Genetic programming‐based approach to elucidate biochemical interaction networks from data

Biochemical systems are characterised by cyclic/reversible reciprocal actions, non‐linear interactions and a mixed relationship structures (linear and non‐linear; static and dynamic). Deciphering the architecture of such systems using measured data to provide quantitative information regarding the nature of relationships that exist between the measured variables is a challenging proposition. Causality detection is one of the methodologies that are applied to elucidate biochemical networks from such data. Autoregressive‐based modelling approach such as granger causality, partial directed coherence, directed transfer function and canonical variate analysis have been applied on different systems for deciphering such interactions, but with limited success. In this study, the authors propose a genetic programming‐based causality detection (GPCD) methodology which blends evolutionary computation‐based procedures along with parameter estimation methods to derive a mathematical model of the system. Application of the GPCD methodology on five data sets that contained the different challenges mentioned above indicated that GPCD performs better than the other methods in uncovering the exact structure with less false positives. On a glycolysis data set, GPCD was able to fill the ‘interaction gaps’ which were missed by other methods.Inspec keywords: autoregressive processes, biochemistry, biology computing, genetic algorithms, parameter estimation, transfer functionsOther keywords: elucidate biochemical interaction networks, biochemical systems, cyclic‐reversible reciprocal actions, nonlinear interactions, autoregressive‐based modelling, granger causality, transfer function, canonical variate analysis, genetic programming‐based causality detection methodology, GPCD methodology, mathematical model, parameter estimation methods     

Effects of tuned mass damper on correlation of wind‐induced responses and combination coefficients of equivalent static wind loads of high‐rise buildings

Tuned mass dampers (TMDs) are employed to control the wind‐induced responses of tall buildings. In the meantime, TMD may have an impact on the correlation of wind‐induced responses and combination coefficients of equivalent static wind loads (ESWLs). First, the mass matrix and stiffness matrix were extracted in this paper in accordance with the structural analysis model of two high‐rise buildings, and on that basis, the wind‐induced vibration responses analysis model with and without TMD was established. Second, the synchronous multipoint wind tunnel test to measure the pressure was performed for two high‐rise buildings, and the time history of wind‐induced vibration responses with and without TMD was studied. Finally, the impact of TMD on the correlation of wind‐induced responses and combination coefficients of ESWLs was discussed. The results of two examples suggest that after the installation of TMD, the increase of ρ_xy was 2.1% to 35.0% and ρ_yz was 2.8% to 45.6% at all wind directions for Building 1, and the increase of ρ_xy was 3.9% to 17.1% and ρ_yz was 6.8% to 38.3% for Building 2. The combination coefficients of ESWLs of two buildings were 3% to 6% larger than that of the original structure. The conclusion of this paper can be referenced by the wind resistant design of high‐rise buildings with TMD.     

Enhancement of field emission characteristics of carbon nanotubes on oxidation

Vertically aligned multi-walled carbon nanotubes (CNTs) were grown on p-type silicon wafer using thermal chemical vapor deposition process and subsequently treated with oxygen plasma for oxidation. It was observed that the electron field emission (EFE) characteristics are enhanced. It showed that the turn-on electric field (E(TOE)) of CNTs decreased from 0.67 (untreated) to 0.26 V/microm (oxygen treated). Raman spectra showed that the numbers of defects are increased, which are generated by oxygen-treatment, and absorbed molecules on the CNTs are responsible for the enhancement of EFE. Scanning electron microscopy and Transmission electron microscopy images were used to identify the quality and physical changes of the nanotube morphology and surfaces; revealing the evidence of enhancement in the field emission properties after oxygen-plasma treatment.     

Carbon nanotube-zirconium dioxide hybrid for defluoridation of water

This study presents the synthesis of zirconia/multi-walled carbon nanotube (ZrO2/MWCNTs) hybrid as a novel sorbent for water defluoridation. The synthesis was facilitated by the high degree of functionalization of MWCNTs using a microwave assisted process. In the final product, nearly 3% of the carbon atoms were attached to ZrO2. The ZrO2/MWCNTs were effective in fluoride removal and mechanistic aspects of the process are presented. The research findings highlight the potential application for the use of MWCNT hybrids in environmental remediation.     

