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Nebot, M. (2020). Bounded masses in two Higgs doublets models, spontaneous CP violation and Z(2) symmetry. Phys. Rev. D, 102(11), 115002–16pp.
Abstract: In two Higgs doublet models (2HDMs) shaped by some unbroken symmetry, imposing perturbativity requirements on the quartic couplings can imply that the allowed masses of all the fundamental scalars are bounded from above. This important property is analyzed in detail for the only two realistic 2HDMs with an exact symmetry, the case with Z(2) symmetry and the case with CP symmetry. It is also noticeable that one exception arises in each case: when the vacuum is assumed to respect the imposed symmetry, a decoupling regime can nevertheless appear without violating perturbativity requirements. In both models with an exact symmetry and no decoupling regime, soft symmetry breaking terms can however lead to a decoupling regime: the possibility that this regime might be unnatural, since it requires some fine-tuning, is also analyzed.
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Botella, F. J., Branco, G. C., & Nebot, M. (2012). The hunt for New Physics in the Flavour Sector with up vector-like quarks. J. High Energy Phys., 12(12), 040–34pp.
Abstract: We analyse the possible presence of New Physics (NP) in the Flavour Sector and evaluate its potential for solving the tension between the experimental values of A(J/Psi KS) and Br(B+ -> tau(+)v(tau)) with respect to the Standard Model (SM) expectations. Updated model independent analyses, where NP contributions are allowed in B-d(0) – (B) over bar (0)(d) and B-s(0) – (B) over bar (0)(s) transitions, suggest the need of New Physics in the bd sector. A detailed analysis of recent Flavour data is then presented in the framework of a simple extension of the SM, where a Q = 2/3 vector-like isosinglet quark is added to the spectrum of the SM. Special emphasis is given to the implications of this model for correlations among various measurable quantities. We include constraints from all the relevant quark flavour sectors and give precise predictions for selected rare processes. We find important deviations from the SM in observables in the bd sector like the semileptonic asymmetry A(SL)(d), B-d(0) -> mu(+)mu(-) and A(SL)(s) – A(SL)(d). Other potential places where NP can show up include A(J/Psi Phi), gamma, K-L(0) -> pi(0)v (v) over bar, t -> Zq and D-0 -> mu(+)mu(-) among others. The experimental data favours in this model the existence of an up vector-like quark with a mass below 600(1000) GeV at 1(2) sigma.
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Bernabeu, J., Botella, F. J., Mavromatos, N. E., & Nebot, M. (2017). The signal of ill-defined CPT weakening entanglement in the B-d system. Eur. Phys. J. C, 77(12), 865–10pp.
Abstract: In the presence of quantum-gravity fluctuations (space-time foam), the CPT operator may be ill-defined. Its perturbative treatment leads to a modification of the Einstein-Podolsky- Rosen correlation of the neutral meson system by adding an entanglement-weakening term of the wrong exchange symmetry, the omega-effect. In the current paper we identify how to probe the complex omega in the entangled B-d system using the flavour (f)-CP(g) eigenstate decay channels: the connection between the intensities for the two timeordered decays (f, g) and (g, f) is lost. Appropriate observables are constructed allowing independent experimental determinations of Re(omega) and Im(omega), disentangled from CPT violation in the evolution Hamiltonian Re(theta) and Im(theta). 2 sigma tensions for both Re(theta) and Im(omega) are shown to be uncorrelated.
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Sanjuan, R., Nebot, M., Chirico, N., Mansky, L. M., & Belshaw, R. (2010). Viral Mutation Rates. J. Virol., 84(19), 9733–9748.
Abstract: Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 10(-8) to 10(-6) s/n/c for DNA viruses and from 10(-6) to 10(-4) s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mutation rate and genome size among RNA viruses, but this result requires further experimental testing. Contrary to some suggestions, the mutation rate of retroviruses is not lower than that of other RNA viruses. We also show that nucleotide substitutions are on average four times more common than insertions/deletions (indels). Finally, we provide estimates of the mutation rate per nucleotide per strand copying, which tends to be lower than that per cell infection because some viruses undergo several rounds of copying per cell, particularly double-stranded DNA viruses. A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut.
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Peris, J. B., Davis, P., Cuevas, J. M., Nebot, M., & Sanjuan, R. (2010). Distribution of Fitness Effects Caused by Single-Nucleotide Substitutions in Bacteriophage f1. Genetics, 185(2), 603–U308.
Abstract: Empirical knowledge of the fitness effects of mutations is important for understanding many evolutionary processes, yet this knowledge is often hampered by several sources of measurement error and bias. Most of these problems can be solved using site-directed mutagenesis to engineer single mutations, an approach particularly suited for viruses due to their small genomes. Here, we used this technique to measure the fitness effect of 100 single-nucleotide substitutions in the bacteriophage f1, a filamentous single-strand DNA virus. We found that approximately one-fifth of all mutations are lethal. Viable ones reduced fitness by 11% on average and were accurately described by a log-normal distribution. More than 90% of synonymous substitutions were selectively neutral, while those affecting intergenic regions reduced fitness by 14% on average. Mutations leading to amino acid substitutions had an overall mean deleterious effect of 37%, which increased to 45% for those changing the amino acid polarity. Interestingly, mutations affecting early steps of the infection cycle tended to be more deleterious than those affecting late steps. Finally, we observed at least two beneficial mutations. Our results confirm that high mutational sensitivity is a general property of viruses with small genomes, including RNA and single-strand DNA viruses infecting animals, plants, and bacteria.
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