Vibrational spectroscopic and electrochemical investigations of multi-centered heme proteins in biomimetic membrane architectures

Membrane proteins play a major role in every living cell. They are the key factors in the cell’s metabolism and in other functions, for example in cell-cell interaction, signal transduction, and transport of ions and nutrients. Cytochrome c oxidase (CcO), as one of the membrane proteins of the respiratory chain, plays a significant role in the energy transformation of higher organisms. CcO is a multi centered heme protein, utilizing redox energy to actively transport protons across the mitochondrial membrane. One aim of this dissertation is to investigate single steps in the mechanism of the ion transfer process coupled to electron transfer, which are not fully understood. The protein-tethered bilayer lipid membrane is a general approach to immobilize membrane proteins in an oriented fashion on a planar electrode embedded in a biomimetic membrane. This system enables the combination of electrochemical techniques with surface enhanced resonance Raman (SERRS), surface enhanced reflection absorption infrared (SEIRAS), and surface plasmon spectroscopy to study protein mediated electron and ion transport processes. The orientation of the enzymes within the surface confined architecture can be controlled by specific site-mutations, i.e. the insertion of a poly-histidine tag to different subunits of the enzyme. CcO can, thus, be oriented uniformly with its natural electron pathway entry pointing either towards or away from the electrode surface. The first orientation allows an ultra-fast direct electron transfer(ET) into the protein, not provided by conventional systems, which can be leveraged to study intrinsic charge transfer processes. The second orientation permits to study the interaction with its natural electron donor cytochrome c. Electrochemical and SERR measurements show conclusively that the redox site structure and the activity of the surface confined enzyme are preserved. Therefore, this biomimetic system offers a unique platform to study the kinetics of the ET processes in order to clarify mechanistic properties of the enzyme. Highly sensitive and ultra fast electrochemical techniques allow the separation of ET steps between all four redox centres including the determination of ET rates. Furthermore, proton transfer coupled to ET could be directly measured and discriminated from other ion transfer processes, revealing novel mechanistic information of the proton transfer mechanism of cytochrome c oxidase. In order to study the kinetics of the ET inside the protein, including the catalytic center, time resolved SEIRAS and SERRS measurements were performed to gain more insight into the structural and coordination changes of the heme environment. The electrical behaviour of tethered membrane systems and membrane intrinsic proteins as well as related charge transfer processes were simulated by solving the respective sets of differential equations, utilizing a software package called SPICE. This helps to understand charge transfer processes across membranes and to develop models that can help to elucidate mechanisms of complex enzymatic processes.

Bioconductor: Open software development for computational biology and bioinformatics

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software paradigms and operational strategies that have allowed a small number of researchers to provide a wide variety of innovative, extensible, software solutions in a relatively short time. The use of an object oriented programming paradigm, the adoption and development of a software package system, designing by contract, distributed development and collaboration with other projects are elements of this project's success. Individually, each of these concepts are useful and important but when combined they have provided a strong basis for rapid development and deployment of innovative and flexible research software for scientific computation. A primary objective of this initiative is achievement of total remote reproducibility of novel algorithmic research results.

Resource-allocation capabilities of commercial project management software. An experimental analysis

When project managers determine schedules for resource-constrained projects, they commonly use commercial project management software packages. Which resource-allocation methods are implemented in these packages is proprietary information. The resource-allocation problem is in general computationally difficult to solve to optimality. Hence, the question arises if and how various project management software packages differ in quality with respect to their resource-allocation capabilities. None of the few existing papers on this subject uses a sizeable data set and recent versions of common software packages. We experimentally analyze the resource-allocation capabilities of Acos Plus.1, AdeptTracker Professional, CS Project Professional, Microsoft Office Project 2007, Primavera P6, Sciforma PS8, and Turbo Project Professional. Our analysis is based on 1560 instances of the precedence- and resource-constrained project scheduling problem RCPSP. The experiment shows that using the resource-allocation feature of these packages may lead to a project duration increase of almost 115% above the best known feasible schedule. The increase gets larger with increasing resource scarcity and with increasing number of activities. We investigate the impact of different complexity scenarios and priority rules on the project duration obtained by the software packages. We provide a decision table to support managers in selecting a software package and a priority rule.

False normal Lung Clearance Index in infants with cystic fibrosis due to software algorithms.

BACKGROUND Lung clearance index (LCI), a marker of ventilation inhomogeneity, is elevated early in children with cystic fibrosis (CF). However, in infants with CF, LCI values are found to be normal, although structural lung abnormalities are often detectable. We hypothesized that this discrepancy is due to inadequate algorithms of the available software package. AIM Our aim was to challenge the validity of these software algorithms. METHODS We compared multiple breath washout (MBW) results of current software algorithms (automatic modus) to refined algorithms (manual modus) in 17 asymptomatic infants with CF, and 24 matched healthy term-born infants. The main difference between these two analysis methods lies in the calculation of the molar mass differences that the system uses to define the completion of the measurement. RESULTS In infants with CF the refined manual modus revealed clearly elevated LCI above 9 in 8 out of 35 measurements (23%), all showing LCI values below 8.3 using the automatic modus (paired t-test comparing the means, P < 0.001). Healthy infants showed normal LCI values using both analysis methods (n = 47, paired t-test, P = 0.79). The most relevant reason for false normal LCI values in infants with CF using the automatic modus was the incorrect recognition of the end-of-test too early during the washout. CONCLUSION We recommend the use of the manual modus for the analysis of MBW outcomes in infants in order to obtain more accurate results. This will allow appropriate use of infant lung function results for clinical and scientific purposes.

