently achievable by other methods. In particular, if such particles exist with masses m_a<0.01[eV] and coupling constant to the electromagnetic field, g>1e-13[1/GeV], then their oscillation signatures are likely to be lurking in the spectra of magnetars, pulsars, and quasars.

astro-ph↗

arXiv2005

Collider Bounds on Pseudoscalars Coupling to Gauge Bosons

We bound the coupling of pseudo-scalar particles to Tr G^G_{QCD} using (the lack of) monojet plus missing E_T events at the Tevatron, and estimate the bounds obtainable from LHC. In addition, we revisit the bounds on the coupling to F^F_{EM} from e^+e^- collider events with single photon and missing E_T final states. This is especially interesting in light of the recent experimental results from the PVLAS collaboration, which we believe can be tested by data which will be available in the near future.

hep-ph↗

arXiv2005

Photon Regeneration from Pseudoscalars at X-ray Laser Facilities

Recently, the PVLAS collaboration has reported an anomalously large rotation of the polarization of light in the presence of a magnetic field. As a possible explanation they consider the existence of a light pseudoscalar particle coupled to two photons. In this note, we propose a method of independently testing this result by using a high-energy photon regeneration experiment (the X-ray analogue of "invisible light shining through walls") using the synchrotron X-rays from a free-electron laser (FEL). With such an experiment the region of parameter space implied by PVLAS could be probed in a matter of minutes.

hep-ph↗

arXiv2005

Non-perturbative orientifold transitions at the conifold

After orientifold projection, the conifold singularity in hypermultiplet moduli space of Calabi-Yau compactifications cannot be avoided by geometric deformations. We study the non-perturbative fate of this singularity in a local model involving O6-planes and D6-branes wrapping the deformed conifold in Type IIA string theory. We classify possible A-type orientifolds of the deformed conifold and find that they cannot all be continued to the small resolution. When passing through the singularity on the deformed side, the O-plane charge generally jumps by the class of the vanishing cycle. To decide which classical configurations are dynamically connected, we construct the quantum moduli space by lifting the orientifold to M-theory as well as by looking at the superpotential. We find a rich pattern of smooth and phase transitions depending on the total sixbrane charge. Non-BPS states from branes wrapped on non-supersymmetric bolts are responsible for a phase transition. We also clarify the nature of a Z_2 valued D0-brane charge in the 6-brane background. Along the way, we obtain a new metric of G_2 holonomy corresponding to an O6-plane on the three sphere of the deformed conifold.

hep-th↗

arXiv2003

(Re)constructing Dimensions

Compactifying a higher-dimensional theory defined in R^{1,3+n} on an n-dimensional manifold {\cal M} results in a spectrum of four-dimensional (bosonic) fields with masses m^2_i = λ_i, where - λ_i are the eigenvalues of the Laplacian on the compact manifold. The question we address in this paper is the inverse: given the masses of the Kaluza-Klein fields in four dimensions, what can we say about the size and shape (i.e. the topology and the metric) of the compact manifold? We present some examples of isospectral manifolds (i.e., different manifolds which give rise to the same Kaluza-Klein mass spectrum). Some of these examples are Ricci-flat, complex and Kähler and so they are isospectral backgrounds for string theory. Utilizing results from finite spectral geometry, we also discuss the accuracy of reconstructing the properties of the compact manifold (e.g., its dimension, volume, and curvature etc) from measuring the masses of only a finite number of Kaluza-Klein modes.

hep-th↗

arXiv2002

Dilaton tadpoles and D-brane interactions in compact spaces

We analyse some physical consequences when supersymmetry is broken by a set of D-branes and/or orientifold planes in Type II string theories. Generically, there are global dilaton tadpoles at the disk level when the transverse space is compact. By taking the toy model of a set of electric charges in a compact space, we discuss two different effects appearing when global tadpoles are not cancelled. On the compact directions a constant term appears that allows to solve the equations of motion. On the non-compact directions Poincaré invariance is broken. We analyse some examples where the Poincaré invariance is broken along the time direction (cosmological models).After that, we discuss how to obtain a finite interaction between D-branes and orientifold planes in the compact space at the supergravity level.

