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.

Effects of turbulent reynolds number on the performance of algebraic flame surface density models for large eddy simulation in the thin reaction zones regime: A direct numerical simulation analysis

A direct numerical simulation (DNS) database of freely propagating statistically planar turbulent premixed flames with a range of different turbulent Reynolds numbers has been used to assess the performance of algebraic flame surface density (FSD) models based on a fractal representation of the flame wrinkling factor. The turbulent Reynolds number Ret has been varied by modifying the Karlovitz number Ka and the Damköhler number Da independently of each other in such a way that the flames remain within the thin reaction zones regime. It has been found that the turbulent Reynolds number and the Karlovitz number both have a significant influence on the fractal dimension, which is found to increase with increasing Ret and Ka before reaching an asymptotic value for large values of Ret and Ka. A parameterisation of the fractal dimension is presented in which the effects of the Reynolds and the Karlovitz numbers are explicitly taken into account. By contrast, the inner cut-off scale normalised by the Zel'dovich flame thickness ηi/δz does not exhibit any significant dependence on Ret for the cases considered here. The performance of several algebraic FSD models has been assessed based on various criteria. Most of the algebraic models show a deterioration in performance with increasing the LES filter width. © 2012 Mohit Katragadda et al.

Reconstruction of arbitrary biochemical reaction networks: A compressive sensing approach

Reconstruction of biochemical reaction networks (BRN) and genetic regulatory networks (GRN) in particular is a central topic in systems biology which raises crucial theoretical challenges in system identification. Nonlinear Ordinary Differential Equations (ODEs) that involve polynomial and rational functions are typically used to model biochemical reaction networks. Such nonlinear models make the problem of determining the connectivity of biochemical networks from time-series experimental data quite difficult. In this paper, we present a network reconstruction algorithm that can deal with ODE model descriptions containing polynomial and rational functions. Rather than identifying the parameters of linear or nonlinear ODEs characterised by pre-defined equation structures, our methodology allows us to determine the nonlinear ODEs structure together with their associated parameters. To solve the network reconstruction problem, we cast it as a compressive sensing (CS) problem and use sparse Bayesian learning (SBL) algorithms as a computationally efficient and robust way to obtain its solution. © 2012 IEEE.

Effect of95 241Am(n, γ) reaction branching ratio on fuel cycle and reactor design characteristics

The growing interest in innovative reactors and advanced fuel cycle designs requires more accurate prediction of various transuranic actinide concentrations during irradiation or following discharge because of their effect on reactivity or spent-fuel emissions, such as gamma and neutron activity and decay heat. In this respect, many of the important actinides originate from the 241Am(n,γ) reaction, which leads to either the ground or the metastable state of 242Am. The branching ratio for this reaction depends on the incident neutron energy and has very large uncertainty in the current evaluated nuclear data files. This study examines the effect of accounting for the energy dependence of the 241Am(n,γ) reaction branching ratio calculated from different evaluated data files for different reactor and fuel types on the reactivity and concentrations of some important actinides. The results of the study confirm that the uncertainty in knowing the 241Am(n,γ) reaction branching ratio has a negligible effect on the characteristics of conventional light water reactor fuel. However, in advanced reactors with large loadings of actinides in general, and 241Am in particular, the branching ratio data calculated from the different data files may lead to significant differences in the prediction of the fuel criticality and isotopic composition. Moreover, it was found that neutron energy spectrum weighting of the branching ratio in each analyzed case is particularly important and may result in up to a factor of 2 difference in the branching ratio value. Currently, most of the neutronic codes have a single branching ratio value in their data libraries, which is sometimes difficult or impossible to update in accordance with the neutron spectrum shape for the analyzed system.

Statistics of reaction progress variable and mixture fraction gradients from DNS of turbulent partially premixed flames

Statistically planar turbulent partially premixed flames for different initial intensities of decaying turbulence have been simulated for global equivalence ratios = 0.7 and 1.0 using three-dimensional, simplified chemistry-based direct numerical simulations (DNS). The simulation parameters are chosen such that the flames represent the thin reaction zones regime combustion. A random bimodal distribution of equivalence ratio is introduced in the unburned gas ahead of the flame to account for the mixture inhomogeneity. The results suggest that the probability density functions (PDFs) of the mixture fraction gradient magnitude |Δξ| (i.e., P(|Δξ|)) can be reasonably approximated using a log-normal distribution. However, this presumed PDF distribution captures only the qualitative nature of the PDF of the reaction progress variable gradient magnitude |Δc| (i.e., P(|Δc|)). It has been found that a bivariate log-normal distribution does not sufficiently capture the quantitative behavior of the joint PDF of |Δξ| and |Δc| (i.e., P(|Δξ|, |Δc|)), and the agreement with the DNS data has been found to be poor in certain regions of the flame brush, particularly toward the burned gas side of the flame brush. Moreover, the variables |Δξ| and |Δc| show appreciable correlation toward the burned gas side of the flame brush. These findings are corroborated further using a DNS data of a lifted jet flame to study the flame geometry dependence of these statistics. © 2013 Copyright Taylor and Francis Group, LLC.

