Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A

Topological frustration in an energetically unfrustrated off-lattice model of the helical protein fragment B of protein A from Staphylococcus aureus was investigated. This Gō-type model exhibited thermodynamic and kinetic signatures of a well-designed two-state folder with concurrent collapse and folding transitions and single exponential kinetics at the transition temperature. Topological frustration is determined in the absence of energetic frustration by the distribution of Fersht φ values. Topologically unfrustrated systems present a unimodal distribution sharply peaked at intermediate φ, whereas highly frustrated systems display a bimodal distribution peaked at low and high φ values. The distribution of φ values in protein A was determined both thermodynamically and kinetically. Both methods yielded a unimodal distribution centered at φ = 0.3 with tails extending to low and high φ values, indicating the presence of a small amount of topological frustration. The contacts with high φ values were located in the turn regions between helices I and II and II and III, intimating that these hairpins are in large part required in the transition state. Our results are in good agreement with all-atom simulations of protein A, as well as lattice simulations of a three- letter code 27-mer (which can be compared with a 60-residue helical protein). The relatively broad unimodal distribution of φ values obtained from the all-atom simulations and that from the minimalist model for the same native fold suggest that the structure of the transition state ensemble is determined mostly by the protein topology and not energetic frustration.

Portable 3D laser-camera calibration system with color fusion for SLAM

Nowadays, the use of RGB-D sensors have focused a lot of research in computer vision and robotics. These kinds of sensors, like Kinect, allow to obtain 3D data together with color information. However, their working range is limited to less than 10 meters, making them useless in some robotics applications, like outdoor mapping. In these environments, 3D lasers, working in ranges of 20-80 meters, are better. But 3D lasers do not usually provide color information. A simple 2D camera can be used to provide color information to the point cloud, but a calibration process between camera and laser must be done. In this paper we present a portable calibration system to calibrate any traditional camera with a 3D laser in order to assign color information to the 3D points obtained. Thus, we can use laser precision and simultaneously make use of color information. Unlike other techniques that make use of a three-dimensional body of known dimensions in the calibration process, this system is highly portable because it makes use of small catadioptrics that can be placed in a simple manner in the environment. We use our calibration system in a 3D mapping system, including Simultaneous Location and Mapping (SLAM), in order to get a 3D colored map which can be used in different tasks. We show that an additional problem arises: 2D cameras information is different when lighting conditions change. So when we merge 3D point clouds from two different views, several points in a given neighborhood could have different color information. A new method for color fusion is presented, obtaining correct colored maps. The system will be tested by applying it to 3D reconstruction.

Portable 3D laser-camera calibration system with color fusion for SLAM

Paper submitted to the 43rd International Symposium on Robotics (ISR2012), Taipei, Taiwan, Aug. 29-31, 2012.

Determination of cyclic and linear siloxanes in wastewater samples by ultrasound-assisted dispersive liquid-liquid microextraction followed by gas chromatography-mass spectrometry

A fast, simple and environmentally friendly ultrasound-assisted dispersive liquid-liquid microextraction (USA-DLLME) procedure has been developed to preconcentrate eight cyclic and linear siloxanes from wastewater samples prior to quantification by gas chromatography-mass spectrometry (GC-MS). A two-stage multivariate optimization approach has been developed employing a Plackett-Burman design for screening and selecting the significant factors involved in the USA-DLLME procedure, which was later optimized by means of a circumscribed central composite design. The optimum conditions were: extractant solvent volume, 13 µL; solvent type, chlorobenzene; sample volume, 13 mL; centrifugation speed, 2300 rpm; centrifugation time, 5 min; and sonication time, 2 min. Under the optimized experimental conditions the method gave levels of repeatability with coefficients of variation between 10 and 24% (n=7). Limits of detection were between 0.002 and 1.4 µg L−1. Calculated calibration curves gave high levels of linearity with correlation coefficient values between 0.991 and 0.9997. Finally, the proposed method was applied for the analysis of wastewater samples. Relative recovery values ranged between 71–116% showing that the matrix had a negligible effect upon extraction. To our knowledge, this is the first time that combines LLME and GC-MS for the analysis of methylsiloxanes in wastewater samples.

