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

Geometric quantum computation using fictitious spin- 1/2 subspaces of strongly dipolar coupled nuclear spins

Geometric phases have been used in NMR, to implement controlled phase shift gates for quantum information processing, only in weakly coupled systems in which the individual spins can be identified as qubits. In this work, we implement controlled phase shift gates in strongly coupled systems, by using non-adiabatic geometric phases, obtained by evolving the magnetization of fictitious spin-1/2 subspaces, over a closed loop on the Bloch sphere. The dynamical phase accumulated during the evolution of the subspaces, is refocused by a spin echo pulse sequence and by setting the delay of transition selective pulses such that the evolution under the homonuclear coupling makes a complete $2\pi$ rotation. A detailed theoretical explanation of non-adiabatic geometric phases in NMR is given, by using single transition operators. Controlled phase shift gates, two qubit Deutsch-Jozsa algorithm and parity algorithm in a qubit-qutrit system have been implemented in various strongly dipolar coupled systems obtained by orienting the molecules in liquid crystal media.Comment: 37 pages, 17 figure

Development and application of the GIM code for the Cyber 203 computer

The GIM computer code for fluid dynamics research was developed. Enhancement of the computer code, implicit algorithm development, turbulence model implementation, chemistry model development, interactive input module coding and wing/body flowfield computation are described. The GIM quasi-parabolic code development was completed, and the code used to compute a number of example cases. Turbulence models, algebraic and differential equations, were added to the basic viscous code. An equilibrium reacting chemistry model and implicit finite difference scheme were also added. Development was completed on the interactive module for generating the input data for GIM. Solutions for inviscid hypersonic flow over a wing/body configuration are also presented

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

Urinary Glycosaminoglycans are Selectively Included into Calcium Oxalate Crystals Precipitated from Whole Human Urine

Urinary glycosaminoglycans are selectively included into calcium oxalate (CaOx) crystals precipitated from whole human urine: The presence of glycosaminoglycans (GAGs) in the organic matrix of urinary stones, and their known effects on CaOx crystallization have prompted speculation regarding their role in CaOx urolithiasis. The aim of this study was to examine the involvement of GAGs in the early stages of CaOx crystallization in human urine. Urine samples were collected from healthy men and CaOx crystallization was induced by the addition of a sodium oxalate load. The crystals were harvested and demineralized, and the GAG content of the resulting extract analysed by cellulose acetate electrophoresis. Only one GAG, heparan sulphate (HS) was detected in the organic matrix of the crystals; chondroitin sulphate (ChS), the most abundant urinary GAG, was conspicuously absent. Further experiments, in which varying amounts of HS and ChS were added to ultrafiltered (10,000 Da) urine prior to induction of calcium oxalate crystallization, showed that ChS was included into the crystals only when HS was absent from the urine. It was concluded that the selective inclusion of GAGs into crystals and stones is a function related more to relative binding affinity than to ambient GAG concentration and that HS and ChS compete for specific binding sites on the crystal surface

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

The prevalence of coeliac disease-associated human leukocyte antigens in South African transplant donors and recipients

Background. Coeliac disease (CD) is an autoimmune condition occurring in genetically predisposed individuals exposed to an environmental trigger. The human leukocyte antigen (HLA) haplotypes HLA-DQ2.5 and HLA-DQ8 have the strongest association with CD, and 90 - 95% of CD patients bear these haplotypes. The susceptibility of the South African (SA) population to CD has not been studied previously.Objectives. To describe the genetic propensity of the SA population to CD.Methods. The South African National Blood Service database was used to analyse the prevalence of HLA-DQ2.5 and HLA-DQ8 in potential donors and recipients of organ transplants. Self-reported ethnic group was used to estimate the prevalence among different population groups.Results. The overall prevalence of HLA-DQ2.5 and HLA-DQ8 was 19.8%. The prevalence was lower in black participants (15.9%) than in whites (28.6%). Coloured (22.0%) and Indian (17.4%) participants had an intermediate prevalence. There was no significant difference between potential transplant donors and recipients.Conclusions. The prevalence of HLA-DQ2.5 and HLA-DQ8 differed among SA study participants of different ethnicities. However, the notion that CD does not occur in black South Africans owing to lack of a genetic predisposition is incorrect

Nominal model predictive control

5 p., to appear in Encyclopedia of Systems and Control, Tariq Samad, John Baillieul (eds.)International audienceModel Predictive Control is a controller design method which synthesizes a sampled data feedback controller from the iterative solution of open loop optimal control problems.We describe the basic functionality of MPC controllers, their properties regarding feasibility, stability and performance and the assumptions needed in order to rigorously ensure these properties in a nominal setting

Multi-walled carbon nanotube sensor coupled with a pre- concentrator nanoporous layer for the detection of benzene at low temperature

International audienceThis work reports the development and study of a resistive gas sensor for benzene detection, based on multi-walled carbon nanotubes (MWCNTs). The MWCNTs were covered with a nanoporous SiO$_2$ layer whose function is to concentrate the pollutant in order to enhance the sensor performances. In this paper, we will describe the preparation of the sensor and highlight the beneficial effects of both the pre-concentration layer and the operating temperature. MWCNT/SiO$_2$-based sensors operating at 125°C are able to detect 50 ppb of benzene in air. Further developments are in progress in order to improve this detection limit