Dynamic bonding of metallic nanocontacts: Insights from experiments and atomistic simulations

The conductance across an atomically narrow metallic contact can be measured by using scanning tunneling microscopy. In certain situations, a jump in the conductance is observed right at the point of contact between the tip and the surface, which is known as “jump to contact” (JC). Such behavior provides a way to explore, at a fundamental level, how bonding between metallic atoms occurs dynamically. This phenomenon depends not only on the type of metal but also on the geometry of the two electrodes. For example, while some authors always find JC when approaching two atomically sharp tips of Cu, others find that a smooth transition occurs when approaching a Cu tip to an adatom on a flat surface of Cu. In an attempt to show that all these results are consistent, we make use of atomistic simulations; in particular, classical molecular dynamics together with density functional theory transport calculations to explore a number of possible scenarios. Simulations are performed for two different materials: Cu and Au in a [100] crystal orientation and at a temperature of 4.2 K. These simulations allow us to study the contribution of short- and long-range interactions to the process of bonding between metallic atoms, as well as to compare directly with experimental measurements of conductance, giving a plausible explanation for the different experimental observations. Moreover, we show a correlation between the cohesive energy of the metal, its Young's modulus, and the frequency of occurrence of a jump to contact.

Spatially extensive summation of contrast-energy is revealed by contrast detection of micro-pattern textures

Vision must analyze the retinal image over both small and large areas to represent fine-scale spatial details and extensive textures. The long-range neuronal convergence that this implies might lead us to expect that contrast sensitivity should improve markedly with the contrast area of the image. But this is at odds with the orthodox view that contrast sensitivity is determined merely by probability summation over local independent detectors. To address this puzzle, I aimed to assess the summation of luminance contrast without the confounding influence of area-dependent internal noise. I measured contrast detection thresholds for novel Battenberg stimuli that had identical overall dimensions (to clamp the aggregation of noise) but were constructed from either dense or sparse arrays of micro-patterns. The results unveiled a three-stage visual hierarchy of contrast summation involving (i) spatial filtering, (ii) long-range summation of coherent textures, and (iii) pooling across orthogonal textures. Linear summation over local energy detectors was spatially extensive (as much as 16 cycles) at Stage 2, but the resulting model is also consistent with earlier classical results of contrast summation (J. G. Robson & N. Graham, 1981), where co-aggregation of internal noise has obscured these long-range interactions.

Degenerate Gases of Strontium for Studies of Quantum Magnetism

We describe the construction and characterization of a new apparatus that can produce degenerate quantum gases of strontium. The realization of degenerate gases is an important first step toward future studies of quantum magnetism. Three of the four stable isotopes of strontium have been cooled into the degenerate regime. The experiment can make nearly pure Bose-Einstein condensates containing approximately 1x10^4 atoms, for strontium-86, and approximately 4x10^5 atoms, for strontium-84. We have also created degenerate Fermi gases of strontium-87 with a reduced temperature, T/T_F of approximately 0.2. The apparatus will be able to produce Bose-Einstein condensates of strontium-88 with straightforward modifications. We also report the first experimental and theoretical results from the strontium project. We have developed a technique to accelerate the continuous loading of strontium atoms into a magnetic trap. By applying a laser addressing the 3P1 to 3S1 transition in our magneto-optical trap, the rate at which atoms populate the magnetically-trapped 3P2 state can be increased by up to 65%. Quantum degenerate gases of atoms in the metastable 3P0 and 3P2 states are a promising platform for quantum simulation of systems with long-range interactions. We have performed an initial numerical study of a method to transfer the ground state degenerate gases that we can currently produce into one of the metastable states via a three-photon transition. Numerical simulations of the Optical Bloch equations governing the three-photon transition indicate that >90% of a ground state degenerate gas can be transferred into a metastable state.

