Formation of a metallic contact: jump to contact revisited

The transition from tunneling to metallic contact between two surfaces does not always involve a jump, but can be smooth. We have observed that the configuration and material composition of the electrodes before contact largely determine the presence or absence of a jump. Moreover, when jumps are found preferential values of conductance have been identified. Through a combination of experiments, molecular dynamics, and first-principles transport calculations these conductance values are identified with atomic contacts of either monomers, dimers, or double-bond contacts.

Mechanical annealing of metallic electrodes at the atomic scale

The process of creating an atomically defined and robust metallic tip is described and quantified using measurements of contact conductance between gold electrodes and numerical simulations. Our experiments show how the same conductance behavior can be obtained for hundreds of cycles of formation and rupture of the nanocontact by limiting the indentation depth between the two electrodes up to a conductance value of approximately 5G0 in the case of gold. This phenomenon is rationalized using molecular dynamics simulations together with density functional theory transport calculations which show how, after repeated indentations (mechanical annealing), the two metallic electrodes are shaped into tips of reproducible structure. These results provide a crucial insight into fundamental aspects relevant to nanotribology or scanning probe microscopies.

Mechanical, electrical, and magnetic properties of Ni nanocontacts

The dynamic deformation upon stretching of Ni nanowires as those formed with mechanically controllable break junctions or with a scanning tunneling microscope is studied both experimentally and theoretically. Molecular dynamics simulations of the breaking process are performed. In addition, and in order to compare with experiments, we also compute the transport properties in the last stages before failure using the first-principles implementation of Landauer's formalism included in our transport package ALACANT.

Data index for energy transfer collisions of atoms and molecules, 1970-1979 /

Mode of access: Internet.

Enhancement of hydrogen physisorption on single-walled carbon nanotubes resulting from defects created by carbon bombardment

The defect effect on hydrogen adsorption on single-walled carbon nanotubes (SWNTs) has been studied by using extensive molecular dynamics simulations and density functional theory (DFT) calculations. It indicates that the defects created on the exterior wall of the SWNTs by bombarding the tube wall with carbon atoms and C-2 dimers at a collision energy of 20 eV can enhance the hydrogen adsorption potential of the SWNTs substantially. The average adsorption energy for a H-2 molecule adsorbed on the exterior wall of a defected (10,10) SWNT is similar to 150 meV, while that for a H-2 molecule adsorbed on the exterior wall of a perfect (10,10) SWNT is similar to 104 meV. The H-2 sticking coefficient is very sensitive to temperature, and has a maximum value around 70 to 90 K. The electron density contours, the local density of states, and the electron transfers obtained from the DFT calculations clearly indicate that the H-2 molecules are all physisorbed on the SWNTs. At temperatures above 200 K, most of the H-2 molecules adsorbed on the perfect SWNT are soon desorbed, but the H-2 molecules can still remain on the defected SWNTs at 300 K. The detailed processes of H-2 molecules adsorbing on and desorbing from the (10,10) SWNTs are demonstrated.

Quantum effect induced reverse kinetic molecular sieving in microporous materials

We report kinetic molecular sieving of hydrogen and deuterium in zeolite rho at low temperatures, using atomistic molecular dynamics simulations incorporating quantum effects via the Feynman-Hibbs approach. We find that diffusivities of confined molecules decrease when quantum effects are considered, in contrast with bulk fluids which show an increase. Indeed, at low temperatures, a reverse kinetic sieving effect is demonstrated in which the heavier isotope, deuterium, diffuses faster than hydrogen. At 65 K, the flux selectivity is as high as 46, indicating a good potential for isotope separation.

Application of a generalized thermodynamic approach to characterize mesoporous materials

Equilibrium adsorption and desorption in mesoporous adsorbents is considered on the basis of rigorous thermodynamic analysis, in which the curvature-dependent solid-fluid potential and the compressibility of the adsorbed phase are accounted for. The compressibility of the adsorbed phase is considered for the first time in the literature in the framework of a rigorous thermodynamic approach. Our model is a further development of continuum thermodynamic approaches proposed by Derjaguin and Broekhoff and de Boer, and it is based on a reference isotherm of a non-porous material having the same chemical structure as that of the pore wall. In this improved thermodynamic model, we incorporated a prescription for transforming the solid-fluid potential exerted by the flat reference surface to the potential inside cylindrical and spherical pores. We relax the assumption that the adsorbed film density is constant and equal to that of the saturated liquid. Instead, the density of the adsorbed fluid is allowed to vary over the adsorbed film thickness and is calculated by an equation of state. As a result, the model is capable to describe the adsorption-desorption reversibility in cylindrical pores having diameter less than 2 nm. The generalized thermodynamic model may be applied to the pore size characterization of mesoporous materials instead of much more time-consuming molecular approaches. (c) 2005 Elsevier B.V. All rights reserved.

