Biomedical subjects

M Marsman

Publications and source records attributed to M Marsman.

4 recordsLinked to original sources

PubMed2006

Relaxed core projector-augmented-wave method.

We extend the full-potential projector-augmented-wave method beyond the frozen core approximation, i.e., include the self-consistent optimization of the core charge density, in such a manner that the valence wave functions remain orthogonal to the core. The method consists of an on-the-fly repseudization of the all-electron problem, solving for the self-consistent core charge density within a spherical approximation. The key ideas in our procedure are to keep the projector functions fixed throughout the electronic minimization and to derive the new pseudopartial waves from these original projector functions, at each step of the electronic minimization procedure. Results of relaxed core calculations for atomic interconfigurational energies, structural energy differences between bulk phases of Fe, atomization energies of a subset of Pople's G2-1 set, and the Rh 3d surface core level shifts for the (log3 x log3)-Rh(111) surface at 1/3 CO coverage are presented.

Journal Article↗

PubMed2006

Screened hybrid density functionals applied to solids.

Hybrid Fock exchange/density functional theory functionals have shown to be very successful in describing a wide range of molecular properties. For periodic systems, however, the long-range nature of the Fock exchange interaction and the resultant large computational requirements present a major drawback. This is especially true for metallic systems, which require a dense Brillouin zone sampling. Recently, a new hybrid functional [HSE03, J. Heyd, G. E. Scuseria, and M. Ernzerhof, J. Chem. Phys. 118, 8207 (2003)] that addresses this problem within the context of methods that evaluate the Fock exchange in real space was introduced. We discuss the advantages the HSE03 functional brings to methods that rely on a reciprocal space description of the Fock exchange interaction, e.g., all methods that use plane wave basis sets. Furthermore, we present a detailed comparison of the performance of the HSE03 and PBE0 functionals for a set of archetypical solid state systems by calculating lattice parameters, bulk moduli, heats of formation, and band gaps. The results indicate that the hybrid functionals indeed often improve the description of these properties, but in several cases the results are not yet on par with standard gradient corrected functionals. This concerns in particular metallic systems for which the bandwidth and exchange splitting are seriously overestimated.

Journal Article↗

PubMed2004

High-coverage oxygen structures on Rh111: adsorbate repulsion and site preference is not enough.

A new O induced structure on Rh(111) displaying a (2 sqaureroot[3] x 2sqaureroot[3])R30 degrees periodicity with an oxygen coverage of 2/3 has been studied by high resolution core level spectroscopy, scanning tunneling microscopy, and density functional theory. Although O favors fcc hollow sites in all other known phases, it occupies both fcc and hcp sites in this structure, which cannot be explained by pairwise adsorbate repulsion only. Both the (2sqaureroot[3] x 2sqaureroot[3])R30 degrees and (2 x 2)-3O structures also exemplify that density-of-states contrast can lead to oxygen adatoms appearing as protrusions in scanning tunneling microscopy images.

Journal Article↗

PubMed2001

The Rab7 effector protein RILP controls lysosomal transport by inducing the recruitment of dynein-dynactin motors.

Many intracellular compartments, including MHC class II-containing lysosomes, melanosomes, and phagosomes, move along microtubules in a bidirectional manner and in a stop-and-go fashion due to the alternating activities of a plus-end directed kinesin motor and a minus-end directed dynein-dynactin motor. It is largely unclear how motor proteins are targeted specifically to different compartments. Rab GTPases recruit and/or activate several proteins involved in membrane fusion and vesicular transport. They associate with specific compartments after activation, which makes Rab GTPases ideal candidates for controlling motor protein binding to specific membranes. We and others [7] have identified a protein, called RILP (for Rab7-interacting lysosomal protein), that interacts with active Rab7 on late endosomes and lysosomes. Here we show that RILP prevents further cycling of Rab7. RILP expression induces the recruitment of functional dynein-dynactin motor complexes to Rab7-containing late endosomes and lysosomes. Consequently, these compartments are transported by these motors toward the minus end of microtubules, effectively inhibiting their transport toward the cell periphery. This signaling cascade may be responsible for timed and selective dynein motor recruitment onto late endosomes and lysosomes.

Adaptor Proteins, Signal Transducing↗