Thermal food processing optimization: Algorithms and software

The algorithms and graphic user interface software package ?OPT-PROx? are developed to meet food engineering needs related to canned food thermal processing simulation and optimization. The adaptive random search algorithm and its modification coupled with penalty function?s approach, and the finite difference methods with cubic spline approximation are utilized by ?OPT-PROx? package (http://tomakechoice. com/optprox/index.html). The diversity of thermal food processing optimization problems with different objectives and required constraints are solvable by developed software. The geometries supported by the ?OPT-PROx? are the following: (1) cylinder, (2) rectangle, (3) sphere. The mean square error minimization principle is utilized in order to estimate the heat transfer coefficient of food to be heated under optimal condition. The developed user friendly dialogue and used numerical procedures makes the ?OPT-PROx? software useful to food scientists in research and education, as well as to engineers involved in optimization of thermal food processing.

Experiences on dynamic simulation software in chemical engineering education

Commercial process simulators are increasing interest in the chemical engineer education. In this paper, the use of commercial dynamic simulation software, D-SPICE® and K-Spice®, for three different chemical engineering courses is described and discussed. The courses cover the following topics: basic chemical engineering, operability and safety analysis and process control. User experiences from both teachers and students are presented. The benefits of dynamic simulation as an additional teaching tool are discussed and summarized. The experiences confirm that commercial dynamic simulators provide realistic training and can be successfully integrated into undergraduate and graduate teaching, laboratory courses and research. © 2012 The Institution of Chemical Engineers.

A stereo-image analysis JAVA software with links to executable and source code

Scientists planning to use underwater stereoscopic image technologies are often faced with numerous problems during the methodological implementations: commercial equipment is too expensive; the setup or calibration is too complex; or the imaging processing (i.e. measuring objects in the stereo-images) is too complicated to be performed without a time-consuming phase of training and evaluation. The present paper addresses some of these problems and describes a workflow for stereoscopic measurements for marine biologists. It also provides instructions on how to assemble an underwater stereo-photographic system with two digital consumer cameras and gives step-by-step guidelines for setting up the hardware. The second part details a software procedure to correct stereo-image pairs for lens distortions, which is especially important when using cameras with non-calibrated optical units. The final part presents a guide to the process of measuring the lengths (or distances) of objects in stereoscopic image pairs. To reveal the applicability and the restrictions of the described systems and to test the effects of different types of camera (a compact camera and an SLR type), experiments were performed to determine the precision and accuracy of two generic stereo-imaging units: a diver-operated system based on two Olympus Mju 1030SW compact cameras and a cable-connected observatory system based on two Canon 1100D SLR cameras. In the simplest setup without any correction for lens distortion, the low-budget Olympus Mju 1030SW system achieved mean accuracy errors (percentage deviation of a measurement from the object's real size) between 10.2 and -7.6% (overall mean value: -0.6%), depending on the size, orientation and distance of the measured object from the camera. With the single lens reflex (SLR) system, very similar values between 10.1% and -3.4% (overall mean value: -1.2%) were observed. Correction of the lens distortion significantly improved the mean accuracy errors of either system. Even more, system precision (spread of the accuracy) improved significantly in both systems. Neither the use of a wide-angle converter nor multiple reassembly of the system had a significant negative effect on the results. The study shows that underwater stereophotography, independent of the system, has a high potential for robust and non-destructive in situ sampling and can be used without prior specialist training.

Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection

SELECTOR is a software package for studying the evolution of multiallelic genes under balancing or positive selection while simulating complex evolutionary scenarios that integrate demographic growth and migration in a spatially explicit population framework. Parameters can be varied both in space and time to account for geographical, environmental, and cultural heterogeneity. SELECTOR can be used within an approximate Bayesian computation estimation framework. We first describe the principles of SELECTOR and validate the algorithms by comparing its outputs for simple models with theoretical expectations. Then, we show how it can be used to investigate genetic differentiation of loci under balancing selection in interconnected demes with spatially heterogeneous gene flow. We identify situations in which balancing selection reduces genetic differentiation between population groups compared with neutrality and explain conflicting outcomes observed for human leukocyte antigen loci. These results and three previously published applications demonstrate that SELECTOR is efficient and robust for building insight into human settlement history and evolution.