Engineering a Quantum Many-body Hamiltonian with Trapped Ions

While fault-tolerant quantum computation might still be years away, analog quantum simulators offer a way to leverage current quantum technologies to study classically intractable quantum systems. Cutting edge quantum simulators such as those utilizing ultracold atoms are beginning to study physics which surpass what is classically tractable. As the system sizes of these quantum simulators increase, there are also concurrent gains in the complexity and types of Hamiltonians which can be simulated. In this work, I describe advances toward the realization of an adaptable, tunable quantum simulator capable of surpassing classical computation. We simulate long-ranged Ising and XY spin models which can have global arbitrary transverse and longitudinal fields in addition to individual transverse fields using a linear chain of up to 24 Yb+ 171 ions confined in a linear rf Paul trap. Each qubit is encoded in the ground state hyperfine levels of an ion. Spin-spin interactions are engineered by the application of spin-dependent forces from laser fields, coupling spin to motion. Each spin can be read independently using state-dependent fluorescence. The results here add yet more tools to an ever growing quantum simulation toolbox. One of many challenges has been the coherent manipulation of individual qubits. By using a surprisingly large fourth-order Stark shifts in a clock-state qubit, we demonstrate an ability to individually manipulate spins and apply independent Hamiltonian terms, greatly increasing the range of quantum simulations which can be implemented. As quantum systems grow beyond the capability of classical numerics, a constant question is how to verify a quantum simulation. Here, I present measurements which may provide useful metrics for large system sizes and demonstrate them in a system of up to 24 ions during a classically intractable simulation. The observed values are consistent with extremely large entangled states, as much as ~95% of the system entangled. Finally, we use many of these techniques in order to generate a spin Hamiltonian which fails to thermalize during experimental time scales due to a meta-stable state which is often called prethermal. The observed prethermal state is a new form of prethermalization which arises due to long-range interactions and open boundary conditions, even in the thermodynamic limit. This prethermalization is observed in a system of up to 22 spins. We expect that system sizes can be extended up to 30 spins with only minor upgrades to the current apparatus. These results emphasize that as the technology improves, the techniques and tools developed here can potentially be used to perform simulations which will surpass the capability of even the most sophisticated classical techniques, enabling the study of a whole new regime of quantum many-body physics.

Spontaneous long and short-range ferroelectric ordering in Pb(0.55)La(0.30)TiO(3) ceramics

In this work, we investigated the temperature dependence of short and long-range ferroelectric ordering in Pb(0.55)La(0.30)TiO(3) relaxor composition. High-resolution x-ray powder diffraction measurements revealed a clear spontaneous macroscopic cubic-to-tetragonal phase transition in the PLT relaxor sample at similar to 60 K below the maximum of the dielectric constant peak (T(m)). Indeed, the x-ray diffraction (XRD) data showed that at 300 K (above T(m) but below the Burns temperature, T(B)) the long-range order structure corresponds to a macroscopic cubic symmetry, space group number 221 (Pm-3m), whereas the data collected at 20 K revealed a macroscopic tetragonal symmetry, space group number 99 (P4mm) with c/a=1.0078, that is comparable to that of a normal ferroelectric. These results show that for samples with tetragonal composition, the long-range ferroelectric order may be recovered spontaneously at cryogenics temperatures, in contrast to ferroelectric samples with rhombohedral symmetry. On the other hand, x-ray absorption spectroscopy investigations intriguingly revealed the existence of local tetragonal disorder around Ti atoms for temperatures far below T(m) and above T(B), for which the sample presents macroscopic tetragonal and cubic symmetries, respectively. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3431024]

Colloidal dipolar interactions in 2D smectic-C films

We use a two-dimensional (2D) elastic free energy to calculate the effective interaction between two circular disks immersed in smectic-C films. For strong homeotropic anchoring, the distortion of the director field caused by the disks generates topological defects that induce an effective interaction between the disks. We use finite elements, with adaptive meshing, to minimize the 2D elastic free energy. The method is shown to be accurate and efficient for inhomogeneities on the length scales set by the disks and the defects, that differ by up to 3 orders of magnitude. We compute the effective interaction between two disk-defect pairs in a simple (linear) configuration. For large disk separations, D, the elastic free energy scales as similar to D-2, confirming the dipolar character of the long-range effective interaction. For small D the energy exhibits a pronounced minimum. The lowest energy corresponds to a symmetrical configuration of the disk-defect pairs, with the inner defect at the mid-point between the disks. The disks are separated by a distance that, is twice the distance of the outer defect from the nearest disk. The latter is identical to the equilibrium distance of a defect nucleated by an isolated disk.

Shielding of ionic interactions by sulfur dioxide in an ionic liquid

The effect of adding SO(2) on the structure and dynamics of 1-butyl-3-methylimidazolium bromide (BMIBr) was investigated by low-frequency Raman spectroscopy and molecular dynamics (MD) simulations. The MD simulations indicate that the long-range structure of neat BMIBr is disrupted resulting in a liquid with relatively low viscosity and high conductivity, but strong correlation of ionic motion persists in the BMIBr-SO(2) mixture due to ionic pairing. Raman spectra within the 5 < omega < 200 cm(-1) range at low temperature reveal the short-time dynamics, which is consistent with the vibrational density of states calculated by MD simulations. Several time correlation functions calculated by MD simulations give further insights on the structural relaxation of BMIBr-SO(2).

