SuSeFLAV 1.2: Program for supersymmetric mass spectra with seesaw mechanism and rare lepton flavor violating decays

Accurate supersymmetric spectra are required to confront data from direct and indirect searches of supersymmetry. SuSeFLAV is a numerical tool capable of computing supersymmetric spectra precisely for various supersymmetric breaking scenarios applicable even in the presence of flavor violation. The program solves MSSM RGEs with complete 3 x 3 flavor mixing at 2-loop level and one loop finite threshold corrections to all MSSM parameters by incorporating radiative electroweak symmetry breaking conditions. The program also incorporates the Type-I seesaw mechanism with three massive right handed neutrinos at user defined mass scales and mixing. It also computes branching ratios of flavor violating processes such as l(j) -> l(i)gamma, l(j) -> 3 l(i), b -> s gamma and supersymmetric contributions to flavor conserving quantities such as (g(mu) - 2). A large choice of executables suitable for various operations of the program are provided. Program summary Program title: SuSeFLAV Catalogue identifier: AEOD_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEOD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 76552 No. of bytes in distributed program, including test data, etc.: 582787 Distribution format: tar.gz Programming language: Fortran 95. Computer: Personal Computer, Work-Station. Operating system: Linux, Unix. Classification: 11.6. Nature of problem: Determination of masses and mixing of supersymmetric particles within the context of MSSM with conserved R-parity with and without the presence of Type-I seesaw. Inter-generational mixing is considered while calculating the mass spectrum. Supersymmetry breaking parameters are taken as inputs at a high scale specified by the mechanism of supersymmetry breaking. RG equations including full inter-generational mixing are then used to evolve these parameters up to the electroweak breaking scale. The low energy supersymmetric spectrum is calculated at the scale where successful radiative electroweak symmetry breaking occurs. At weak scale standard model fermion masses, gauge couplings are determined including the supersymmetric radiative corrections. Once the spectrum is computed, the program proceeds to various lepton flavor violating observables (e.g., BR(mu -> e gamma), BR(tau -> mu gamma) etc.) at the weak scale. Solution method: Two loop RGEs with full 3 x 3 flavor mixing for all supersymmetry breaking parameters are used to compute the low energy supersymmetric mass spectrum. An adaptive step size Runge-Kutta method is used to solve the RGEs numerically between the high scale and the electroweak breaking scale. Iterative procedure is employed to get the consistent radiative electroweak symmetry breaking condition. The masses of the supersymmetric particles are computed at 1-loop order. The third generation SM particles and the gauge couplings are evaluated at the 1-loop order including supersymmetric corrections. A further iteration of the full program is employed such that the SM masses and couplings are consistent with the supersymmetric particle spectrum. Additional comments: Several executables are presented for the user. Running time: 0.2 s on a Intel(R) Core(TM) i5 CPU 650 with 3.20 GHz. (c) 2012 Elsevier B.V. All rights reserved.

MolBridge: a program for identifying nonbonded interactions in small molecules and biomolecular structures

Identification and analysis of nonbonded interactions within a molecule and with the surrounding molecules are an essential part of structural studies, given the importance of these interactions in defining the structure and function of any supramolecular entity. MolBridge is an easy to use algorithm based purely on geometric criteria that can identify all possible nonbonded interactions, such as hydrogen bond, halogen bond, cation-pi, pi-pi and van der Waals, in small molecules as well as biomolecules. The user can either upload three-dimensional coordinate files or enter the molecular ID corresponding to the relevant database. The program is available in a standalone form and as an interactive web server with Jmol and JME incorporated into it. The program is freely downloadable and the web server version is also available at http://nucleix.mbu.iisc.ernet.in/molbridge/index.php.

SUB1 Plays a Negative Role during Starvation Induced Sporulation Program in Saccharomyces cerevisiae

Saccharomyces cerevisiae Sub1 is involved in several cellular processes such as, transcription initiation, elongation, mRNA processing and DNA repair. It has also been reported to provide cellular resistance during conditions of oxidative DNA damage and osmotic stress. Here, we report a novel role of SUB1 during starvation stress-induced sporulation, which leads to meiosis and spore formation in diploid yeast cells. Deletion of SUB1 gene significantly increased sporulation efficiency as compared to the wild-type cells in S288c genetic background. Whereas, the sporulation functions of the sub1(Y66A) missense mutant were similar to Sub1. SUB1 transcript and protein levels are downregulated during sporulation, in highly synchronized and sporulation proficient wild-type SK1 cells. The changes in Sub1 levels during sporulation cascade correlate with the induction of middle sporulation gene expression. Deletion of SUB1 increased middle sporulation gene transcript levels with no effect on their induction kinetics. In wild-type cells, Sub1 associates with chromatin at these loci in a temporal pattern that correlates with their enhanced gene expression seen in sub1. cells. We show that SUB1 genetically interacts with HOS2, which led us to speculate that Sub1 might function with Set3 repressor complex during sporulation. Positive Cofactor 4, human homolog of Sub1, complemented the sub1. sporulation phenotype, suggesting conservation of function. Taken together, our results suggest that SUB1 acts as a negative regulator of sporulation.

Role of gas in supporting grand spiral structure

The density wave theory for the grand-design two-armed spiral pattern in galaxies is successful in explaining several observed features. However, the long-term persistence of this spiral structure is a serious problem since the group transport would destroy it within about a billion years as shown in a classic paper by Toomre. In this paper, we include the low-velocity dispersion component, namely gas, on an equal footing with stars in the formulation of the density wave theory, and obtain the dispersion relation for this coupled system. We show that the inclusion of gas makes the group transport slower by a factor of few, thus allowing the pattern to persist longer - for several billion years. Though still less than the Hubble time, this helps in making the spiral structure more long-lived. Further we show that addition of gas is essential to get a stable wave for the observed pattern speed for the Galaxy, which otherwise is not possible for a one-component stellar disc.

SUPPORTING ENVIRONMENTALLY-BENIGN DESIGN ELUCIDATING ENVIRONMENTAL IMPACT PROPAGATION IN CONCEPTUAL DESIGN PHASE BY SAPPHIRE MODEL OF CAUSALITY

Conceptual Design Phase is the most critical for design decisions and their impact on the Environment. It is also a phase of many `unknowns' making it flexible and allowing exploration of many solutions. Thus, it is a challenge to determine the most Environmentally-benign Solution or Concept to be translated in to a `good' product. The SAPPhIRE Model captures the various levels of abstractions present in Conceptual Design by Outcomes and defines a Solution-variant as a set of verifiable and quantifiable Outcomes. The Causality explains the propagation of Environmental Impact across Outcomes at varying levels of abstraction, suggesting that the Environmental Impact of an Outcome at a certain level can be represented as a collation of Environmental Impact information of all the Outcomes at each of its subsequent lower levels of abstraction. Thus a ball-park impact value can be associated with the higher-levels of abstraction, thereby supporting design decisions taken earlier on in Conceptual Design directing towards Environmentally-benign Design.