Theoretical Study of the Phosphoryl Transfer Reaction from ATP to Dha Catalyzed by DhaK from Escherichia coli

Protein kinases, representing one of the largest protein families involved in almost all aspects of cell life, have become one of the most important targets for the development of new drugs to be used in, for instance, cancer treatments. In this article an exhaustive theoretical study of the phosphoryl transfer reaction from adenosine triphosphate (ATP) to dihydroxyacetone (Dha) catalyzed by DhaK from Escherichia coli (E. coli) is reported. Two different mechanisms, previously proposed for the phosphoryl transfer from ATP to the hydroxyl side chain of specific serine, threonine, or tyrosine residues, have been explored based on the generation of free energy surfaces (FES) computed with hybrid QM/MM potentials. The results suggest that the substrate-assisted phosphoryl and proton-transfer mechanism is kinetically more favorable than the mechanism where an aspartate would be activating the Dha. Although the details of the mechanisms appear to be dramatically dependent on the level of theory employed in the calculations (PM3/MM, B3LYP:PM3/MM, or B3LYP/MM), the transition states (TSs) for the phosphoryl transfer step appear to be described as a concerted step with different degrees of synchronicity in the breaking and forming bonds process in both explored mechanisms. Residues of the active site belonging to different subunits of the protein, such as Gly78B, Thr79A, Ser80A, Arg178B, and one Mg2+ cation, would be stabilizing the transferred phosphate in the TS. Asp109A would have a structural role by posing the Dha and other residues of the active site in the proper orientation. The information derived from our calculations not only reveals the role of the enzyme and the particular residues of its active site, but it can assist in the rational design of new more specific inhibitors

Use of nanofiltration membrane technology for ceramic industry wastewater treatment

A study has been undertaken of an advanced wastewater treatment approach using polymer nanofiltration membranes, in an attempt to obtain water of sufficient quality to allow it to be reused in the same production process or, alternatively, to be discharged without any problems. The study has initially focused on the removal of organic matter (reduction of COD) and the most representative ions present in the wastewater, such as Na+ , Mg2+, Cl- , and SO4 2- . In a first part of the study, with a view to optimising the experimental phase, a simulation has been performed of the nanofiltration process using the NanoFlux software. Among other things, the simulation allows the most suitable membranes to be selected as a function of the permeate flow rate and desired level of retention in the substances to be removed. The subsequent experimentation was carried out in a laboratory tangential filtration system that works with flat membranes. It was found that retention values of about 90% were obtained for the studied substances, with a good permeate flow rate, using low operating pressures. These results demonstrate the feasibility of the studied technology and its potential as a treatment for improving ceramic industry wastewater qualit

The translationally-invariant coupled cluster method in coordinate space

We study a formulation of the translationally-invariant coupled cluster method in coordinate space. Previous calculations in configuration space showed poor convergence, a problem that the new formulation is expected to remedy. This question is investigated for a system of bosons interacting through the Wigner part of the Afnan-Tang S3 interaction, where previous results exist.Facultad de Ciencias Exacta

Embedding method for the scattering phase in strongly correlated quantum dots

The embedding method for the calculation of the conductance through interacting systems connected to single channel leads is generalized to obtain the full complex transmission amplitude that completely characterizes the effective scattering matrix of the system at the Fermi energy. We calculate the transmission amplitude as a function of the gate potential for simple diamond-shaped lattice models of quantum dots with nearest neighbor interactions. In our simple models we do not generally observe an interaction dependent change in the number of zeroes or phase lapses that depend only on the symmetry properties of the underlying lattice. Strong correlations separate and reduce the widths of the resonant peaks while preserving the qualitative properites of the scattering phase.Comment: 11 pages, 3 figures. Proceedings of the Workshop on Advanced Many-Body and Statistical Methods in Mesoscopic Systems, Constanta, Romania, June 27th - July 2nd 2011. To appear in Journal of Physics: Conference Serie

Translationally-invariant coupled-cluster method for finite systems

The translational invariant formulation of the coupled-cluster method is presented here at the complete SUB(2) level for a system of nucleons treated as bosons. The correlation amplitudes are solution of a non-linear coupled system of equations. These equations have been solved for light and medium systems, considering the central but still semi-realistic nucleon-nucleon S3 interaction.Comment: 16 pages, 2 Postscript figures, to be published in Nucl. Phys.

On the Origin of the -4.4 eV Band in CdTe(100)"

We calculate the bulk- (infinite system), (100)-bulk-projected- and (100)-Surface-projected Green's functions using the Surface Green's Function Matching method (SGFM) and an empirical tight-binding hamiltonian with tight-binding parameters (TBP) that describe well the bulk band structure of CdTe. In particular, we analyze the band (B--4) arising at --4.4 eV from the top of the valence band at $\Gamma$ according to the results of Niles and H\"ochst and at -4.6 eV according to Gawlik {\it et al.} both obtained by Angle-resolved photoelectron spectroscopy (ARPES). We give the first theoretical description of this band.Comment: 17 pages, Rev-TEX, CIEA-Phys. 02/9