Efficient accommodation of local minima in watershed model calibration

The Gauss-Marquardt-Levenberg (GML) method of computer-based parameter estimation, in common with other gradient-based approaches, suffers from the drawback that it may become trapped in local objective function minima, and thus report optimized parameter values that are not, in fact, optimized at all. This can seriously degrade its utility in the calibration of watershed models where local optima abound. Nevertheless, the method also has advantages, chief among these being its model-run efficiency, and its ability to report useful information on parameter sensitivities and covariances as a by-product of its use. It is also easily adapted to maintain this efficiency in the face of potential numerical problems (that adversely affect all parameter estimation methodologies) caused by parameter insensitivity and/or parameter correlation. The present paper presents two algorithmic enhancements to the GML method that retain its strengths, but which overcome its weaknesses in the face of local optima. Using the first of these methods an intelligent search for better parameter sets is conducted in parameter subspaces of decreasing dimensionality when progress of the parameter estimation process is slowed either by numerical instability incurred through problem ill-posedness, or when a local objective function minimum is encountered. The second methodology minimizes the chance of successive GML parameter estimation runs finding the same objective function minimum by starting successive runs at points that are maximally removed from previous parameter trajectories. As well as enhancing the ability of a GML-based method to find the global objective function minimum, the latter technique can also be used to find the locations of many non-global optima (should they exist) in parameter space. This can provide a useful means of inquiring into the well-posedness of a parameter estimation problem, and for detecting the presence of bimodal parameter and predictive probability distributions. The new methodologies are demonstrated by calibrating a Hydrological Simulation Program-FORTRAN (HSPF) model against a time series of daily flows. Comparison with the SCE-UA method in this calibration context demonstrates a high level of comparative model run efficiency for the new method. (c) 2006 Elsevier B.V. All rights reserved.

The cost of uniqueness in groundwater model calibration

Calibration of a groundwater model requires that hydraulic properties be estimated throughout a model domain. This generally constitutes an underdetermined inverse problem, for which a Solution can only be found when some kind of regularization device is included in the inversion process. Inclusion of regularization in the calibration process can be implicit, for example through the use of zones of constant parameter value, or explicit, for example through solution of a constrained minimization problem in which parameters are made to respect preferred values, or preferred relationships, to the degree necessary for a unique solution to be obtained. The cost of uniqueness is this: no matter which regularization methodology is employed, the inevitable consequence of its use is a loss of detail in the calibrated field. This, ill turn, can lead to erroneous predictions made by a model that is ostensibly well calibrated. Information made available as a by-product of the regularized inversion process allows the reasons for this loss of detail to be better understood. In particular, it is easily demonstrated that the estimated value for an hydraulic property at any point within a model domain is, in fact, a weighted average of the true hydraulic property over a much larger area. This averaging process causes loss of resolution in the estimated field. Where hydraulic conductivity is the hydraulic property being estimated, high averaging weights exist in areas that are strategically disposed with respect to measurement wells, while other areas may contribute very little to the estimated hydraulic conductivity at any point within the model domain, this possibly making the detection of hydraulic conductivity anomalies in these latter areas almost impossible. A study of the post-calibration parameter field covariance matrix allows further insights into the loss of system detail incurred through the calibration process to be gained. A comparison of pre- and post-calibration parameter covariance matrices shows that the latter often possess a much smaller spectral bandwidth than the former. It is also demonstrated that, as all inevitable consequence of the fact that a calibrated model cannot replicate every detail of the true system, model-to-measurement residuals can show a high degree of spatial correlation, a fact which must be taken into account when assessing these residuals either qualitatively, or quantitatively in the exploration of model predictive uncertainty. These principles are demonstrated using a synthetic case in which spatial parameter definition is based oil pilot points, and calibration is Implemented using both zones of piecewise constancy and constrained minimization regularization. (C) 2005 Elsevier Ltd. All rights reserved.

