Automated nanoflow liquid chromatography/tandem mass spectrometric identification of proteins from Shewanella putrefaciens separated by two-dimensional polyacrylamide gel electrophoresis

The implementation of nanoflow liquid chromatography offers unique opportunities for automation of proteomics research. We demonstrate that automated nanoflow LC/MS/MS allowed the unambiguous identification of proteins from the omnipotent bacterium Shewanella putrefaciens, based on similarity searches against the completely determined genome of related microorganisms and against non-redundant databases. Total protein extracts were separated by 2-dimensional polyacrylamide electrophoresis. Only 1/20th of a tryptic digest mixture obtained from a single Coomassie Blue stained spot was loaded on the nanoflow LC column using a preconcentration/desalting step, and analyzed on-line on a hybrid quadrupole time-of-flight mass spectrometer with an automated MS-to-MS/MS switching protocol. This method allowed the de novo peptide sequence determination of several tryptic fragments and the identification of different proteins. CopyrightCopyright 2000 John Wiley & Sons, Ltd.     

Vibrational spectra of molecules in the Hartree–Fock dielectric screening approach

Traditionally, the calculation of the vibrational spectra of molecules involves at one point or another a numerical differentiation procedure. Such a method has some serious drawbacks both in efficiency and in accuracy. In this paper, an alternative method based on linear response theory is presented. The second derivative of the ground-state energy is expressed in terms of the electron density response matrix by means of perturbation theory. The unperturbed wave functions are obtained from the Hartree–Fock equation. First-order perturbation theory applied to this equation leads to the Hartree–Fock linear response. As an illustration of this method the vibrational frequency of a H₂ molecule is calculated. The result is 1.348 × 10¹⁴ Hz as compared to the experimental value of 1.319 × 10¹⁴ Hz. This method is also applicable in the calculation of the phonon dispersion curves of solids.     

Dynamical exchange effects in a two-dimensional many-polaron gas

We calculate the influence of dynamical exchange effects on the response properties and the static properties of a two-dimensional many-polaron gas. These effects are not manifested in the random-phase approximation which is widely used in the analysis of the many-polaron system. Here they are taken into account by using a dielectric function derived in the time-dependent Hartree-Fock formalism. At weak electron-phonon coupling, we find that dynamical exchange effects lead to substantial corrections to the random-phase approximation results for the ground state energy, the effective mass, and the optical conductivity of the polaron system. Furthermore, we show that the reduction of the spectral weight of the optical absorption spectrum at frequencies above the longitudinal optical phonon frequency, due to many-body effects, is overestimated by the random-phase approximation.Received: 24 December 2003, Published online: 9 April 2004PACS: 71.45.Gm Exchange, correlation, dielectric and magnetic response functions, plasmons - 71.10.Pm Fermions in reduced dimensions (anyons, composite fermions, Luttinger liquid, etc.) - 71.38.Fp Large or Fröhlich polarons     

The energy loss function of the polaron gas

The energy loss function Im 1/K(π, ω) of a gas of polarons is calculated in the RPA approximation. For typical densities of degenerate polar semiconductors, the energy loss function has pronounced structure. Up to three resonances appear. The coupled phonon-plasmon resonance, with frequency between ω_TO and ω_LO, leads to an extremely sharp peak in Im 1/K(π, ω), for appropriate values of wavevector and densities.