Modeling contact formation between atomic-sized gold tips via molecular dynamics

The formation and rupture of atomic-sized contacts is modelled by means of molecular dynamics simulations. Such nano-contacts are realized in scanning tunnelling microscope and mechanically controlled break junction experiments. These instruments routinely measure the conductance across the nano-sized electrodes as they are brought into contact and separated, permitting conductance traces to be recorded that are plots of conductance versus the distance between the electrodes. One interesting feature of the conductance traces is that for some metals and geometric configurations a jump in the value of the conductance is observed right before contact between the electrodes, a phenomenon known as jump-to-contact. This paper considers, from a computational point of view, the dynamics of contact between two gold nano-electrodes. Repeated indentation of the two surfaces on each other is performed in two crystallographic orientations of face-centred cubic gold, namely (001) and (111). Ultimately, the intention is to identify the structures at the atomic level at the moment of first contact between the surfaces, since the value of the conductance is related to the minimum cross-section in the contact region. Conductance values obtained in this way are determined using first principles electronic transport calculations, with atomic configurations taken from the molecular dynamics simulations serving as input structures.

Study of zinc protein ligands in a halophilic enzyme

Glucose dehydrogenase (EC 1.1.1.47) from the halophilic Archaeon Haloferax mediterranei belongs to the medium-chain alcohol dehydrogenase superfamily and requires a zinc ion for catalysis. The zinc ion is coordinated by a histidine, a water molecule and two other ligands from the protein or the substrate, which vary during the catalytic cycle of the enzyme. In many enzymes of this superfamily one of the zinc ligands is commonly cysteine, which is replaced by an aspartate residue at position 38 in the halophilic enzyme. This change has been only observed in glucose dehydrogenases from extremely halophilic microorganisms belonging to the Archaea Domain. This paper describes biochemical studies and structural comparisons to analyze the role of sequence differences between thermophilic and halophilic glucose dehydrogenases which contain a zinc ion within the protein surrounded by three ligands. Whilst the catalytic activity of the D38C GlcDH mutant is reduced, its thermal stability is enhanced, consistent with the greater structural similarity between this mutant and the homologous thermophilic enzyme from Thermoplasma acidophilum.