Nonmetallic inclusion modification and its effect on the final properties of a linepipe steel

Five linepipe type steels were produced in order to study the effect of calcium and magnesium injection on their final properties. Two of these steels were at the extremes of the sulphide range i.e. 0.003 and 0.017% sulphur with no injection attempted; thereby, providing standards to compare with the injected steels. The oxygen level varied from 21 to 63 p.p.m. The cast ingots were controlled-rolled and isothermally rolled in order to study the deformation characteristics of the residual non-metallic inclusions. The structure and cleanliness of these steels was evaluated metallographically using the light microscope, SEM, and image analysis and the results related to their Charpy toughness and HIC resistance. Increasing sulphur levels decreased final properties of the steel. In the untreated state, with as little as 0.003% sulphur, test orientation was highly influential. Modification of sulphur bearing steels was achieved with low modifying element to sulphur ratios provided that the oxygen content was very low. Injection of calcium into steel caused interaction with oxide and sulphide inclusions which was biased toward oxide reduction relative to sulphur removal. Magnesium again reduced oxides and appeared to be linked with aluminia containing inclusions in the final product. It produced improved toughness values relative to a similar sulphur containing calcium treated steel. The results of this work could be extended to establish the mechanism of inclusion modification with magnesium additions to sulphur bearing steels.

Effect of poor curing conditions and remedies on the durability of steel in concrete

An investigation was undertaken to study the effect of poor curing simulating hot climatic conditions and remedies on the durability of steel in concrete. Three different curing environments were used i.e. (1) Saturated Ca(OH)2 solution at 20°C, (2) Saturated Ca(OH)2 solution at 50°C and (3) Air at 50°C at 30% relative humidity. The third curing condition corresponding to the temperature and relative humidity typical of Middle Eastern Countries. The nature of the hardened cement paste matrix, cured under the above conditions was studied by means of Mercury Intrusion Porosimetry for measuring pore size distribution. The results were represented as total pore volume and initial pore entry diameter. The Scanning Electron Microscope was used to look at morphological changes during hydration, which were compared to the Mercury Intrusion Porosimetry results. X-ray defraction and Differential Thermal Analysis techniques were also employed for looking at any phase transformations. Polymer impregnation was used to reduce the porosity of the hardened cement pastes, especially in the case of the poorly cured samples. Carbonation rates of unimpregnated and impregnated cements were determined. Chloride diffusion studies were also undertaken to establish the effect of polymer impregnation and blending of the cements. Finally the corrosion behaviour of embedded steel bars was determined by the technique of Linear Polarisation. The steel was embedded in both untreated and polymer impregnated hardened cement pastes placed in either a solution containing NaCl or an environmental cabinet which provided carbonation at 40°C and 50% relative humidity.

Performance improvement of asymmetrical filtered 40GB/s RZ-DPSK receiver design-strong filtering considerations

We present a novel differential phase shift keying receiver design under strong optical filtering. The receiver design is based on asymmetrical filtering at the destructive port of the Mach Zehnder Interferometer. The asymmetrical filtered receiver design can significantly increase performance by 2 to 4.7dB in calculated "Q".

Effects of crack length and shape on the fracture toughness of a high strength steel 300m

The results of fracture toughness tests on a high strength steel 300m are presented. These results show (i) that in the presence of through-thickness cracks the toughness remains constant down to (a/W)-ratios as low as 0.01 and failure loads up to 0.85σy, and (ii) that the material is more resistant to crack growth when the cracks are semi-elliptical in shape, giving a toughness value which is almost 25 per cent higher than the through-thickness one. Three independent stress analyses are used to obtain stress intensity values for the semi-elliptical cracks and additional confirmation of the increase in toughness comes from stretch zone measurements.

The analysis of potentiostatic transients applied to the corrosion of steel in concrete

Potentiostatically induced current transients obtained on a range of reinforced concrete specimens were analysed to give estimates of the polarisation resistance and interfacial capacitance. The polarisation resistance was compared with the values obtained using more conventional DC methods of analysis and, while it was consistently lower, it was within the error normally attributed to the polarisation resistance method of corrosion rate determination. The interfacial capacitance values determined increased from 0.44 F m -2 for passive steel (polarisation resistance of 132 Ω m 2) to 26.5 F m -2 for active steel (polarisation resistance of 0.34 Ω m 2). This has a dominant effect on the time required for potentiostatically induced current transients to reach a steady state with a longer time being required by actively corroding steel. By contrast the potential decay time constants describing galvanostatically or coulostatically induced potential transients decrease with an increase in corrosion rate and values less than 25 s for active specimens and greater than 40 s for passive specimens were determined in this work. © 1997 Elsevier Science Ltd.