Long- and medium-range components of the nuclear force in quark-model based calculations

Quark-model descriptions of the nucleon-nucleon interaction contain two main ingredients, a quark-exchange mechanism for the short-range repulsion and meson exchanges for the medium- and long-range parts of the interaction. We point out the special role played by higher partial waves, and in particular the (1)F(3), as a very sensitive probe for the meson-exchange pan employed in these interaction models. In particular, we show that the presently available models fail to provide a reasonable description of higher partial waves and indicate the reasons for this shortcoming.

TiO2-Cu photocatalysts: A study on the long- and short-range chemical environment of the dopant

In this study, the short- and long-range chemical environments of Cu dopant in TiO2 photocatalyst have been investigated. The Cu-doped and undoped TiO2 specimens were prepared by the sol-gel approach employing CuSO4·5H2O and Ti(O-iPr)4 precursors and subjecting the dried gels to thermal treatment at 400 and 500 C. The photocatalytic activity, investigated by methylene blue degradation under sunlight irradiation, showed a significantly higher efficiency of Cu-doped samples than that of pure TiO2. The X-ray diffraction results showed the presence of anatase phase for samples prepared at 400 and 500 C. No crystalline CuSO4 phase was detected below 500 C. It was also found that doping decreases the crystallite size in the (004) and (101) directions. Infrared spectroscopy results indicated that the chemical environment of sulfate changes as a function of thermal treatment, and UV-vis spectra showed that the band gap decreases with thermal treatment and Cu doping, showing the lowest value for the 400 C sample. X-ray absorption fine structure measurements and analysis refinements revealed that even after thermal treatment and photocatalytic assays, the Cu2+ local order is similar to that of CuSO4, containing, however, oxygen vacancies. X-ray photoelectron spectroscopy data, limited to the near surface region of the catalyst, evidenced, besides CuSO4, the presence of Cu1+ and CuO phases, indicating the active role of Cu in the TiO2 lattice. © 2013 Springer Science+Business Media New York.

Electrostatic potentials and polarization effects in proton-molecule interactions by means of multipoles from the quantum theory of atoms in molecules

Some atomic multipoles (charges, dipoles and quadrupoles) from the Quantum Theory of Atoms in Molecules (QTAIM) and CHELPG charges are used to investigate interactions between a proton and a molecule (F2, Cl2, BF, AlF, BeO, MgO, LiH, H2CO, NH3, PH3, BF3, and CO2). Calculations were done at the B3LYP/6-311G(3d,3p) level. The main aspect of this work is the investigation of polarization effects over electrostatic potentials and atomic multipoles along a medium to long range of interaction distances. Large electronic charge fluxes and polarization changes are induced by a proton mainly when this positive particle approaches the least electronegative atom of diatomic heteronuclear molecules. The search for simple equations to describe polarization on electrostatic potentials from QTAIM quantities resulted in linear relations with r-4 (r is the interaction distance) for many cases. Moreover, the contribution from atomic dipoles to these potentials is usually the most affected contribution by polarization what reinforces the need for these dipoles to a minimal description of purely electrostatic interactions. Finally, CHELPG charges provide a description of polarization effects on electrostatic potentials that is in disagreement with physical arguments for certain of these molecules. (c) 2012 Wiley Periodicals, Inc.

Multiple attractors, long chaotic transients, and failure in small-world networks of excitable neurons.

We study the dynamical states of a small-world network of recurrently coupled excitable neurons, through both numerical and analytical methods. The dynamics of this system depend mostly on both the number of long-range connections or ?shortcuts?, and the delay associated with neuronal interactions. We find that persistent activity emerges at low density of shortcuts, and that the system undergoes a transition to failure as their density reaches a critical value. The state of persistent activity below this transition consists of multiple stable periodic attractors, whose number increases at least as fast as the number of neurons in the network. At large shortcut density and for long enough delays the network dynamics exhibit exceedingly long chaotic transients, whose failure times follow a stretched exponential distribution. We show that this functional form arises for the ensemble-averaged activity if the failure time for each individual network realization is exponen- tially distributed

RNA tertiary interactions in the large ribosomal subunit: The A-minor motif

Analysis of the 2.4-Å resolution crystal structure of the large ribosomal subunit from Haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif that stabilizes RNA tertiary and quaternary structures. This motif is termed the A-minor motif, because it involves the insertion of the smooth, minor groove edges of adenines into the minor groove of neighboring helices, preferentially at C-G base pairs, where they form hydrogen bonds with one or both of the 2′ OHs of those pairs. A-minor motifs stabilize contacts between RNA helices, interactions between loops and helices, and the conformations of junctions and tight turns. The interactions between the 3′ terminal adenine of tRNAs bound in either the A site or the P site with 23S rRNA are examples of functionally significant A-minor interactions. The A-minor motif is by far the most abundant tertiary structure interaction in the large ribosomal subunit; 186 adenines in 23S and 5S rRNA participate, 68 of which are conserved. It may prove to be the universally most important long-range interaction in large RNA structures.

