The flavor puzzle in multi-Higgs models

We reconsider the flavor problem in the models with two Higgs doublets. By studying two generation toy models, we look for flavor basis independent constraints on Yukawa couplings that will give us the mass hierarchy while keeping all Yukawa couplings of the same order. We then generalize our findings to the full three generation Standard Model. We find that we need two constraints on the Yukawa couplings to generate the observed mass hierarchy, and a slight tuning of Yukawa couplings of order 10%, much less than the Standard Model. We briefly study how these constraints can be realized, and show how flavor changing currents are under control for $K-\bar{K}$ mixing in the near-decoupling limit.Comment: 26 pages, typos are corrected, references are added, the final versio

An Adaptive Fast Multipole Boundary Element Method for Poisson−Boltzmann Electrostatics

The numerical solution of the Poisson−Boltzmann (PB) equation is a useful but a computationally demanding tool for studying electrostatic solvation effects in chemical and biomolecular systems. Recently, we have described a boundary integral equation-based PB solver accelerated by a new version of the fast multipole method (FMM). The overall algorithm shows an order N complexity in both the computational cost and memory usage. Here, we present an updated version of the solver by using an adaptive FMM for accelerating the convolution type matrix-vector multiplications. The adaptive algorithm, when compared to our previous nonadaptive one, not only significantly improves the performance of the overall memory usage but also remarkably speeds the calculation because of an improved load balancing between the local- and far-field calculations. We have also implemented a node-patch discretization scheme that leads to a reduction of unknowns by a factor of 2 relative to the constant element method without sacrificing accuracy. As a result of these improvements, the new solver makes the PB calculation truly feasible for large-scale biomolecular systems such as a 30S ribosome molecule even on a typical 2008 desktop computer

11^{11}B NMR study of pure and lightly carbon doped MgB2_2 superconductors

We report a $^{11}$B NMR line shape and spin-lattice relaxation rate ($1/(T_1T)$) study of pure and lightly carbon doped MgB$_{2-x}$C$_{x}$ for $x=0$, 0.02, and 0.04, in the vortex state and in magnetic field of 23.5 kOe. We show that while pure MgB$_2$ exhibits the magnetic field distribution from superposition of the normal and the Abrikosov state, slight replacement of boron with carbon unveils the magnetic field distribution of the pure Abrikosov state. This indicates a considerable increase of $H_{c2}^c$ with carbon doping with respect to pure MgB$_2$. The spin-lattice relaxation rate $1/(T_1T)$ demonstrates clearly the presence of a coherence peak right below $T_c$ in pure MgB$_2$, followed by a typical BCS decrease on cooling. However, at temperatures lower than $\approx 10$K strong deviation from the BCS behavior is observed, probably from residual contribution of the vortex dynamics. In the carbon doped systems both the coherence peak and the BCS temperature dependence of $1/(T_1T)$ weaken, an effect attributed to the gradual shrinking of the $\sigma$ hole cylinders of the Fermi surface with electron doping.Comment: 8 pages, 6 figures, submitted to Phys. Rev.

Automated DNA mutation detection using universal conditions direct sequencing: application to ten muscular dystrophy genes

<p>Abstract</p> <p>Background</p> <p>One of the most common and efficient methods for detecting mutations in genes is PCR amplification followed by direct sequencing. Until recently, the process of designing PCR assays has been to focus on individual assay parameters rather than concentrating on matching conditions for a set of assays. Primers for each individual assay were selected based on location and sequence concerns. The two primer sequences were then iteratively adjusted to make the individual assays work properly. This generally resulted in groups of assays with different annealing temperatures that required the use of multiple thermal cyclers or multiple passes in a single thermal cycler making diagnostic testing time-consuming, laborious and expensive.</p> <p>These factors have severely hampered diagnostic testing services, leaving many families without an answer for the exact cause of a familial genetic disease. A search of GeneTests for sequencing analysis of the entire coding sequence for genes that are known to cause muscular dystrophies returns only a small list of laboratories that perform comprehensive gene panels.</p> <p>The hypothesis for the study was that a complete set of universal assays can be designed to amplify and sequence any gene or family of genes using computer aided design tools. If true, this would allow automation and optimization of the mutation detection process resulting in reduced cost and increased throughput.</p> <p>Results</p> <p>An automated process has been developed for the detection of deletions, duplications/insertions and point mutations in any gene or family of genes and has been applied to ten genes known to bear mutations that cause muscular dystrophy: DMD; CAV3; CAPN3; FKRP; TRIM32; LMNA; SGCA; SGCB; SGCG; SGCD. Using this process, mutations have been found in five DMD patients and four LGMD patients (one in the FKRP gene, one in the CAV3 gene, and two likely causative heterozygous pairs of variations in the CAPN3 gene of two other patients). Methods and assay sequences are reported in this paper.</p> <p>Conclusion</p> <p>This automated process allows laboratories to discover DNA variations in a short time and at low cost.</p

Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation

Central in the variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett.2006, 96, 087802 and J. Chem. Phys.2006, 124, 084905] of molecular solvation is a mean-field free-energy functional of all possible solute–solvent interfaces or dielectric boundaries. Such a functional can be minimized numerically by a level-set method to determine stable equilibrium conformations and solvation free energies. Applications to nonpolar systems have shown that the level-set VISM is efficient and leads to qualitatively and often quantitatively correct results. In particular, it is capable of capturing capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states as found in molecular dynamics (MD) simulations. In this work, we introduce into the VISM the Coulomb-field approximation of the electrostatic free energy. Such an approximation is a volume integral over an arbitrary shaped solvent region, requiring no solutions to any partial differential equations. With this approximation, we obtain the effective boundary force and use it as the “normal velocity” in the level-set relaxation. We test the new approach by calculating solvation free energies and potentials of mean force for small and large molecules, including the two-domain protein BphC. Our results reveal the importance of coupling polar and nonpolar interactions in the underlying molecular systems. In particular, dehydration near the domain interface of BphC subunits is found to be highly sensitive to local electrostatic potentials as seen in previous MD simulations. This is a first step toward capturing the complex protein dehydration process by an implicit-solvent approach

Determining Supersymmetric Parameters With Dark Matter Experiments

In this article, we explore the ability of direct and indirect dark matter experiments to not only detect neutralino dark matter, but to constrain and measure the parameters of supersymmetry. In particular, we explore the relationship between the phenomenological quantities relevant to dark matter experiments, such as the neutralino annihilation and elastic scattering cross sections, and the underlying characteristics of the supersymmetric model, such as the values of mu (and the composition of the lightest neutralino), m_A and tan beta. We explore a broad range of supersymmetric models and then focus on a smaller set of benchmark models. We find that by combining astrophysical observations with collider measurements, mu can often be constrained far more tightly than it can be from LHC data alone. In models in the A-funnel region of parameter space, we find that dark matter experiments can potentially determine m_A to roughly +/-100 GeV, even when heavy neutral MSSM Higgs bosons (A, H_1) cannot be observed at the LHC. The information provided by astrophysical experiments is often highly complementary to the information most easily ascertained at colliders.Comment: 46 pages, 76 figure