The effect of clearance on shrouded and unshrouded turbines at two levels of reaction

In this paper, the effect of seal clearance on the efficiency of a turbine with a shrouded rotor is compared with the effect of the tip clearance when the same turbine has an unshrouded rotor. The shrouded versus unshrouded comparison was undertaken for two turbine stage designs one having 50% reaction, the other having 24% reaction. Measurements for a range of clearances, including very small clearances, showed three important phenomena. Firstly, as the clearance is reduced, there is a "break-even clearance" at which both the shrouded turbine and the unshrouded turbine have the same efficiency. If the clearance is reduced further, the unshrouded turbine performs better than the shrouded turbine, with the difference at zero clearance termed the "offset loss." This is contrary to the traditional assumption that both shrouded and unshrouded turbines have the same efficiency at zero clearance. The physics of the break-even clearance and the offset loss are discussed. Secondly, the use of a lower reaction had the effect of reducing the tip leakage efficiency penalty for both the shrouded and the unshrouded turbines. In order to understand the effect of reaction on the tip leakage, an analytical model was used and it was found that the tip leakage efficiency penalty should be understood as the dissipated kinetic energy rather than either the tip leakage mass flow rate or the tip leakage loss coefficient. Thirdly, it was also observed that, at a fixed flow coefficient, the fractional change in the output power with clearance was approximately twice the fractional change in efficiency with clearance. This was explained by using an analytical model. © 2014 by ASME.

Direct epitaxial growth of θ-Ni2Si by reaction of a thin Ni(10 at.% Pt) film with Si(1 0 0) substrate

The reaction between an 11 nm Ni(10 at.% Pt) film on a Si substrate has been examined by in situ X-ray diffraction (XRD), atom probe tomography (APT) and transmission electron microscopy (TEM). In situ XRD experiments show the unusual formation of a phase without an XRD peak through consumption of the metal. According to APT, this phase has an Si concentration gradient in accordance with the θ-Ni2Si metastable phase. TEM analysis confirms the direct formation of θ-Ni2Si in epitaxy on Si(1 0 0) with two variants of the epitaxial relationship. © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A detection method for grass carp hemorrhagic virus (GCHV) based on a reverse transcription polymerase chain reaction

A rapid, sensitive and highly specific detection method for grass carp hemorrhagic virus (GCHV) based on a reverse transcription-polymerase chain reaction (RT-PCR) has been developed. Two pairs of PCR primers were synthesized according to the cloned cDNA sequences of the GCHV-861 strain. For each primer combination, only one specific major product was obtained when amplification was performed by using the genomic dsRNA of GCHV-861 strain. The lengths of their expected products were 320 and 223 bp, respectively. No products were obtained when nucleic acids other than GCHV-861 genomic RNA were used as RT-PCR templates. To assess the sensitivity of the method, dilutions of purified GCHV-861 dsRNA total genome (0.01 pg up to 1000 pg) were amplified and quantities of as little as 0.1 pg of purified dsRNA were detectable when the amplification product was analyzed by 1.5% agarose gel electrophoresis. This technique could detect GCHV-861 not only in infected cell culture fluids, but also in infected grass carp Ctenopharyngodon idellus and rare minnow Gobiocypris rarus with or without hemorrhagic symptoms. The results show that the RT-PCR amplification method is useful for the direct detection of GCHV.

Wear resistance of reaction sintered alumina/mullite composites

Alumina and alumina/mullite composites with mullite content of 0.96-8.72 vol.% were subjected to an abrasive wear test under loads of 0.1-2.0 N with a ball-on-disc apparatus. The wear rate and area fraction of pullout f(po) on the worn surfaces were measured. The wear resistances of the alumina/mullite composites were better by a factor of 1-2 than that of pure alumina. The main wear mechanism of alumina is fracture wear, and for alumina/mullite composites, fracture wear and plastic wear mechanisms work together. The influence of mechanical properties on wear resistance was estimated by Evans' method. It was found that the wear rate depends on f(po), and the primary reason for the better wear resistance of alumina/mullite composites is the reduction off, induced by fracture mode transition. (c) 2007 Elsevier B.V. All rights reserved.

Parasitic reaction and its effect on the growth rate of AlN by metalorganic chemical vapor deposition

The Al composition of metalorganic chemical vapor deposition (MOCVD)-grown AlGaN alloy layers is found to be greatly influenced by the parasitic reaction between ammonia (NH3) and trimethylaluminum (TMAI). The growth process of AlN is carefully investigated by monitoring the in situ optical reflection. The abnormal dependencies of growth rate on growth temperature, reactor pressure, and flux of NH3 are observed and can be well explained by the effect of parasitic reaction. The increase of growth rate with increasing flux of TMAI is found to depend on the growth temperature and reactor pressure due to the presence of parasitic effect. A relatively low growth temperature and a reduced reactor pressure are suggested for the effective decrease of parasitic reaction during the MOCVD growth of AlN and probably lead to a more effective incorporation of Al into the AlGaN layers. (c) 2005 Elsevier B.V. All rights reserved.