When the path is never shortest: a reality check on shortest path biocomputation

Shortest path problems are a touchstone for evaluating the computing performance and functional range of novel computing substrates. Much has been published in recent years regarding the use of biocomputers to solve minimal path problems such as route optimisation and labyrinth navigation, but their outputs are typically difficult to reproduce and somewhat abstract in nature, suggesting that both experimental design and analysis in the field require standardising. This chapter details laboratory experimental data which probe the path finding process in two single-celled protistic model organisms, Physarum polycephalum and Paramecium caudatum, comprising a shortest path problem and labyrinth navigation, respectively. The results presented illustrate several of the key difficulties that are encountered in categorising biological behaviours in the language of computing, including biological variability, non-halting operations and adverse reactions to experimental stimuli. It is concluded that neither organism examined are able to efficiently or reproducibly solve shortest path problems in the specific experimental conditions that were tested. Data presented are contextualised with biological theory and design principles for maximising the usefulness of experimental biocomputer prototypes.Comment: To appear in: Adamatzky, A (Ed.) Shortest path solvers. From software to wetware. Springer, 201

A comparison of GC-FID and PTR-MS toluene measurements in ambient air under conditions of enhanced monoterpene loading

Toluene was measured using both a gas chromatographic system (GC), with a flame ionization detector (FID), and a proton transfer reaction-mass spectrometer (PTR-MS) at the AIRMAP atmospheric monitoring station Thompson Farm (THF) in rural Durham, NH during the summer of 2004. Simultaneous measurements of monoterpenes, including alpha- and beta-pinene, camphene, Delta(3)-carene, and d-limonene, by GC-FID demonstrated large enhancements in monoterpene mixing ratios relative to toluene, with median and maximum enhancement ratios of similar to 2 and similar to 30, respectively. A detailed comparison between the GC-FID and PTR-MS toluene measurements was conducted to test the specificity of PTR-MS for atmospheric toluene measurements under conditions often dominated by biogenic emissions. We derived quantitative estimates of potential interferences in the PTR-MS toluene measurements related to sampling and analysis of monoterpenes, including fragmentation of the monoterpenes and some of their primary carbonyl oxidation products via reactions with H(3)O(+), O(2)(+) and NO(+) in the PTR-MS drift tube. The PTR-MS and GC-FID toluene measurements were in good quantitative agreement and the two systems tracked one another well from the instrumental limits of detection to maximum mixing ratios of similar to 0.5 ppbv. A correlation plot of the PTR-MS versus GC-FID toluene measurements was described by the least squares regression equation y=(1.13 +/- 0.02)x-(0.008 +/- 0.003) ppbv, suggesting a small similar to 13% positive bias in the PTR-MS measurements. The bias corresponded with a similar to 0.055 ppbv difference at the highest measured toluene level. The two systems agreed quantitatively within the combined 1 sigma measurement precisions for 60% of the measurements. Discrepancies in the measured mixing ratios were not well correlated with enhancements in the monoterpenes. Better quantitative agreement between the two systems was obtained by correcting the PTR-MS measurements for contributions from monoterpene fragmentation in the PTR-MS drift tube; however, the improvement was minor (\u3c10%). Interferences in the PTRMS measurements from fragmentation of the monoterpene oxidation products pinonaldehyde, caronaldehyde and alpha-pinene oxide were also likely negligible. A relatively large and variable toluene background in the PTR-MS instrument likely drove the measurement bias; however, the precise contribution was difficult to accurately quantify and thus was not corrected for in this analysis. The results from THF suggest that toluene can be reliably quantified by PTR-MS using our operating conditions (drift tube pressure, temperature and voltage of 2.0 mbar, 45 degrees C and 600V, respectively) under the ambient compositions probed. This work extends the range of field conditions under which PTR-MS validation studies have been conducted

Effect of anisotropy and destructuration on behavior of Haarajoki test embankment

