The structure and organization within the membrane of the helices composing the pore-forming domain of Bacillus thuringiensis δ-endotoxin are consistent with an “umbrella-like” structure of the pore

The aim of this study was to elucidate the mechanism of membrane insertion and the structural organization of pores formed by Bacillus thuringiensis δ-endotoxin. We determined the relative affinities for membranes of peptides corresponding to the seven helices that compose the toxin pore-forming domain, their modes of membrane interaction, their structures within membranes, and their orientations relative to the membrane normal. In addition, we used resonance energy transfer measurements of all possible combinatorial pairs of membrane-bound helices to map the network of interactions between helices in their membrane-bound state. The interaction of the helices with the bilayer membrane was also probed by a Monte Carlo simulation protocol to determine lowest-energy orientations. Our results are consistent with a situation in which helices α4 and α5 insert into the membrane as a helical hairpin in an antiparallel manner, while the other helices lie on the membrane surface like the ribs of an umbrella (the “umbrella model”). Our results also support the suggestion that α7 may serve as a binding sensor to initiate the structural rearrangement of the pore-forming domain.

Case study of the effects of atmospheric aerosols and regional haze on agriculture: An opportunity to enhance crop yields in China through emission controls?

The effect of atmospheric aerosols and regional haze from air pollution on the yields of rice and winter wheat grown in China is assessed. The assessment is based on estimates of aerosol optical depths over China, the effect of these optical depths on the solar irradiance reaching the earth’s surface, and the response of rice and winter wheat grown in Nanjing to the change in solar irradiance. Two sets of aerosol optical depths are presented: one based on a coupled, regional climate/air quality model simulation and the other inferred from solar radiation measurements made over a 12-year period at meteorological stations in China. The model-estimated optical depths are significantly smaller than those derived from observations, perhaps because of errors in one or both sets of optical depths or because the data from the meteorological stations has been affected by local pollution. Radiative transfer calculations using the smaller, model-estimated aerosol optical depths indicate that the so-called “direct effect” of regional haze results in an ≈5–30% reduction in the solar irradiance reaching some of China’s most productive agricultural regions. Crop-response model simulations suggest an ≈1:1 relationship between a percentage increase (decrease) in total surface solar irradiance and a percentage increase (decrease) in the yields of rice and wheat. Collectively, these calculations suggest that regional haze in China is currently depressing optimal yields of ≈70% of the crops grown in China by at least 5–30%. Reducing the severity of regional haze in China through air pollution control could potentially result in a significant increase in crop yields and help the nation meet its growing food demands in the coming decades.

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

We describe a procedure for the generation of chemically accurate computer-simulation models to study chemical reactions in the condensed phase. The process involves (i) the use of a coupled semiempirical quantum and classical molecular mechanics method to represent solutes and solvent, respectively; (ii) the optimization of semiempirical quantum mechanics (QM) parameters to produce a computationally efficient and chemically accurate QM model; (iii) the calibration of a quantum/classical microsolvation model using ab initio quantum theory; and (iv) the use of statistical mechanical principles and methods to simulate, on massively parallel computers, the thermodynamic properties of chemical reactions in aqueous solution. The utility of this process is demonstrated by the calculation of the enthalpy of reaction in vacuum and free energy change in aqueous solution for a proton transfer involving methanol, methoxide, imidazole, and imidazolium, which are functional groups involved with proton transfers in many biochemical systems. An optimized semiempirical QM model is produced, which results in the calculation of heats of formation of the above chemical species to within 1.0 kcal/mol (1 kcal = 4.18 kJ) of experimental values. The use of the calibrated QM and microsolvation QM/MM (molecular mechanics) models for the simulation of a proton transfer in aqueous solution gives a calculated free energy that is within 1.0 kcal/mol (12.2 calculated vs. 12.8 experimental) of a value estimated from experimental pKa values of the reacting species.