Efficient -tensor determination and NH assignment of paramagnetic proteins

Anisotropic magnetic susceptibility tensors chi of paramagnetic metal ions are manifested in pseudocontact shifts, residual dipolar couplings, and other paramagnetic observables that present valuable long-range information for structure determinations of protein-ligand complexes. A program was developed for automatic determination of the chi-tensor anisotropy parameters and amide resonance assignments in proteins labeled with paramagnetic metal ions. The program requires knowledge of the three-dimensional structure of the protein, the backbone resonance assignments of the diamagnetic protein, and a pair of 2D N-15-HSQC or 3D HNCO spectra recorded with and without paramagnetic metal ion. It allows the determination of reliable chi-tensor anisotropy parameters from 2D spectra of uniformly N-15-labeled proteins of fairly high molecular weight. Examples are shown for the 185-residue N-terminal domain of the subunit epsilon from E. coli DNA polymerase III in complex with the subunit theta and La3+ in its diamagnetic and Dy3+, Tb3+, and Er3+ in its paramagnetic form.

Molecular recognition of an RNA trafficking element by heterogeneous nuclear ribonucleoprotein A2

Heterogeneous nuclear ribonucleoprotein (hnRNP) A2 is a multitasking protein involved in RNA packaging, alternative splicing of pre-mRNA. telomere maintenance, cytoplasmic RNA trafficking, and translation. It binds short segments of single-stranded nucleic acids, including the A2RE11 RNA element that is necessary and sufficient for cytoplasmic transport of a subset of rnRNAs in oligodendrocytes and neurons. We have explored the structures of hnRNP A2, its RNA recognition motifs (RRMs) and Gly-rich module, and the RRM complexes with A2RE11. Circular dichroism spectroscopy showed that the secondary structure of the first 189 residues of hnRNP A2 parallels that of the tandem beta alpha beta beta alpha beta RRMs of its paralogue, hnRNP A1, previously deduced from X-ray diffraction studies. The unusual GRD was shown to have substantial beta-sheet and beta-turn structure. Sedimentation equilibrium and circular dichroism results were consistent with the tandem RRM region being monomeric and supported earlier evidence for the binding of two A2RE11 oligoribonucleotides to this domain, in contrast to the protein dimer formed by the complex of hnRNP A1 with the telomeric ssDNA repeat. A three-dimensional structure for the N-terminal, two-RRM-containing segment of hnRNP A2 was derived by homology modeling. This structure was used to derive a model for the complex with A2RE11 using the previously described interaction of pairs of stacked nucleotides with aromatic residues on the RRM beta-sheet platforms, conserved in other RRM-RNA complexes, together with biochemical data and molecular dynamics-based observations of inter-RRM mobility.

Quantum effects on adsorption and diffusion of hydrogen and deuterium in microporous materials

Monte Carlo and molecular dynamics simulations and neutron scattering experiments are used to study the adsorption and diffusion of hydrogen and deuterium in zeolite Rho in the temperature range of 30-150 K. In the molecular simulations, quantum effects are incorporated via the Feynman-Hibbs variational approach. We suggest a new set of potential parameters for hydrogen, which can be used when Feynman-Hibbs variational approach is used for quantum corrections. The dynamic properties obtained from molecular dynamics simulations are in excellent agreement with the experimental results and show significant quantum effects on the transport at very low temperature. The molecular dynamics simulation results show that the quantum effect is very sensitive to pore dimensions and under suitable conditions can lead to a reverse kinetic molecular sieving with deuterium diffusing faster than hydrogen.

The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions

The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard box types without these constraints. Three different proteins of varying size, shape, and secondary structure content were examined in the study. The statistical significance of differences in RMSD, radius of gyration, solvent-accessible surface, number of hydrogen bonds, and secondary structure content between proteins, box types, and the application or not of rotational constraints has been assessed. Furthermore, the differences in the collective modes for each protein between different boxes and the application or not of rotational constraints have been examined. In total 105 simulations were performed, and the results compared using a three-way multivariate analysis of variance (MANOVA) for properties derived from the trajectories and a three-way univariate analysis of variance (ANOVA) for collective modes. It is shown that application of roto-translational constraints does not have a statistically significant effect on the results obtained from the different simulations. However, the choice of simulation box was found to have a small (5-10%), but statistically significant effect on the behavior of two of the three proteins included in the study. (c) 2005 Wiley Periodicals, Inc.