This paper investigates the influence of anisotropy and destructuration on the behavior of Haarajoki test embankment, which was built by the Finnish National Road Administration as a noise barrier in 1997 on a soft clay deposit. Half of the embankment is constructed on an area improved with prefabricated vertical drains, while the other half is constructed on the natural deposit without any ground improvement. The construction and consolidation of the embankment is analyzed with the finite-element method using three different constitutive models to represent the soft clay. Two recently proposed constitutive models, namely S-CLAY1 which accounts for initial and plastic strain induced anisotropy, and its extension, called S-CLAY1S which accounts, additionally, for interparticle bonding and degradation of bonds, were used in the analysis. For comparison, the problem is also analyzed with the isotropic modified cam clay model. The results of the numerical analyses are compared with the field measurements. The simulations reveal the influence that anisotropy and destructuration have on the behavior of an embankment on soft clay

The Impact of Phase Equilibrium Cloud Models on GCM Simulations of GJ~1214b

We investigate the impact of clouds on the atmosphere of GJ~1214b using the radiatively-coupled, phase-equilibrium cloud model {\sc EddySed} coupled to the {\sc Unified Model} general circulation model. We find that, consistent with previous investigations, high metallicity ($100\times$ solar) and clouds with large vertical extents (a sedimentation factor of $f_\mathrm{sed} = 0.1$) are required to best match the observations, although metallicities even higher than those investigated here may be required to improve agreement further. We additionally find that in our case which best matches the observations ($f_\mathrm{sed}=0.1$), the velocity structures change relative to the clear sky case with the formation of a superrotating jet being suppressed, although further investigation is required to understand the cause of the suppression. The increase in cloud extent with $f_\mathrm{sed}$ results in a cooler planet due to a higher albedo, causing the atmosphere to contract. This also results in a reduced day-night contrast seen in the phase curves, although the introduction of cloud still results in a reduction of the phase offset. We additionally investigate the impact the the {\sc Unified Model}'s pseudo-spherical irradiation scheme on the calculation of heating rates, finding that the introduction of nightside shortwave heating results in slower mid-latitude jets compared to the plane parallel irradiation scheme used in previous works. We also consider the impact of a gamma distribution, as opposed to a log-normal distribution, for the distribution of cloud particle radii and find the impact to be relatively minor.Comment: Accepted to MNRA

Performance of Sensitivity based NMPC Updates in Automotive Applications

In this work we consider a half car model which is subject to unknown but measurable disturbances. To control this system, we impose a combination of model predictive control without stabilizing terminal constraints or cost to generate a nominal solution and sensitivity updates to handle the disturbances. For this approach, stability of the resulting closed loop can be guaranteed using a relaxed Lyapunov argument on the nominal system and Lipschitz conditions on the open loop change of the optimal value function and the stage costs. For the considered example, the proposed approach is realtime applicable and corresponding results show significant performance improvements of the updated solution with respect to comfort and handling properties.Comment: 6 pages, 2 figure

A gas chromatographic instrument for measurement of hydrogen cyanide in the lower atmosphere

A gas-chromatographic (GC) instrument was developed for measuring hydrogen cyanide (HCN) in the lower atmosphere. The main features of the instrument are (1) a cryogen-free cooler for sample dehumidification and enrichment, (2) a porous polymer PLOT column for analyte separation, (3) a flame thermionic detector (FTD) for sensitive and selective detection, and (4) a dynamic dilution system for calibration. We deployed the instrument for a ∼4 month period from January–June, 2010 at the AIRMAP atmospheric monitoring station Thompson Farm 2 (THF2) in rural Durham, NH. A subset of measurements made during 3–31 March is presented here with a detailed description of the instrument features and performance characteristics. The temporal resolution of the measurements was ~20 min, with a 75 s sample capture time. The 1σ measurement precision was <10% and the instrument response linearity was excellent on a calibration scale of 0.10–0.75 ppbv (±5%). The estimated method detection limit (MDL) and accuracy were 0.021 ppbv and 15%, respectively. From 3–31 March 2010, ambient HCN mixing ratios ranged from 0.15–1.0 ppbv (±15%), with a mean value of 0.36 ± 0.16 ppbv (1σ). The approximate mean background HCN mixing ratio of 0.20 ± 0.04 ppbv appeared to agree well with tropospheric column measurements reported previously. The GC-FTD HCN measurements were strongly correlated with acetonitrile (CH<sub>3</sub>CN) measured concurrently with a proton transfer-reaction mass spectrometer (PTR-MS), as anticipated given our understanding that the nitriles share a common primary biomass burning source to the global atmosphere. The nitriles were overall only weakly correlated with carbon monoxide (CO), which is reasonable considering the greater diversity of sources for CO. However, strong correlations with CO were observed on several nights under stable atmospheric conditions and suggest regional combustion-based sources for the nitriles. These results demonstrate that the GC-FTD instrument is capable of making long term, in-situ measurements of HCN in the lower atmosphere. To date, similar measurements have not been performed, yet they are critically needed to (1) better evaluate the regional scale distribution of HCN in the atmosphere and (2) discern the influence of biomass burning on surface air composition in remote regions