Design, synthesis and thermal behaviour of a series of well-defined clickable and triggerable sulfonate polymers

In the printing industry, the exploitation of triggerable materials that can have their surface properties altered on application of a post-deposition external stimulus has been crucial for the production of robust layers and patterns. To this end, herein, a series of clickable poly(R-alkyl p-styrene sulfonate) homopolymers, with systematically varied thermally-labile protecting groups, has been synthesised via reversible addition-fragmentation chain transfer (RAFT) polymerisation. The polymer range has been designed to offer varied post-deposition thermal treatment to switch them from hydrophobic to hydrophilic. Suitable RAFT conditions have been identified to produce well-defined homopolymers (Đ, Mw/Mn < 1.11 in all cases) at high monomer conversions (>80% for all but one monomer) with controllable molar mass. Poly(p-styrene sulfonate) with an isobutyl protecting group has been shown to be the most readily thermolysed polymer that remains stable at room temperature, and was thus investigated further by incorporation into a diblock copolymer, P3HT-b-PiBSS, by click chemistry. The strategy for preparation of thermal modifiable block copolymers exploiting R-protected p-styrene sulfonates and azide-alkyne click chemistry presented herein allows the design of new, roll-to-roll processable materials for potential application in the printing industry, particularly organic electronics.

Integrated optimisation of surface roughness and tool performance when face milling 416 SS

Tool life is an important factor to be considered during the optimisation of a machining process since cutting parameters can be adjusted to optimise tool changing, reducing cost and time of production. Also the performance of a tool is directly linked to the generated surface roughness and this is important in cases where there are strict surface quality requirements. The prediction of tool life and the resulting surface roughness in milling operations has attracted considerable research efforts. The research reported herein is focused on defining the influence of milling cutting parameters such as cutting speed, feed rate and axial depth of cut, on three major tool performance parameters namely, tool life, material removal and surface roughness. The research is seeking to define methods that will allow the selection of optimal parameters for best tool performance when face milling 416 stainless steel bars. For this study the Taguchi method was applied in a special design of an orthogonal array that allows studying the entire parameter space with only a number of experiments representing savings in cost and time of experiments. The findings were that the cutting speed has the most influence on tool life and surface roughness and very limited influence on material removal. By last tool life can be judged either from tool life or volume of material removal.

Experimental data of CO2, CO3, Omega calcite saturation, pH values, alpha and epsilon fractionation factors, and Dd18O calctite-water

The oxygen isotopic composition (d18O) of calcium carbonate of planktonic calcifying organisms is a key tool for reconstructing both past seawater temperature and salinity. The calibration of paloeceanographic proxies relies in general on empirical relationships derived from field experiments on extant species. Laboratory experiments have more often than not revealed that variables other than the target parameter influence the proxy signal, which makes proxy calibration a challenging task. Understanding these secondary or "vital" effects is crucial for increasing proxy accuracy. We present data from laboratory experiments showing that oxygen isotope fractionation during calcification in the coccolithophore Calcidiscus leptoporus and the calcareous dinoflagellate Thoracosphaera heimii is dependent on carbonate chemistry of seawater in addition to its dependence on temperature. A similar result has previously been reported for planktonic foraminifera, supporting the idea that the [CO3]2- effect on d18O is universal for unicellular calcifying planktonic organisms. The slopes of the d18O/[CO3]2- relationships range between -0.0243 per mil/(µmol/kg) (calcareous dinoflagellate T. heimii) and the previously published -0.0022 per mil/(µmol/kg) (non-symbiotic planktonic foramifera Orbulina universa), while C. leptoporus has a slope of -0.0048 per mil/(µmol/kg). We present a simple conceptual model, based on the contribution of d18O-enriched [HCO3]- to the [CO3]2- pool in the calcifying vesicle, which can explain the [CO3]2- effect on d18O for the different unicellular calcifiers. This approach provides a new insight into biological fractionation in calcifying organisms. The large range in d18O/[CO3]2- slopes should possibly be explored as a means for paleoreconstruction of surface [CO3]2-, particularly through comparison of the response in ecologically similar planktonic organisms.