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We propose a viable minimal model with spontaneous CP violation in the framework of a two Higgs doublet model. The model is based on a generalised Branco–Grimus–Lavoura model with a flavoured \\[\\mathbb {Z}_2\\] symmetry, under which two of the quark families are even and the third one is odd. The lagrangian respects CP invariance, but the vacuum has a CP violating phase, which is able to generate a complex CKM matrix, with the rephasing invariant strength of CP violation compatible with experiment. The question of scalar mediated flavour changing neutral couplings is carefully studied. In particular we point out a deep connection between the generation of a complex CKM matrix from a vacuum phase and the appearance of scalar FCNC. The scalar sector is presented in detail, showing that the new scalars are necessarily lighter than 1 TeV. A complete analysis of the model including the most relevant constraints is performed, showing that it is viable and that it has definite implications for the observation of New Physics signals in, for example, flavour changing Higgs decays or the discovery of the new scalars at the LHC. We give special emphasis to processes like \\[t\\rightarrow \\mathrm{h}c,\\mathrm{h}u\\], as well as \\[\\mathrm{h}\\rightarrow bs, bd\\], which are relevant for the LHC and the ILC.

A bstract We study quark flavor violating interactions mediated by the Higgs boson h . We consider observables involving a third generation quark, of both the up and the down quark sectors, like h → bs and t → ch . Using an effective field theory approach we systematically list all the possible tree-level ultraviolet completions, which comprise models with vector-like quarks and/or extra scalars. We provide upper bounds on the flavor violating transitions allowed by current limits stemming from low energy processes, such as meson mixing and b → s γ. We find that scenarios with vector-like quarks always have very suppressed flavor-violating transitions, while a general Two-Higgs-Doublet Model may have a sizeable rate. To study the latter case in detail, we perform a full numerical simulation taking into account all relevant theoretical and phenomenological constraints. Our results show that BR( t → ch ) [BR( h → bs )] are still allowed at the sub-percent [percent] level, which are being [may be] explored at the LHC [future colliders]. Finally, we have found that the mild mass-splitting discrepancy with respect to the SM in the B s meson system can be accommodated in the Two-Higgs-Doublet Model. If confirmed, it yields the prediction BR( h → bs ) ≃ 10 −4 , if the new contribution to the mass-splitting is dominated by tree-level Higgs boson exchange.

We propose a class of two Higgs doublet models where there are flavour changing neutral currents (FCNC) at tree level, but under control due to the introduction of a discrete symmetry in the full Lagrangian. It is shown that in this class of models, one can have simultaneously FCNC in the up and down sectors, in contrast to the situation encountered in the renormalisable and minimal flavour violating 2HDM models put forward by Branco et al. (Phys Lett B 380:119, 1996 ). The intensity of FCNC is analysed and it is shown that in this class of models one can respect all the strong constraints from experiment without unnatural fine-tuning. It is pointed out that the additional sources of flavour and CP violation are such that they can enhance significantly the generation of the Bbaryon asymmetry of the Universe, with respect to the standard model.

We conjecture the existence of a relation between elementary scalars and fermions, making it plausible the existence of three Higgs doublets. We introduce a Trinity Principle (TP) which, given the fact that there are no massless quarks, requires the existence of a minimum of three Higgs doublets. The TP states that each row of the mass matrix of a quark of a given charge should receive the contribution from one and only one scalar doublet and furthermore a given scalar doublet should contribute to one and only one row of the mass matrix of a quark of a given charge. This principle is analogous to the Natural Flavour Conservation (NFC) of Glashow and Weinberg with the key distinction that NFC required the introduction of a flavour blind symmetry, while the TP requires a flavoured symmetry, to be implemented in a natural way. We provide two examples which satisfy the Trinity Principle based on Z 3 and Z 2 × Z 2 ′ flavoured symmetries, and show that they are the minimal multi-Higgs extensions of the Standard Model where CP can be imposed as a symmetry of the full Lagrangian and broken by the vacuum, without requiring soft-breaking terms. We show that the vacuum phases are sufficient to generate a complex CKM matrix, in agreement with experiment. The above mentioned flavoured symmetries lead to a strong reduction in the number of parameters in the Yukawa interactions, enabling a control of the Scalar Flavour Changing Neutral Couplings (SFCNC). We analyse some of the other physical implications of the two models, including an estimate of the enhancement of the Baryon Asymmetry of the Universe provided by the new sources of CP violation, and a discussion of the strength of their tree-level SFCNC.