hep-th↗

arXiv2002

Complex structure moduli stability in toroidal compactifications

In this paper we present a classification of possible dynamics of closed string moduli within specific toroidal compactifications of Type II string theories due to the NS-NS tadpole terms in the reduced action. They appear as potential terms for the moduli when supersymmetry is broken due to the presence of D-branes. We particularise to specific constructions with two, four and six-dimensional tori, and study the stabilisation of the complex structure moduli at the disk level. We find that, depending on the cycle on the compact space where the brane is wrapped, there are three possible cases: i) there is a solution inside the complex structure moduli space, and the configuration is stable at the critical point, ii) the moduli fields are driven towards the boundary of the moduli space, iii) there is no stable solution at the minimum of the potential and the system decays into a set of branes.

hep-th↗

arXiv2002

M-theory lift of brane-antibrane systems and localised closed string tachyons

We discuss the lift of certain D6-antiD6-brane systems to M-theory. These are purely gravitational configurations with a bolt singularity. When reduced along a trivial circle, and for large bolt radius, the bolt is related to a non-supersymmetric orbifold type of singularity where some closed string tachyons are expected in the twisted sectors. This is a kind of open-closed string duality that relates open string tachyons on one side and localised tachyons in the other. We consider the evolution of the system of branes from M-theory point of view. This evolution gives rise to a brane-antibrane annihilation on the brane side. On the gravity side, the evolution is related to a reduction of the order of the orbifold and to a contraction of the bolt to a nut or flat space if the system has non-vanishing or vanishing charge, respectively. We also consider the inverse process of reducing a non-supersymmetric orbifold to a D6-brane system. For $C^2/Z_N\times Z_M$, the reduced system is a fractional D6-brane at an orbifold singularity $C/Z_M$.

hep-th↗

arXiv2000

Z_N x Z_M orientifolds with and without discrete torsion

We discuss compact four-dimensional Z_N x Z_M type IIB orientifolds. We take a systematic approach to classify the possible models and construct them explicitely. The supersymmetric orientifolds of this type have already been constructed some time ago. We find that there exist several consistent orientifolds for each of the discrete groups Z_2 x Z_2, Z_2 x Z_4, Z_4 x Z_4, Z_2 x Z_6, Z_2 x Z_6' and Z_6 x Z_6 if anti-D5-branes are introduced. Supersymmetry is broken by the open strings ending on antibranes. The rank of the gauge group is reduced by a factor two if the underlying orbifold space has discrete torsion.

hep-th↗

arXiv2000

D=4, N=1 orientifolds with vector structure

We construct compact type IIB orientifolds with discrete groups Z_4, Z_6, Z_6', Z_8, Z_12 and Z_12'. These models are N=1 supersymmetric in D=4 and have vector structure. The possibility of having vector structure in Z_N orientifolds with even N arises due to an alternative Omega-projection in the twisted sectors. Some of the models without vector structure are known to be inconsistent because of uncancelled tadpoles. We show that vector structure leads to a sign flip in the twisted Klein bottle contribution. As a consequence, all the tadpoles can be cancelled by introducing D9-branes and D5-branes.

hep-th↗

arXiv2000

Orientifolds with discrete torsion

We show how discrete torsion can be implemented in D=4, N=1 type IIB orientifolds. Some consistency conditions are found from the closed string and open string spectrum and from tadpole cancellation. Only real values of the discrete torsion parameter are allowed, i.e. epsilon=+-1. Orientifold models are related to real projective representations. In a similar way as complex projective representations are classified by H^2(Gamma,C^*)=H^2(Gamma,U(1)), real projective representations are characterized by H^2(Gamma,R^*)=H^2(Gamma,Z_2). Four different types of orientifold constructions are possible. We classify these models and give the spectrum and the tadpole cancellation conditions explicitly.

hep-th↗