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.

Intrinsic state lifetimes in Pd103 and Cd106,107

The mean-lifetimes, τ, of various medium-spin excited states in Pd103 and Cd106,107 have been deduced using the Recoil Distance Doppler Shift technique and the Differential Decay Curve Method. In Cd106, the mean-lifetimes of the Iπ=12+ state at Ex=5418 keV and the Iπ=11- state at Ex=4324 keV have been deduced as 11.4(17)ps and 8.2(7)ps, respectively. The associated β2 deformation within the axially-symmetric deformed rotor model for these states are 0.14(1) and 0.14(1), respectively. The β2 deformation of 0.14(1) for the Iπ=12+ state in Cd106 compares with a predicted β2 value from total Routhian surface (TRS) calculations of 0.17. In addition, the mean-lifetimes of the yrast Iπ=152- states in Pd103 (at Ex=1262 keV) and Cd107 (at Ex=1360 keV) have been deduced to be 31.2(44)ps and 31.4(17)ps, respectively, corresponding to β2 values of 0.16(1) and 0.12(1) assuming axial symmetry. Agreement with TRS calculations are good for Pd103 but deviate for that predicted for Cd107. © 2007 The American Physical Society.

Efficient generation of one-group cross sections for coupled Monte Carlo depletion calculations

Coupled Monte Carlo depletion systems provide a versatile and an accurate tool for analyzing advanced thermal and fast reactor designs for a variety of fuel compositions and geometries. The main drawback of Monte Carlo-based systems is a long calculation time imposing significant restrictions on the complexity and amount of design-oriented calculations. This paper presents an alternative approach to interfacing the Monte Carlo and depletion modules aimed at addressing this problem. The main idea is to calculate the one-group cross sections for all relevant isotopes required by the depletion module in a separate module external to Monte Carlo calculations. Thus, the Monte Carlo module will produce the criticality and neutron spectrum only, without tallying of the individual isotope reaction rates. The onegroup cross section for all isotopes will be generated in a separate module by collapsing a universal multigroup (MG) cross-section library using the Monte Carlo calculated flux. Here, the term "universal" means that a single MG cross-section set will be applicable for all reactor systems and is independent of reactor characteristics such as a neutron spectrum; fuel composition; and fuel cell, assembly, and core geometries. This approach was originally proposed by Haeck et al. and implemented in the ALEPH code. Implementation of the proposed approach to Monte Carlo burnup interfacing was carried out through the BGCORE system. One-group cross sections generated by the BGCORE system were compared with those tallied directly by the MCNP code. Analysis of this comparison was carried out and led to the conclusion that in order to achieve the accuracy required for a reliable core and fuel cycle analysis, accounting for the background cross section (σ0) in the unresolved resonance energy region is essential. An extension of the one-group cross-section generation model was implemented and tested by tabulating and interpolating by a simplified σ0 model. A significant improvement of the one-group cross-section accuracy was demonstrated.

Motor learning of novel dynamics is not represented in a single global coordinate system: evaluation of mixed coordinate representations and local learning.

Successful motor performance requires the ability to adapt motor commands to task dynamics. A central question in movement neuroscience is how these dynamics are represented. Although it is widely assumed that dynamics (e.g., force fields) are represented in intrinsic, joint-based coordinates (Shadmehr R, Mussa-Ivaldi FA. J Neurosci 14: 3208-3224, 1994), recent evidence has questioned this proposal. Here we reexamine the representation of dynamics in two experiments. By testing generalization following changes in shoulder, elbow, or wrist configurations, the first experiment tested for extrinsic, intrinsic, or object-centered representations. No single coordinate frame accounted for the pattern of generalization. Rather, generalization patterns were better accounted for by a mixture of representations or by models that assumed local learning and graded, decaying generalization. A second experiment, in which we replicated the design of an influential study that had suggested encoding in intrinsic coordinates (Shadmehr and Mussa-Ivaldi 1994), yielded similar results. That is, we could not find evidence that dynamics are represented in a single coordinate system. Taken together, our experiments suggest that internal models do not employ a single coordinate system when generalizing and may well be represented as a mixture of coordinate systems, as a single system with local learning, or both.

Flexible representations of dynamics are used in object manipulation.

To manipulate an object skillfully, the brain must learn its dynamics, specifying the mapping between applied force and motion. A fundamental issue in sensorimotor control is whether such dynamics are represented in an extrinsic frame of reference tied to the object or an intrinsic frame of reference linked to the arm. Although previous studies have suggested that objects are represented in arm-centered coordinates [1-6], all of these studies have used objects with unusual and complex dynamics. Thus, it is not known how objects with natural dynamics are represented. Here we show that objects with simple (or familiar) dynamics and those with complex (or unfamiliar) dynamics are represented in object- and arm-centered coordinates, respectively. We also show that objects with simple dynamics are represented with an intermediate coordinate frame when vision of the object is removed. These results indicate that object dynamics can be flexibly represented in different coordinate frames by the brain. We suggest that with experience, the representation of the dynamics of a manipulated object may shift from a coordinate frame tied to the arm toward one that is linked to the object. The additional complexity required to represent dynamics in object-centered coordinates would be economical for familiar objects because such a representation allows object use regardless of the orientation of the object in hand.

Kinetics of the chemical looping oxidation of H2 by a co-precipitated mixture of CuO and Al2O3

Chemical-looping combustion (CLC) has the inherent property of separating CO2 from flue gases. Instead of air, it uses an oxygen-carrier, usually in the form of a metal oxide, to provide oxygen for combustion. When used for the combustion of gaseous fuels, such as natural gas, or synthesis gas from the gasification of coal, the technique gives a stream of CO2 which, on an industrial scale, would be sufficiently pure for geological sequestration. An important issue is the form of the metal oxide, since it must retain its reactivity through many cycles of complete reduction and oxidation. Here, we report on the rates of oxidation of one constituent of synthesis gas, H2, by co-precipitated mixtures of CuO+Al2O3 using a laboratory-scale fluidised bed. To minimise the influence of external mass transfer, and also of errors in the measurement of [H2], particles sized to 355-500μm were used at low [H2], with the temperature ranging from 450 to 900°C. Under such conditions, the reaction was slow enough for meaningful measurements of the intrinsic kinetics to be made. The reaction was found to be first order with respect to H2. Above ∼800°C, the reaction of CuO was fast and conformed to the shrinking core mechanism, proceeding via the intermediate, Cu2O, in: 2CuO+H2→Cu2O+H2O, ΔH1073 K0=- 116.8 kJ/mol; Cu2O+H2→2Cu+H2O, ΔH1073 K0-80.9 kJ/mol. After oxidation of the products Cu and Cu2O back to CuO, the kinetics in subsequent cycles of chemical looping oxidation of H2 could be approximated by those in the first. Interestingly, the carrier was found to react at temperatures as low as 300°C. The influence of the number of cycles of reduction and oxidation is explored. Comparisons are drawn with previous work using reduction by CO. Finally, these results indicate that the kinetics of reaction of the oxygen carrier with gasifier synthesis gases is very much faster than rates of gasification of the original fuel. © 2010 The Institution of Chemical Engineers.