Topologically invariant reaction coordinates for simulating multistate chemical reactions.

Evaluating free energy profiles of chemical reactions in complex environments such as solvents and enzymes requires extensive sampling, which is usually performed by potential of mean force (PMF) techniques. The reliability of the sampling depends not only on the applied PMF method but also the reaction coordinate space within the dynamics is biased. In contrast to simple geometrical collective variables that depend only on the positions of the atomic coordinates of the reactants, the E(gap) reaction coordinate (the energy difference obtained by evaluating a suitable force field using reactant and product state topologies) has the unique property that it is able to take environmental effects into account leading to better convergence, a more faithful description of the transition state ensemble and therefore more accurate free energy profiles. However, E(gap) requires predefined topologies and is therefore inapplicable for multistate reactions, in which the barrier between the chemically equivalent topologies is comparable to the reaction activation barrier, because undesired "side reactions" occur. In this article, we introduce a new energy-based collective variable by generalizing the E(gap) reaction coordinate such that it becomes invariant to equivalent topologies and show that it yields more well behaved free energy profiles than simpler geometrical reaction coordinates.

Geometry and interaction of structures in homogeneous isotropic turbulence

A strategy to extract turbulence structures from direct numerical simulation (DNS) data is described along with a systematic analysis of geometry and spatial distribution of the educed structures. A DNS dataset of decaying homogeneous isotropic turbulence at Reynolds number Reλ = 141 is considered. A bandpass filtering procedure is shown to be effective in extracting enstrophy and dissipation structures with their smallest scales matching the filter width, L. The geometry of these educed structures is characterized and classified through the use of two non-dimensional quantities, planarity' and filamentarity', obtained using the Minkowski functionals. The planarity increases gradually by a small amount as L is decreased, and its narrow variation suggests a nearly circular cross-section for the educed structures. The filamentarity increases significantly as L decreases demonstrating that the educed structures become progressively more tubular. An analysis of the preferential alignment between the filtered strain and vorticity fields reveals that vortical structures of a given scale L are most likely to align with the largest extensional strain at a scale 3-5 times larger than L. This is consistent with the classical energy cascade picture, in which vortices of a given scale are stretched by and absorb energy from structures of a somewhat larger scale. The spatial distribution of the educed structures shows that the enstrophy structures at the 5η scale (where η is the Kolmogorov scale) are more concentrated near the ones that are 3-5 times larger, which gives further support to the classical picture. Finally, it is shown by analysing the volume fraction of the educed enstrophy structures that there is a tendency for them to cluster around a larger structure or clusters of larger structures. Copyright © 2012 Cambridge University Press.

Homogeneous pinhole free 1 nm Al2O3 tunnel barriers on graphene

We report on the topographical and electrical characterisations of 1 nm thick Al2O3 dielectric films on graphene. The Al 2O3 is grown by sputtering a 0.6 nm Al layer on graphene and subsequentially oxidizing it in an O2 atmosphere. The Al 2O3 layer presents no pinholes and is homogeneous enough to act as a tunnel barrier. A resistance-area product in the mega-ohm micrometer-square range is found. Comparatively, the growth of Al 2O3 by evaporation does not lead to well-wetted films on graphene. Application of this high quality sputtered tunnel barrier to efficient spin injection in graphene is discussed. © 2012 American Institute of Physics.

Consensus on homogeneous manifolds

The present paper considers distributed consensus algorithms for agents evolving on a connected compact homogeneous (CCH) manifold. The agents track no external reference and communicate their relative state according to an interconnection graph. The paper first formalizes the consensus problem for synchronization (i.e. maximizing the consensus) and balancing (i.e. minimizing the consensus); it thereby introduces the induced arithmetic mean, an easily computable mean position on CCH manifolds. Then it proposes and analyzes various consensus algorithms on manifolds: natural gradient algorithms which reach local consensus equilibria; an adaptation using auxiliary variables for almost-global synchronization or balancing; and a stochastic gossip setting for global synchronization. It closes by investigating the dependence of synchronization properties on the attraction function between interacting agents on the circle. The theory is also illustrated on SO(n) and on the Grassmann manifolds. ©2009 IEEE.

A duality principle for homogeneous vectorfields with applications

A duality transformation principle was proposed for converting a positive order homogeneous vectorfield into a negative order homogeneous vectorfield. The principle also converted a uniformly locally asymptotically stable differential equation into a uniformly bounded differential equation. The duality transformations included the geometric framework for homogeneity and the removal of origin from the state space.

Assessment of homogeneous thorium/uranium fuel for pressurized water reactors

The homogeneous ThO2-UO2 fuel cycle option for a pressurized water reactor (PWR) of current technology is investigated. The fuel cycle assessment was carried out by calculating the main performance parameters: natural uranium and separative work requirements, fuel cycle cost, and proliferation potential of the spent fuel. These performance parameters were compared with a corresponding slightly enriched (all-U) fuel cycle applied to a PWR of current technology. The main conclusion derived from this comparison is that fuel cycle requirements and fuel cycle cost for the mixed Th/U fuel are higher in comparison with those of the all-U fuel. A comparison and analysis of the quantity and isotopic composition of discharged Pu indicate that the Th/U fuel cycle provides only a moderate improvement of the proliferation resistance. Thus, the overall conclusion of the investigation is that there is no economic justification to introduce Th into a light water reactor fuel cycle as a homogeneous ThO2-UO2 mixture.

Thorium fuel cycles for light water reactors: homogeneous design

The proliferation potential of the present light water reactor (LWR) fuel cycle is related primarily to the quantity and the quality of the residual Pu contained in the spent-fuel stockpile, although other potentially “weapons usable” materials are also a concern. Thorium-based nuclear fuel produces much smaller amounts of Pu in comparison with standard LWR fuel, and consequently, it is more proliferation resistant than conventional slightly enriched all-U fuel; the long-term toxicity of the spent-fuel stockpile is also reduced

Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Twin plane re-entrant mechanism for catalytic nanowire growth.

A twin-plane based nanowire growth mechanism is established using Au catalyzed Ge nanowire growth as a model system. Video-rate lattice-resolved environmental transmission electron microscopy shows a convex, V-shaped liquid catalyst-nanowire growth interface for a ⟨112⟩ growth direction that is composed of two Ge {111} planes that meet at a twin boundary. Unlike bulk crystals, the nanowire geometry allows steady-state growth with a single twin boundary at the nanowire center. We suggest that the nucleation barrier at the twin-plane re-entrant groove is effectively reduced by the line energy, and hence the twin acts as a preferential nucleation site that dictates the lateral step flow cycle which constitutes nanowire growth.

Co-catalytic absorption layers for controlled laser-induced chemical vapor deposition of carbon nanotubes.

The concept of co-catalytic layer structures for controlled laser-induced chemical vapor deposition of carbon nanotubes is established, in which a thin Ta support layer chemically aids the initial Fe catalyst reduction. This enables a significant reduction in laser power, preventing detrimental positive optical feedback and allowing improved growth control. Systematic study of experimental parameters combined with simple thermostatic modeling establishes general guidelines for the effective design of such catalyst/absorption layer combinations. Local growth of vertically aligned carbon nanotube forests directly on flexible polyimide substrates is demonstrated, opening up new routes for nanodevice design and fabrication.