Order independent structural alignment of circularly permuted proteins

Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because current detection methods can miss many occurances, mistaking random repeats as circular permutation. Here we develop a method for detecting circularly permuted proteins from structural comparison. Sequence order independent alignment of protein structures can be regarded as a special case of the maximum-weight independent set problem, which is known to be computationally hard. We develop an efficient approximation algorithm by repeatedly solving relaxations of an appropriate intermediate integer programming formulation, we show that the approximation ratio is much better then the theoretical worst case ratio of $r = 1/4$. Circularly permuted proteins reported in literature can be identified rapidly with our method, while they escape the detection by publicly available servers for structural alignment.Comment: 5 pages, 3 figures, Accepted by IEEE-EMBS 2004 Conference Proceeding

Minimal SUGRA Model and Collider Signals

The SUSY signals in the dominant stau-neutralino coannihilation region at a 500(800) GeV linear collider are investigated. The region is consistent with the WMAP measurement of the cold dark matter relic density as well as all other current experimental bounds within the mSUGRA framework. The signals are characterized by an existence of very low-energy tau leptons in the final state due to small mass difference between stau_1 and chi_1 (5-15 GeV). We study the accuracy of the mass difference measurement with a 1^deg active mask to reduce a huge SM two-photon background.Comment: 4 pages, 3 figures, Talk presented at ICHEP04, Aug.16-22, Beijing, China, Numerical typos in Table 5 and 6 are corrected, no changes in figures and in other numerical result

Comparison theorem for a nonlinear boundary value problem on time scales

AbstractWe prove a comparison theorem for the lower and upper solutions of a nonlinear two point boundary value problem on time scales. This theorem plays an important role in the development of the method of generalized quasilinearization on time scales

Modification of the Unitarity Relation for sin2beta-Vub in Supersymmetric Models

Recently, a more than 2sigma discrepancy has been observed between the well measured inclusive value of Vub and the predicted value of Vub from the unitarity triangle fit using the world average value of sin2beta. We attempt to resolve this tension in the context of grand unified SO(10) and SU(5) models where the neutrino mixing matrix is responsible for flavor changing neutral current at the weak scale and the models with non-proportional A-terms (can be realized simply in the context of intersecting D-brane models) and investigate the interplay between the constraints arising from B_{s,d}-\bar B_{s,d} mixings, epsilon_K, Br(tau -> mu gamma), Br(mu -> e gamma) and a fit of this new discrepancy. We also show that the ongoing measurement of the phase of Bs mixing will be able to identify the grand unified model. The measurement of Br(tau -> e gamma) will also be able to test these scenarios, especially the models with non-proportional A-terms.Comment: 20 pages, 4 figures. Minor corrections, references adde

Correlation between direct dark matter detection and Br(B_s -> mu mu) with a large phase of B_s - anti-B_s mixing

We combine the analyses for flavor changing neutral current processes and dark matter solutions in minimal-type supersymmetric grand unified theory (GUT) models, SO(10) and SU(5), with a large B_s - anti-B_s mixing phase and large tan beta. For large tan beta, the double penguin diagram dominates the SUSY contribution to the B_s - anti-B_s mixing amplitude. Also, the Br(B_s -> mu mu) constraint becomes important as it grows as tan^6 beta, although it can still be suppressed by large pseudoscalar Higgs mass m_A. We investigate the correlation between B_s -> mu mu and the dark matter direct detection cross-section through their dependence on m_A. In the minimal-type of SU(5) with type I seesaw, the large mixing in neutrino Dirac couplings results in large lepton flavor violating decay process tau to mu gamma, which in turn sets upper bound on m_A. In the SO(10) case, the large mixing can be chosen to be in the Majorana couplings instead, and the constraint from Br(tau -> mu gamma) can be avoided. The heavy Higgs funnel region turns out to be an interesting possibility in both cases and the direct dark matter detection should be possible in the near future in these scenarios.Comment: 19 pages, 8 figure

Geometrically Nonlinear Vibrations of Functionally Graded Shallow Shells

An original method for investigation of geometrically nonlinear vibrations of functionally graded shallow shells and plates with complex planform is presented. Shells under consideration are made from a composite of ceramics and metal. Power law of volume fraction distribution of materials through thickness is chosen. Mathematical statement is implemented in the framework of the refined geometrically nonlinear theory of the shallow shells of the first order (Timoshenko type). The proposed approach combines the application of the Rfunctions theory (RFM), variational Ritz method, procedure by Bubnov-Galerkin and Runge-Kutta method. Due to use of this combined algorithm it is possible to reduce the initial nonlinear system of motion equations with partial derivatives to a nonlinear system of ordinary differential equations. Investigation task of functionally graded shallow shells with arbitrary planform and different types of boundary conditions is carried out by the proposed method. Test problems and numerical results have been presented for one-mode approximation in time. In future, the developed method may be extended to investigation of geometrically nonlinear forced vibrations of functionally graded shallow shells with complex planform