The Computational Chemistry Grid (CCG) is a three-year, National Middleware Initiative program to develop cyberinfrastructure for the chemistry community. CCG is led by the University of Kentucky and involves collaborating sites at Louisiana State University, Ohio Supercomputing Center, Texas Advanced Computing Center, and the National Center for Supercomputing Applications. This paper discusses experiences developing the CCG cyberinfrastructure in the first year of the project. Special attention is paid to September 1, 2005. technological issues faced as well as issues raised running the CCG in production. The final section of the paper looks forward to challenges foreseen in the remaining two years.

Floquet theory is applied to systems whose Hamiltonians are periodic in time. Specifically, the application deals with the sinusoidal Hamiltonians for the semiclassical approximation of the radiationquantum-molecule interaction in an intense field. For these types of Hamiltonians new time symmetries are shown to exist in the Floquet solutions and consequently to yield three useful properties. Three formal approaches to the Floquet solutions are compared. Also the Floquet-state "mean energy" is shown to play the major role in the static part of the molecular-state energy fluctuations. Numerical application to the dynamics of the diatomic HF vibrotor shows multistate participation in both the oneand two-photon excitations, and "resonance interaction" between the oneand two-photon absorption is observed. Also, Magnus approximations to the exact numerical calculations show excellent agreement.Reinhardt, and Chu have applied Floquet theory to hydrogen atom multiphoton ionization, while Leasure and Wyatt, and Leasure, Wyatt, and Milfeld have applied it to a "larger" system, the rotating diatomic. Floquet theory has even been used in the studies of molecular multiphoton dissociation by Leforestier and Wyatt (in one study, Floquet states were used in conjunction with R-matrix theory, and in the other, with the investigation of the optical potential9}. Some of the earlier applications are given in a review of the quantum "twolevel problem" by Dion and Hirschfelder, ' which also includes a description of the nine Floquet theorem s.More theoretically oriented studies including Floquet analysis (also known as the quasienergy method) have expanded the work of Shirley, " Ritus, ' and Zeldovich' to include slowly modulated oscillatory Hamiltonians, ' development of an extended Hilbert-space formalism, ' approximation of the propagator to simplify the dynamics, and investigation of a new notion of energy ("mean energy"), ' to name some examples. In this study, both the theory and application of the Floquet formalism are extended. We begin in 27 72 molecular dynamics. Also, the relationship between the Floquet and fundamental propagators is defined. In Sec. III new symmetries in the Floquet solutions for the semiclassical Hamiltonian are derived. These properties can be used to shorten computations. In Sec. IV, different Floquet formalisms are related, with an emphasis on the role of the Floquet characteristic exponents (or quasienergies). A new method is presented for correlating molecular energies to the Floquet characteristic exponents in multistate systems. Also, we introduce a measure of the molecular-state energy and find that the constant energy term is a linear combination of the Floquet state mean energies, while fluctuations are determined by the Floquet characteristic exponents.Presented in Sec. V are formal expressions for the Magnus propagator, up to fifth order, and a note on their derivation. Also, we have derived the thirdorder interaction picture, and the thirdand fourth-order Schrodinger picture matrix elements ...

A 3-D model of human thromboxane A2 synthase (TXAS) was constructed using a homology modeling approach based on information from the 2.0 A crystal structure of the hemoprotein domains of cytochrome P450BM-3 and P450cam. P450BM-3 is a bacterial fatty acid monooxygenase resembling eukaryotic microsomal cytochrome P450s in primary structure and function. TXAS shares 26.4% residue identity and 48.4% residue similarity with the P450BM-3 hemoprotein domain. The homology score between TXAS and P450BM-3 is much higher than that between TXAS and P450cam. Alignment between TXAS and the P450BM-3 hemoprotein domain or P450cam was determined through sequence searches. The P450BM-3 or P450cam main-chain coordinates were applied to the TXAS main chain in those segments where the two sequences were well aligned. These segments were linked to one another using a fragment search method, and the side chains were added to produce a 3-D model for TXAS. A TXAS substrate, prostaglandin H2 (PGH2) was docked into the TXAS cavity corresponding to the arachidonic acid binding pocket in P450BM-3 or camphor binding site in P450cam. Regions of the heme and putative PGH2 binding cavities in the TXAS model were identified and analyzed. The segments and residues involved in the active-site pocket of the TXAS model provide reasonable candidates for TXAS protein engineering and inhibitor design. Comparison of the TXAS model based on P450BM-3 with another TXAS model based on the P450cam structure indicated that P450BM-3 is a more suitable template for homology modeling of TXAS.

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