Ab initio synthesis of linearly compensated zoom lenses by evolutionary programming

An approach for ab initio synthesis of the thin lens structure of linearly compensated zoom lenses is reported. This method uses evolutionary programming that explores the available configuration space formed by powers of the individual components, the intercomponent separations, and the relative movement parameters of the moving components. Useful thin lens structures of optically and linearly compensated zoom lens systems are obtained by suitable formulation of the merit function of optimization. This paper reports our investigations on three-component zoom lens structures. Illustrative numerical results are presented.     

A new method for estimation of elastic properties of sintered iron powder compacts from ultrasonic longitudinal velocity

A new methodology has been proposed for estimation of elastic moduli of iron powder compacts solely based on longitudinal ultrasonic velocity. New correlations have been semianalytically derived between the elastic moduli and the longitudinal ultrasonic velocity. The moduli estimated on the basis of the suggested methodology agreed reasonably well with data reported for iron powder compacts in the literature. The proposed method can be a potent tool for quick and accurate, nondestructive estimation of elastic properties for porous materials through ultrasonic measurements.     

Statistical adaptive sensing by detectors with spectrally overlapping bands

It has recently been reported that by using a spectral-tuning algorithm, the photocurrents of multiple detectors with spectrally overlapping responsivities can be optimally combined to synthesize, within certain limits, the response of a detector with an arbitrary responsivity. However, it is known that the presence of noise in the photocurrent can degrade the performance of this algorithm significantly, depending on the choice of the responsivity spectrum to be synthesized. We generalize this algorithm to accommodate noise. The results are applied to quantum-dot mid-infrared detectors with bias-dependent spectral responses. Simulation and experiment are used to show the ability of the algorithm to reduce the adverse effect of noise on its spectral-tuning capability.     

Dynamic control of arabinose and xylose utilization in E. coli

The common bacterium Escherichia coli (E. coli) can utilize the pentose sugars arabinose and xylose for growth and energy. When fed both these sugars, the bacterium preferentially utilizes arabinose and only when all the arabinose is exhausted from the media does it start to use xylose. This hierarchical utilization of the two sugars is dictated by two proteins: AraC and XylR. These proteins act as controllers of sugar utilization and dictate the timing and rate of utilization of these sugars. While the biochemical interactions defining individual arabinose and xylose utilization systems are well understood, it is not completely understood how the hierarchical utilization is maintained by the bacterium, and how the regulatory crosstalk between the two systems facilitates this hierarchy. To help answer these questions, in this work, we systematically experimentally characterize the regulatory crosstalk between the two sugar utilization systems. Our work demonstrates extensive interaction between the two sugar systems. Specifically, data from our experiments suggest that the xylose system can regulate arabinose gene expression and consequently, cellular physiology dynamically via promiscuous transport and maybe through cross interactions between regulator and non‐cognate sugar. Put together, we demonstrate that arabinose and xylose utilization networks exhibit an example of distributed control in a biological system. This design likely ensures that the system does not fail under perturbations (mutations). Our results help understand multi‐process control in biological systems and bring to light design criteria for synthetic biology applications.

     

Scaling the SIESTA magnetohydrodynamics equilibrium code

We report the results of a scaling effort that increases both the speed and resolution of the SIESTA magnetohydrodynamics equilibrium code. SIESTA is capable of computing three‐dimensional plasma equilibria with magnetic islands at high spatial resolutions for toroidally confined plasmas. Starting with a small‐scale parallel implementation, we identified scale‐dependent bottlenecks of the code and developed scalable alternatives for each performance‐significant functionality, cumulatively improving both its runtime speed (on the same number of processors) and its scalability (across larger number of processors) by an order of magnitude. The net outcome is an improvement in speed by over 10‐fold, utilizing a few thousand processors, enabling SIESTA to simulate high spatial‐resolution scenarios in under an hour for the first time. Copyright © 2012 John Wiley & Sons, Ltd.