A grammatical approach to the modeling of an autonomous robot

Virtual Worlds Generator is a grammatical model that is proposed to define virtual worlds. It integrates the diversity of sensors and interaction devices, multimodality and a virtual simulation system. Its grammar allows the definition and abstraction in symbols strings of the scenes of the virtual world, independently of the hardware that is used to represent the world or to interact with it. A case study is presented to explain how to use the proposed model to formalize a robot navigation system with multimodal perception and a hybrid control scheme of the robot. The result is an instance of the model grammar that implements the robotic system and is independent of the sensing devices used for perception and interaction. As a conclusion the Virtual Worlds Generator adds value in the simulation of virtual worlds since the definition can be done formally and independently of the peculiarities of the supporting devices.

Type A aortic dissection model to improve endovascular research and technologies.

OBJECTIVE Type A aortic dissection is a life-threatening disease requiring immediate surgical treatment. With emerging catheter-based technologies, endovascular stent-graft implantation to treat aneurysms and dissections has become a standardized procedure. However, endovascular treatment of the ascending aorta remains challenging. Thus we designed an ascending aortic dissection model to allow simulation of endovascular treatment. METHODS Five formalin-fixed human aortas were prepared. The ascending aorta was opened semicircularly in the middle portion and the medial layer was separated from the intima. The intimal tube was readapted using running monofilament sutures. The preparations were assessed by 128-slice computed tomography. A bare-metal stent was implanted for thoracic endovascular aortic repair in 4 of the aortic dissection models. RESULTS Separation of the intimal and medial layer of the aorta was considered to be sufficient because computed tomography showed a clear image of the dissection membrane in each aorta. The dissection was located 3.9 ± 1.4 cm proximally from the aortic annulus, with a length of 4.6 ± 0.9 cm. Before stent implantation, the mean distance from the intimal flap to the aortic wall was measured as 0.63 ± 0.163 cm in the ascending aorta. After stent implantation, this distance decreased to 0.26 ± 0.12 cm. CONCLUSION This model of aortic dissection of the ascending human aorta was reproducible with a comparable pathological and morphological appearance. The technique and model can be used to evaluate new stent-graft technologies to treat type A dissection and facilitate training for surgeons.

A probabilistic assessment of calcium carbonate export and dissolution in the modern ocean

The marine cycle of calcium carbonate (CaCO3) is an important element of the carbon cycle and co-governs the distribution of carbon and alkalinity within the ocean. However, CaCO3 export fluxes and mechanisms governing CaCO3 dissolution are highly uncertain. We present an observationally constrained, probabilistic assessment of the global and regional CaCO3 budgets. Parameters governing pelagic CaCO3 export fluxes and dissolution rates are sampled using a Monte Carlo scheme to construct a 1000-member ensemble with the Bern3D ocean model. Ensemble results are constrained by comparing simulated and observation-based fields of excess dissolved calcium carbonate (TA*). The minerals calcite and aragonite are modelled explicitly and ocean–sediment fluxes are considered. For local dissolution rates, either a strong or a weak dependency on CaCO3 saturation is assumed. In addition, there is the option to have saturation-independent dissolution above the saturation horizon. The median (and 68 % confidence interval) of the constrained model ensemble for global biogenic CaCO3 export is 0.90 (0.72–1.05) Gt C yr−1, that is within the lower half of previously published estimates (0.4–1.8 Gt C yr−1). The spatial pattern of CaCO3 export is broadly consistent with earlier assessments. Export is large in the Southern Ocean, the tropical Indo–Pacific, the northern Pacific and relatively small in the Atlantic. The constrained results are robust across a range of diapycnal mixing coefficients and, thus, ocean circulation strengths. Modelled ocean circulation and transport timescales for the different set-ups were further evaluated with CFC11 and radiocarbon observations. Parameters and mechanisms governing dissolution are hardly constrained by either the TA* data or the current compilation of CaCO3 flux measurements such that model realisations with and without saturation-dependent dissolution achieve skill. We suggest applying saturation-independent dissolution rates in Earth system models to minimise computational costs.