Transport diffusion of gases is rapid in flexible carbon nanotu

Molecular dynamics simulations of rigid, defect-free single-walled carbon nanotubes have previously suggested that the transport diffusivity of gases adsorbed in these materials can be orders of magnitude higher than any other nanoporous material (A. I. Skoulidas et al., Phys. Rev. Lett. 2002, 89, 185901). These simulations must overestimate the molecular diffusion coefficients because they neglect energy exhange between the diffusing molecules and the nanotube. Recently, Jakobtorweihen et al. have reported careful simulations of molecular self-diffusion that allow nanotube flexibility (Phys. Rev. Lett. 2005, 95, 044501). We have used the efficient thermostat developed by Jakobtorweihen et al. to examine the influence of nanotube flexibility on the transport diffusion of CH4 in (20,0) and (15,0) nanotubes. The inclusion of nanotube flexibility reduces the transport diffusion relative to the rigid nanotube by roughly an order of magnitude close to zero pressure, but at pressures above about I bar the transport diffusivities for flexible and rigid nanotubes are very similar, differing by less than a factor or two on average. Hence, the transport diffusivities are still extremely large compared to other known materials when flexibility is taken into account.

Transport of simple fluids in nanopores: Theory and simulation

A theory is discussed of single-component transport in nanopores, recently developed by Bhatia and coworkers. The theory considers the oscillatory motion of molecules between diffuse wall collisions, arising from the fluid-wall interaction, along with superimposed viscous flow due to fluid-fluid interaction. The theory is tested against molecular dynamics simulations for hydrogen, methane, and carbon tetrafluoride flow in cylindrical nanopores in silica. Although exact at low densities, the theory performs well even at high densities, with the density dependency of the transport coefficient arising from viscous effects. Such viscous effects are reduced at high densities because of the large increase in viscosity, which explains the maximum in the transport coefficient with increase in density. Further, it is seen that in narrow pore sizes of less than two molecular diameters, where a complete monolayer cannot form on the surface, the mutual interference of molecules on opposite sides of the cross section can reduce the transport coefficient, and lead to a maximum in the transport coefficient with increasing density. The theory is also tested for the case of partially diffuse reflection and shows the viscous contribution to be negligible when the reflection is nearly specular. (c) 2005 American Institute of Chemical Engineers AIChE J, 52: 29-38, 2006.

Simulation of glassy state relaxations in polymers: A static analysis of methyl group and methoxy group rotation in poly(vinyl methyl ether)

We show that the simple quasi-static technique, also called the adiabatic mapping technique, can be used to determine the energetics of rotation of methyl and methoxy groups in amorphous poly(vinyl methyl ether) even though the latter process is too slow to be amenable to direct molecular dynamics simulation. For the methyl group rotation, we find that the mean and standard deviation of the simulated rotational barrier heights agree well with experimental data from quasi-elastic neutron scattering. In the case of the methoxy groups we find that just 4% of the groups contribute more than 90% of the observed dielectric relaxation strength. The groups which make the most contribution are those which, by virtue of their particular conformation and local environment, have two alternative positions of similar energy.

Implementation of particle-scale rotation in the 3-d Lattice Solid Model

In this study, 3-D Lattice Solid Model (LSMearth or LSM) was extended by introducing particle-scale rotation. In the new model, for each 3-D particle, we introduce six degrees of freedom: Three for translational motion, and three for orientation. Six kinds of relative motions are permitted between two neighboring particles, and six interactions are transferred, i.e., radial, two shearing forces, twisting and two bending torques. By using quaternion algebra, relative rotation between two particles is decomposed into two sequence-independent rotations such that all interactions due to the relative motions between interactive rigid bodies can be uniquely decided. After incorporating this mechanism and introducing bond breaking under torsion and bending into the LSM, several tests on 2-D and 3-D rock failure under uni-axial compression are carried out. Compared with the simulations without the single particle rotational mechanism, the new simulation results match more closely experimental results of rock fracture and hence, are encouraging. Since more parameters are introduced, an approach for choosing the new parameters is presented.