The study of genetic interactions (epistasis) is central to the understanding of genome organization and evolution. A general correlation between epistasis and genomic complexity has been recently shown, such that in simpler genomes epistasis is antagonistic on average (mutational effects tend to cancel each other out), whereas a transition towards synergistic epistasis occurs in more complex genomes (mutational effects strengthen each other). Here, we use a simple network model to identify basic features explaining this correlation. We show that, in small networks with multifunctional nodes, lack of redundancy, and absence of alternative pathways, epistasis is antagonistic on average. In contrast, lack of multi-functionality, high connectivity, and redundancy favor synergistic epistasis. Moreover, we confirm the previous finding that epistasis is a covariate of mutational robustness: in less robust networks it tends to be antagonistic whereas in more robust networks it tends to be synergistic. We argue that network features associated with antagonistic epistasis are typically found in simple genomes, such as those of viruses and bacteria, whereas the features associated with synergistic epistasis are more extensively exploited by higher eukaryotes.

We show how a novel fine-tuning problem present in the Standard Model can be solved through the introduction of a Z 6 flavour symmetry, together with three Q = - 1 / 3 quarks, three Q = 2 / 3 quarks, as well as a complex singlet scalar. The Z 6 symmetry is extended to the additional fields and it is an exact symmetry of the Lagrangian, only softly broken in the scalar potential, in order to avoid the domain-wall problem. Specific examples are given and a phenomenological analysis of the main features of the model is presented. It is shown that even for vector-like quarks with masses accessible at the LHC, one can have realistic quark masses and mixing, while respecting the strict constraints on processes arising from flavour changing neutral currents. The vector-like quark decay channels are also described.

The immune system should constitute a strong selective pressure promoting viral genetic diversity and evolution. However, HIV shows lower sequence variability at T-cell epitopes than elsewhere in the genome, in contrast with other human RNA viruses. Here, we propose that epitope conservation is a consequence of the particular interactions established between HIV and the immune system. On one hand, epitope recognition triggers an anti-HIV response mediated by cytotoxic T-lymphocytes (CTLs), but on the other hand, activation of CD4(+) helper T lymphocytes (TH cells) promotes HIV replication. Mathematical modeling of these opposite selective forces revealed that selection at the intrapatient level can promote either T-cell epitope conservation or escape. We predict greater conservation for epitopes contributing significantly to total immune activation levels (immunodominance), and when TH cell infection is concomitant to epitope recognition (trans-infection). We suggest that HIV-driven immune activation in the lymph nodes during the chronic stage of the disease may offer a favorable scenario for epitope conservation. Our results also support the view that some pathogens draw benefits from the immune response and suggest that vaccination strategies based on conserved TH epitopes may be counterproductive.

We study two-Higgs-doublet models (2HDM) where Abelian symmetries have been introduced, leading to a drastic reduction in the number of free parameters in the 2HDM. Our analysis is inspired in BGL models, where, as the result of a symmetry of the Lagrangian, there are tree-level scalar mediated Flavour-Changing-Neutral-Currents, with the flavour structure depending only on the CKM matrix. A systematic analysis is done on the various possible schemes, which are classified in different classes, depending on the way the extra symmetries constrain the matrices of couplings defining the flavour structure of the scalar mediated neutral currents. All the resulting flavour textures of the Yukawa couplings are stable under renormalisation since they result from symmetries imposed at the Lagrangian level. We also present a brief phenomenological analysis of the most salient features of each class of symmetry constrained 2HDM.

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 -effect. In the current paper we identify how to probe the complex in the entangled -system using the flavour ( )-CP( ) eigenstate decay channels: the connection between the intensities for the two time-ordered decays ( ,  ) and ( ,  ) is lost. Appropriate observables are constructed allowing independent experimental determinations of Re( ) and Im( ), disentangled from CPT violation in the evolution Hamiltonian Re( ) and Im( ). tensions for both Re( ) and Im( ) are shown to be uncorrelated.

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.