Whole of life cycle cost analysis in bridge rehabilitation

The report presents a methodology for whole of life cycle cost analysis of alternative treatment options for bridge structures, which require rehabilitation. The methodology has been developed after a review of current methods and establishing that a life cycle analysis based on a probabilistic risk approach has many advantages including the essential ability to consider variability of input parameters. The input parameters for the analysis are identified as initial cost, maintenance, monitoring and repair cost, user cost and failure cost. The methodology utilizes the advanced simulation technique of Monte Carlo simulation to combine a number of probability distributions to establish the distribution of whole of life cycle cost. In performing the simulation, the need for a powerful software package, which would work with spreadsheet program, has been identified. After exploring several products on the market, @RISK software has been selected for the simulation. In conclusion, the report presents a typical decision making scenario considering two alternative treatment options.

Power quality enhanced operation and control of a microgrid based custom power park

This paper describes the operation of a microgrid that contains a custom power park (CPP). The park may contain an unbalanced and/or nonlinear load and the microgrid may contain many dis-tributed generators (DGs). One of the DGs in the microgrid is used as a compensator to achieve load compensation. A new method is proposed for current reference generation for load compensation, which takes into account the real and reactive power to be supplied by the DG connected to the compensator. The real and reactive power from the DGs and the utility source is tightly regulated assuming that dedicated communication channels are available. Therefore this scheme is most suitable in cases where the loads in CPP and DGs are physically located close to each other. The proposal is validated through extensive simulation studies using EMTDC/PSCAD software package (version 4.2).

Project diagnostics : assessing the condition of projects and identifying poor health combing forces

In many cases, construction projects do not achieve the objectives that the project participants set for them. If participants could better understand how their project is performing overall, at various stages of its delivery, then the opportunities to achieve project success would almost certainly be greater. This paper documents a method of assessing the status of a project, at a point in its design or construction phase, or after completion. The status is assessed in terms of up to seven (7) key success factors. Any evidence of less than adequate performance in these performance areas is scrutinised to seek out the root causes of why this situation is happening. Using these identified root causes of under performance, general suggestions can then be made as to how to return the project to good health. A software package that assists in assessing the status of the project has been developed. The package is currently being calibrated before commercial release.

LCADesign

LCADesign software package is a real-time environmental impact calculator for commercial property that works directly from the building designer's model. It enables developers, building designers, architects, engineers, builders, manufacturers and government bodies to optimise the eco-impact of a building as the design model evolves instead of waiting months for expert analysis. By integrating with the Building Information Models (BIMs) generated by 3D computer-aided drafting, LCADesign builds eco-efficiency into the design stage and measures the environmental values and risks of materials in commercial buildings

Near real-time prediction of Zenith Tropospheric Delays for position estimation over long-baseline CORS network

This paper presents the preliminary results in establishing a strategy for predicting Zenith Tropospheric Delay (ZTD) and relative ZTD (rZTD) between Continuous Operating Reference Stations (CORS) in near real-time. It is anticipated that the predicted ZTD or rZTD can assist the network-based Real-Time Kinematic (RTK) performance over long inter-station distances, ultimately, enabling a cost effective method of delivering precise positioning services to sparsely populated regional areas, such as Queensland. This research firstly investigates two ZTD solutions: 1) the post-processed IGS ZTD solution and 2) the near Real-Time ZTD solution. The near Real-Time solution is obtained through the GNSS processing software package (Bernese) that has been deployed for this project. The predictability of the near Real-Time Bernese solution is analyzed and compared to the post-processed IGS solution where it acts as the benchmark solution. The predictability analyses were conducted with various prediction time of 15, 30, 45, and 60 minutes to determine the error with respect to timeliness. The predictability of ZTD and relative ZTD is determined (or characterized) by using the previously estimated ZTD as the predicted ZTD of current epoch. This research has shown that both the ZTD and relative ZTD predicted errors are random in nature; the STD grows from a few millimeters to sub-centimeters while the predicted delay interval ranges from 15 to 60 minutes. Additionally, the RZTD predictability shows very little dependency on the length of tested baselines of up to 1000 kilometers. Finally, the comparison of near Real-Time Bernese solution with IGS solution has shown a slight degradation in the prediction accuracy. The less accurate NRT solution has an STD error of 1cm within the delay of 50 minutes. However, some larger errors of up to 10cm are observed.

Engaging students in large classes using Elluminate

The advancement of online teaching environments during the past several years presents an exciting opportunity to extend existing teaching methodologies. The software package known as Elluminate is one example of a virtual classroom, facilitating the provision of real time interaction, collaboration and group meetings. This paper will examine the use of Elluminate in the teaching of large classes. The use of such technology for large classes is of particular interest, as large classes are often, unfairly, associated with a reputation for being impersonal as well as notions of conveyor belt learning. In this paper the potential to extend teaching and learning opportunities using Elluminate, in the context of large classes, will be explored. It will be shown that the use of technology such as Elluminate can assist in providing students with a more flexible means of accessing academic support, as well as allowing for a customised delivery of course content so as to focus learning outcomes.

A parametric study of imaging subsurface objects using ground penetrating radar

A parametric study was carried out to investigate the effects on reconstructed images from a ground penetrating radar (GPR) due to (a) the centre frequency of the GPR excitation pulse, (b) the height of transmitting and receiving antennas above ground level, and (c) the proximity of the buried objects. An integrated software package was developed to streamline the computer simulation based on synthetic data generated by GPRMax.