Controlling tetramer formation, subunit rotation and DNA ligation during Hin-catalyzed DNA inversion.

Two critical steps controlling serine recombinase activity are the remodeling of dimers into the chemically active synaptic tetramer and the regulation of subunit rotation during DNA exchange. We identify a set of hydrophobic residues within the oligomerization helix that controls these steps by the Hin DNA invertase. Phe105 and Met109 insert into hydrophobic pockets within the catalytic domain of the same subunit to stabilize the inactive dimer conformation. These rotate out of the catalytic domain in the dimer and into the subunit rotation interface of the tetramer. About half of residue 105 and 109 substitutions gain the ability to generate stable synaptic tetramers and/or promote DNA chemistry without activation by the Fis/enhancer element. Phe106 replaces Phe105 in the catalytic domain pocket to stabilize the tetramer conformation. Significantly, many of the residue 105 and 109 substitutions support subunit rotation but impair ligation, implying a defect in rotational pausing at the tetrameric conformer poised for ligation. We propose that a ratchet-like surface involving Phe105, Met109 and Leu112 within the rotation interface functions to gate the subunit rotation reaction. Hydrophobic residues are present in analogous positions in other serine recombinases and likely perform similar functions

Quantum phase transition and engineering in two-component BEC in optical lattices

In this paper we review recent progress in studying quantum phase transitions in one- and two-component Bose-Einstein condensates (BEC) in optical lattices. These phase transitions involve the emergence and disappearance of quantum coherence over whole optical lattice and of linear superposition of macroscopic quantum states. The latter may provide new means to engineer and to manipulate novel macroscopic quantum states and novel coherent atomic beams for quantum information processing, quantum computing etc.Comment: Format: LaTex2e. 7 pages, no figure. Talk at the Yang Symposium (in honor of C.N. Yang's 80th birthday), Beijing, China, June 2002. To appear in the Proceeding

Estimating exploitable stock biomass for the Maine green sea urchin (Strongylocentrotus droebachiensis) fishery using a spatial statistics approach

The objective of this study was to investigate the spatial patterns in green sea urchin (Strongylocentrotus droebachiensis) density off the coast of Maine, using data from a fishery-independent survey program, to estimate the exploitable biomass of this species. The dependence of sea urchin variables on the environment, the lack of stationarity, and the presence of discontinuities in the study area made intrinsic geostatistics inappropriate for the study; therefore, we used triangulated irregular networks (TINs) to characterize the large-scale patterns in sea urchin density. The resulting density surfaces were modified to include only areas of the appropriate substrate type and depth zone, and were used to calculate total biomass. Exploitable biomass was estimated by using two different sea urchin density threshold values, which made different assumptions about the fishing industry. We observed considerable spatial variability on both small and large scales, including large-scale patterns in sea urchin density related to depth and fishing pressure. We conclude that the TIN method provides a reasonable spatial approach for generating biomass estimates for a fishery unsuited to geostatistics, but we suggest further studies into uncertainty estimation and the selection of threshold density values

Analytic Expression for Exact Ground State Energy Based on an Operator Method for a Class of Anharmonic Potentials

A general procedure based on shift operators is formulated to deal with anharmonic potentials. It is possible to extract the ground state energy analytically using our method provided certain consistency relations are satisfied. Analytic expressions for the exact ground state energy have also been derived specifically for a large class of the one-dimensional oscillator with cubic-quartic anharmonic terms. Our analytical results can be used to check the accuracy of existing numerical methods, for instance the method of state-dependent diagonalization. Our results also agree with the asymptotic behavior in the divergent pertubative expansion of quartic harmonic oscillator.Comment: LaTeX with six figure (gif) files; Submitted to Phys. Rev.