A Library of Self-Consistent Simulated Exoplanet Atmospheres

We present a publicly available library of model atmospheres with radiative-convective equilibrium Pressure-Temperature ($P$-$T$) profiles fully consistent with equilibrium chemical abundances, and the corresponding emission and transmission spectrum with R$\sim$5000 at 0.2 $\mu$m decreasing to R$\sim$35 at 30 $\mu$m, for 89 hot Jupiter exoplanets, for four re-circulation factors, six metallicities and six C/O ratios. We find the choice of condensation process (local/rainout) alters the $P$-$T$ profile and thereby the spectrum substantially, potentially detectable by JWST. We find H$^-$ opacity can contribute to form a strong temperature inversion in ultra-hot Jupiters for C/O ratios $\geq$ 1 and can make transmission spectra features flat in the optical, alongside altering the entire emission spectra. We highlight how adopting different model choices such as thermal ionisation, opacities, line-wing profiles and the methodology of varying the C/O ratio, effects the $P$-$T$ structure and the spectrum. We show the role of Fe opacity to form primary/secondary inversion in the atmosphere. We use WASP-17b and WASP-121b as test cases to demonstrate the effect of grid parameters across their full range, while highlighting some important findings, concerning the overall atmospheric structure, chemical transition regimes and their observables. Finally, we apply this library to the current transmission and emission spectra observations of WASP-121b, which shows H$_2$O and tentative evidence for VO at the limb, and H$_2$O emission feature indicative of inversion on the dayside, with very low energy redistribution, thereby demonstrating the applicability of library for planning and interpreting observations of transmission and emission spectrum.Comment: 26 pages, 19 figures in the main paper. 13 pages, 6 figures, 3 tables in the supplementary material attached with the main paper here. Accepted for Publication in MNRAS. Full grid of model P-T profiles, chemical abundances, transmission and emission spectra, contribution functions are available here, https://drive.google.com/drive/folders/1zCCe6HICuK2nLgnYJFal7W4lyunjU4J

A Cilia-inspired Closed-loop Sensor-actuator Array

© 2018, Jilin University. Cilia are finger-like cell-surface organelles that are used by certain varieties of aquatic unicellular organisms for motility, sensing and object manipulation. Initiated by internal generators and external mechanical and chemical stimuli, coordinated undulations of cilia lead to the motion of a fluid surrounding the organism. This motion transports micro-particles towards an oral cavity and provides motile force. Inspired by the emergent properties of cilia possessed by the pond organism P. caudatum, we propose a novel smart surface with closed-loop control using sensor-actuators pairings that can manipulate objects. Each vibrating motor actuator is controlled by a localised microcontroller which utilises proximity sensor information to initiate actuation. The circuit boards are designed to be plug-and-play and are infinitely up-scalable and reconfigurable. The smart surface is capable of moving objects at a speed of 7.2 millimetres per second in forward or reverse direction. Further development of this platform will include more anatomically similar biomimetic cilia and control