Criteria for the Classification of System and Bath Variables in Nonadiabatic Dynamics: Application to Pyrazine

The present work deals with the system-bath separation of the vibrational modes involved in a nonadiabatic system. System modes are the strongly interacting modes which dominate the overall dynamics and, hence, need a near-exact treatment. Bath modes have relatively weaker couplings and can be approximately treated. Thus, the exponential bottleneck involved in computations is controlled by the size of the system-subspace. The aim of this work is to put forward a set of criteria that provides clear guidelines for choosing the system degrees of freedom. The extent of wave packet dephasing caused by repeated crossings across the surface of curve-crossing is the basis for distinction between system and bath modes. The mechanisms of the wave packet dephasing and the criteria are discussed in detail. Numerically converged results presented for the 24-mode pyrazine and 3-mode spin-boson model validate the efficiency of these criteria.

Understanding of the C-H stretch region of infra-red spectroscopy: an analysis of the final state wavefunctions

The nature of the wavefunctions associated with the final states in the CH stretching region of several medium sized molecules is analysed. The number of optically bright transitions is much larger than the number of CH oscillators present in the molecule, and they are spread over a range of about 300 cm^-1. Several of them are clustered together within about 5 cm^-1 with near equal intensities. The final states of all these transitions are superpositions of multiple zeroth order states. In almost all of such superpositions, no single zeroth order state has more than 50% weight. Several multiquantum states, with three to four quanta of excitation dominate the final states, with the CH chromophore contributing only a small weightage. Thus the band structure of the CH stretch region is due to several optically bright transitions whose final states are superpositions of low frequency multiquantum states with the CH chromophore contributing only a small weight to make them spectroscopically active.

A Gaussian Wave Packet Propagation Approach to Vibrationally Resolved Optical Spectra at Non-Zero Temperatures

An effective time dependent approach based on a method that is similar to the Gaussian wave packet propagation (GWP) technique of Heller is developed for the computation of vibrationally resolved electronic spectra at finite temperatures in the harmonic, Franck-Condon/Hertzberg-Teller approximations. Since the vibrational thermal density matrix of the ground electronic surface and the time evolution operator on that surface commute, it is possible to write the spectrum generating correlation function as a trace of the time evolved doorway state. In the stated approximations, the doorway state is a superposition of the harmonic oscillator zero and one quantum eigenfunctions and thus can be propagated by the GWP. The algorithm has an O(N(3)) dependence on the number of vibrational modes. An application to pyrene absorption spectrum at two temperatures is presented as a proof of the concept.

SilkSatDb: a microsatellite database of the silkworm, Bombyx mori

The SilkSatDb (silkmoth microsatellite database) (http://www.cdfd.org.in/silksatdb) is a relational database of microsatellites extracted from the available expressed sequence tags and whole genome shotgun sequences of the silkmoth, Bombyx mori. The database has been rendered with a simple and robust web-based search facility, developed using PHP. The SilkSatDb also stores information on primers developed and validated in the laboratory. Users can retrieve information on the microsatellite and the protocols used, along with informative figures and polymorphism status of those microsatellites. In addition, the interface is coupled with Autoprimer, a primer-designing program, using which users can design primers for the loci of interest.