Parallel Tempering Algorithm for Conformational Studies of Biological Molecules

The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by the new method. This is demonstrated by performing simulations with high statistics for one of the simplest peptides, Met-enkephalin. The numerical effectiveness of the new technique was found to be much better than traditional methods and is comparable to sophisticated methods like generalized ensemble techniques.Comment: Latex, ps-files included; to appear in Chem. Phys. Let

Simulated Annealing with Tsallis Weights - A Numerical Comparison

We discuss the use of Tsallis generalized mechanics in simulated annealing algorithms. For a small peptide it is shown that older implementations are not more effective than regular simulated annealing in finding ground state configurations. We propose a new implementation which leads to an improvement over regular simulated annealing.Comment: Late

On non-round points of the boundary of the numerical range and an application to non-selfadjoint Schr\"odinger operators

We show that non-round boundary points of the numerical range of an unbounded operator (i.e. points where the boundary has infinite curvature) are contained in the spectrum of the operator. Moreover, we show that non-round boundary points, which are not corner points, lie in the essential spectrum. This generalizes results of H\"ubner, Farid, Spitkovsky and Salinas and Velasco for the case of bounded operators. We apply our results to non-selfadjoint Schr\"odinger operators, showing that in this case the boundary of the numerical range can be non-round only at points where it hits the essential spectrum.Comment: Shortened version. To appear in Journal of Spectral Theor

Stochastic dynamics simulations in a new generalized ensemble

We develop a formulation for molecular dynamics, Langevin, and hybrid Monte Carlo algorithms in the recently proposed generalized ensemble that is based on a physically motivated realisation of Tsallis weights. The effectiveness of the methods are tested with an energy function for a protein system. Simulations in this generalized ensemble by the three methods are performed for a penta peptide, Met-enkephalin. For each algorithm, it is shown that from only one simulation run one can not only find the global-minimum-energy conformation but also obtain probability distributions in canonical ensemble at any temperature, which allows the calculation of any thermodynamic quantity as a function of temperature.Comment: to appear in Chem. Phy. Let

Measurement of phi_s at LHCb

A time dependent angular analysis of the decay mode $B_s \rightarrow J/\psi \phi$ allows for the measurement of the mixing induced CP-violating phase $\phi_s$. Within the Standard Model $\phi_s$ is theoretically precisely predicted to be very small, however many Standard Model extensions predict sizeable contributions to this phase. The current experimental knowledge of $\phi_s$ has very larger uncertainties. However already with the data expected to be delivered within the next year, the LHCb experiment at the Large Hadron Collider at CERN, has the potential to improve significantly existing measurements. In a data set of up to 37.5 pb$^{-1}$ taken in 2010, first physics signals in the LHCb detector are reconstructed and their properties are compared to Monte Carlo predictions. Based on recently published measurements of $b\bar{b}$ cross-sections from the LHCb collaboration, the sensitivity on the $CP$ violating phase $\phi_s$ in the decay $B_s \rightarrow J/\psi \phi$ is evaluated. Additionally an alternative method to potentially extract complementary information on $\phi_s$ from the measurement of the asymmetry in semileptonic final states is presented.Comment: Proceedings of CKM2010, the 6th International Workshop on the CKM Unitarity Triangle, University of Warwick, UK, 6-10 September 201