MPN+, a putative catalytic motif found in a subset of MPN domain proteins from eukaryotes and prokaryotes, is critical for Rpn11 function

Background  

Three macromolecular assemblages, the lid complex of the proteasome, the COP9-Signalosome (CSN) and the eIF3 complex, all consist of multiple proteins harboring MPN and PCI domains. Up to now, no specific function for any of these proteins has been defined, nor has the importance of these motifs been elucidated. In particular Rpn11, a lid subunit, serves as the paradigm for MPN-containing proteins as it is highly conserved and important for proteasome function.     

Parameterized matching with mismatches

The problem of approximate parameterized string searching consists of finding, for a given text t=t₁t₂…t_n and pattern p=p₁p₂…p_m over respective alphabets Σ_t and Σ_p, the injection π_i from Σ_p to Σ_t maximizing the number of matches between π_i(p) and t_it_i+1…t_i+m−1 (i=1,2,…,n−m+1). We examine the special case where both strings are run-length encoded, and further restrict to the case where one of the alphabets is binary. For this case, we give a construction working in time O(n+(r_p×r_t)α(r_t)log(r_t)), where r_p and r_t denote the number of runs in the corresponding encodings for y and x, respectively, and α is the inverse of the Ackermann's function.     

Three level atom optics in dipole traps and waveguides

An analogy is explored between a setup of three atomic traps coupled via tunneling and an internal atomic three-level system interacting with two laser fields. Within this scenario we describe a STIRAP like process which allows to move an atom between the ground states of two trapping potentials and analyze its robustness. This analogy is extended to other robust and coherent transport schemes and to systems of more than a single atom. Finally it is applied to manipulate external degrees of freedom of atomic wave packets propagating in waveguides.     

Optimizing the efficiency in high order harmonic generation optimization by two-color fields

We address the problem of the optimization of high-order harmonic generation by two laser fields of frequencies and respectively, through a theoretical approach. The parameters that are investigated are the two lasers intensities as well as the relative phase between the two fields. We show that a moderate, but significant increase of efficiency can be achieved in that context and give the domain of optimized parameters. Moreover, we quantitatively investigate the gain and set the limitation of the optimization using such coherent control methods. Received 3 March 2000 and Received in final form 4 May 2000     

Entangling strings of neutral atoms in 1D atomic pipeline structures

We study a string of neutral atoms with nearest neighbor interaction in a 1D beam splitter configuration, where the longitudinal motion is controlled by a moving optical lattice potential. The dynamics of the atoms crossing the beam splitter maps to a 1D spin model with controllable time dependent parameters, which allows the creation of maximally entangled states of atoms by crossing a quantum phase transition. Furthermore, we show that this system realizes protected quantum memory, and we discuss the implementation of one- and two-qubit gates in this setup.