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.

Reversible nanoscale switching of polytwin orientation in a ferroelectric thin film induced by a local electric field

The response to a local, tip-induced electric field of ferroelastic domains in thin polycrystalline lead zirconate titanate films with predominantly (110) orientation has been studied using Enhanced Piezoresponse Force Microscopy. Two types of reversible polytwin switching between well-defined orientations have been observed. When a-c domains are switched to other forms of a-c domains, the ferroelastic domain walls rotate in-plane by 109.5°, and when a-c domains are switched to c-c domains (or vice-versa), the walls rotate by 54.75°. © 2013 AIP Publishing 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.

Reversible tuning of the wettability of carbon nanotube arrays: the effect of ultraviolet/ozone and vacuum pyrolysis treatments.

Among diverse types of synthetic materials, arrays of vertically aligned carbon nanotubes have attracted the most attention, mainly because of their exceptional mechanical, electrical, optical, and thermal properties. However, their wetting properties are yet to be understood. In this present study, oxygenated surface functional groups have been identified as a vital factor in controlling the wetting properties of carbon nanotube arrays. The results presented herein indeed show that a combination of ultraviolet/ozone and vacuum pyrolysis treatments can be used to vary the surface concentration of these functional groups such that the carbon nanotube array can be repeatedly switched between hydrophilic and hydrophobic.

Dipole assisted photogated switch in spiropyran grafted polyaniline nanowires

In this work we show dipole-assisted photogated switching by covalent grafting of photoactive molecules to conducting polymers. Photochromic spiropyran molecules were covalently attached to polyaniline (PANI) nanowires via N-alkylation reaction to the quinoic part of PANI. Upon irradiation with ultraviolet light spiropyran transformed to a large dipole containing molecule, merocyanine form. We show that this transformation leads to a substantial (ca. 2 orders of magnitude) increase in conductance of the photochromic PANI nanowires, which were evident by an increase in field-effect mobility and calculated band gap narrowing of the system. Finally, this transformation was found to be fully reversible with no significant photofatigue. © 2011 American Chemical Society.

A reversible infinite HMM using normalised random measures

Copyright 2014 by the author(s). We present a nonparametric prior over reversible Markov chains. We use completely random measures, specifically gamma processes, to construct a countably infinite graph with weighted edges. By enforcing symmetry to make the edges undirected we define a prior over random walks on graphs that results in a reversible Markov chain. The resulting prior over infinite transition matrices is closely related to the hierarchical Dirichlet process but enforces reversibility. A reinforcement scheme has recently been proposed with similar properties, but the de Finetti measure is not well characterised. We take the alternative approach of explicitly constructing the mixing measure, which allows more straightforward and efficient inference at the cost of no longer having a closed form predictive distribution. We use our process to construct a reversible infinite HMM which we apply to two real datasets, one from epigenomics and one ion channel recording.

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.

Spin dynamics in the second subband of a quasi-two-dimensional system studied in a single-barrier heterostructure by time-resolved Kerr rotation

Spin dynamics in the first and second subbands have been examined simultaneously by time resolved Kerr rotation in a single-barrier heterostructure of a 500 nm thick GaAs absorption layer. By scanning the wavelengths of the probe and pump beams towards the short wavelength in the zero magnetic field, the spin coherent time T-2(1)* in the 1st subband E-1 decreases in accordance with the D'yakonov-Perel' (DP) spin decoherence mechanism. Meanwhile, the spin coherence time T-2(2)* in the 2nd subband E-2 remains very low at wavelengths longer than 810 nm, and then is dramatically enhanced afterwards. At 803 nm, T-2(2)* (450 ps) becomes ten times longer than T-2(1)* (50 ps). A new feature has been discovered at the wavelength of 811nm under the bias of -0.3V (807nm under the bias of -0.6V) that the spin coherence times (T-2(1)* and T-2(2)*) and the effective g* factors (vertical bar g*(E-1)vertical bar and vertical bar g*(E-2)vertical bar) all display a sudden change, presumably due to the "resonant" spin exchange coupling between two spin opposite bands. Copyright (C) EPLA, 2008.