On the magnitude of the electrostatic contribution to ligand-DNA interactions.

A model based on the nonlinear Poisson-Boltzmann equation is used to study the electrostatic contribution to the binding free energy of a simple intercalating ligand, 3,8-diamino-6-phenylphenanthridine, to DNA. We find that the nonlinear Poisson-Boltzmann model accurately describes both the absolute magnitude of the pKa shift of 3,8-diamino-6-phenylphenanthridine observed upon intercalation and its variation with bulk salt concentration. Since the pKa shift is directly related to the total electrostatic binding free energy of the charged and neutral forms of the ligand, the accuracy of the calculations implies that the electrostatic contributions to binding are accurately predicted as well. Based on our results, we have developed a general physical description of the electrostatic contribution to ligand-DNA binding in which the electrostatic binding free energy is described as a balance between the coulombic attraction of a ligand to DNA and the disruption of solvent upon binding. Long-range coulombic forces associated with highly charged nucleic acids provide a strong driving force for the interaction of cationic ligands with DNA. These favorable electrostatic interactions are, however, largely compensated for by unfavorable changes in the solvation of both the ligand and the DNA upon binding. The formation of a ligand-DNA complex removes both charged and polar groups at the binding interface from pure solvent while it displaces salt from around the nucleic acid. As a result, the total electrostatic binding free energy is quite small. Consequently, nonpolar interactions, such as tight packing and hydrophobic forces, must play a significant role in ligand-DNA stability.

Van der Waals-corrected density functional theory: benchmarking for hydrogen-nanotube and nanotube-nanotube interactions

Density functional theory (DFT) is a powerful approach to electronic structure calculations in extended systems, but suffers currently from inadequate incorporation of long-range dispersion, or Van der Waals (VdW) interactions. VdW-corrected DFT is tested for interactions involving molecular hydrogen, graphite, single-walled carbon nanotubes (SWCNTs), and SWCNT bundles. The energy correction, based on an empirical London dispersion term with a damping function at short range, allows a reasonable physisorption energy and equilibrium distance to be obtained for H-2 on a model graphite surface. The VdW-corrected DFT calculation for an (8, 8) nanotube bundle reproduces accurately the experimental lattice constant. For H-2 inside or outside an (8, 8) SWCNT, we find the binding energies are respectively higher and lower than that on a graphite surface, correctly predicting the well known curvature effect. We conclude that the VdW correction is a very effective method for implementing DFT calculations, allowing a reliable description of both short-range chemical bonding and long-range dispersive interactions. The method will find powerful applications in areas of SWCNT research where empirical potential functions either have not been developed, or do not capture the necessary range of both dispersion and bonding interactions.

Identifying optimal lipid raft characteristics required to promote nanoscale protein-protein interactions on the plasma membrane

The dynamic lateral segregation of signaling proteins into microdomains is proposed to facilitate signal transduction, but the constraints on microdomain size, mobility, and diffusion that might realize this function are undefined. Here we interrogate a stochastic spatial model of the plasma membrane to determine how microdomains affect protein dynamics. Taking lipid rafts as representative microdomains, we show that reduced protein mobility in rafts segregates dynamically partitioning proteins, but the equilibrium concentration is largely independent of raft size and mobility. Rafts weakly impede small-scale protein diffusion but more strongly impede long-range protein mobility. The long-range mobility of raft-partitioning and raft-excluded proteins, however, is reduced to a similar extent. Dynamic partitioning into rafts increases specific interprotein collision rates, but to maximize this critical, biologically relevant function, rafts must be small (diameter, 6 to 14 nm) and mobile. Intermolecular collisions can also be favored by the selective capture and exclusion of proteins by rafts, although this mechanism is generally less efficient than simple dynamic partitioning. Generalizing these results, we conclude that microdomains can readily operate as protein concentrators or isolators but there appear to be significant constraints on size and mobility if microdomains are also required to function as reaction chambers that facilitate nanoscale protein-protein interactions. These results may have significant implications for the many signaling cascades that are scaffolded or assembled in plasma membrane microdomains.