Stable carbon isotope record and geochemistry of late Miocene-early Pliocene sediments from DSDP Site 90-590 in the Tasman Sea

Biogenic components of sediment accumulated at high rates beneath frontal zones of the Indian and Pacific oceans during the late Miocene and early Pliocene. The delta13C of bulk and foraminiferal carbonate also decreased during this time interval. Although the two observations may be causally linked, and signify a major perturbation in global biogeochemical cycling, no site beneath a frontal zone has independent records of export production and delta13C on multiple carbonate phases across the critical interval of interest. Deep Sea Drilling Project (DSDP) site 590 lies beneath the Tasman Front (TF), an eddy-generating jetstream in the southwest Pacific Ocean. To complement previous delta13C records of planktic and benthic foraminifera at this location, late Neogene records of CaCO3 mass accumulation rate (MAR), Ca/Ti, Ba/Ti, Al/Ti, and of bulk carbonate and foraminiferal delta13C were constructed at site 590. The delta13C records include bulk sediment, bulk sediment fractions (<63 µm and 5-25 µm), and the planktic foraminifera Globigerina bulloides, Globigerinoides sacculifer (with and without sac), and Orbulina universa. Using current time scales, CaCO3 MARs, Ca/Ti, Al/Ti and Ba/Ti ratios are two to three times higher in upper Miocene and lower Pliocene sediment relative to overlying and underlying units. A significant decrease also occurs in all delta13C records. All evidence indicates that enhanced export production - the 'biogenic bloom' - extended to the southwest Pacific Ocean between ca. 9 and 3.8 Ma, and this phenomenon is coupled with changes in delta13C - the 'Chron C3AR carbon shift'. However, CaCO3 MARs peak ca. 5 Ma whereas elemental ratios are highest ca. 6.5 Ma; foraminiferal delta13C starts to decrease ca. 8 Ma whereas bulk carbonate delta13C begins to drop ca. 5.6 Ma. Temporal discrepancies between the records can be explained by changes in the upwelling regime at the TF, perhaps signifying a link between changes in ocean-atmosphere circulation change and widespread primary productivity.

Data mining and simulation: a grey relationship demonstration

Fuzzy data has grown to be an important factor in data mining. Whenever uncertainty exists, simulation can be used as a model. Simulation is very flexible, although it can involve significant levels of computation. This article discusses fuzzy decision-making using the grey related analysis method. Fuzzy models are expected to better reflect decision-making uncertainty, at some cost in accuracy relative to crisp models. Monte Carlo simulation is used to incorporate experimental levels of uncertainty into the data and to measure the impact of fuzzy decision tree models using categorical data. Results are compared with decision tree models based on crisp continuous data.

Using simulation for facility design: a case study

A discrete event simulation model was developed and used to estimate the storage area required for a proposed overseas textile manufacturing facility. It was found that the simulation was able to achieve this because of its ability to both store attribute values and to show queuing levels at an individual product level. It was also found that the process of undertaking the simulation project initiated useful discussions regarding the operation of the facility. Discrete event simulation is shown to be much more than an exercise in quantitative analysis of results and an important task of the simulation project manager is to initiate a debate among decision makers regarding the assumptions of how the system operates.

Dynamic simulation of chemical plant

This thesis describes the design and implementation of a new dynamic simulator called DASP. It is a computer program package written in standard Fortran 77 for the dynamic analysis and simulation of chemical plants. Its main uses include the investigation of a plant's response to disturbances, the determination of the optimal ranges and sensitivities of controller settings and the simulation of the startup and shutdown of chemical plants. The design and structure of the program and a number of features incorporated into it combine to make DASP an effective tool for dynamic simulation. It is an equation-oriented dynamic simulator but the model equations describing the user's problem are generated from in-built model equation library. A combination of the structuring of the model subroutines, the concept of a unit module, and the use of the connection matrix of the problem given by the user have been exploited to achieve this objective. The Executive program has a structure similar to that of a CSSL-type simulator. DASP solves a system of differential equations coupled to nonlinear algebraic equations using an advanced mixed equation solver. The strategy used in formulating the model equations makes it possible to obtain the steady state solution of the problem using the same model equations. DASP can handle state and time events in an efficient way and this includes the modification of the flowsheet. DASP is highly portable and this has been demonstrated by running it on a number of computers with only trivial modifications. The program runs on a microcomputer with 640 kByte of memory. It is a semi-interactive program, with the bulk of all input data given in pre-prepared data files with communication with the user is via an interactive terminal. Using the features in-built in the package, the user can view or modify the values of any input data, variables and parameters in the model, and modify the structure of the flowsheet of the problem during a simulation session. The program has been demonstrated and verified using a number of example problems.

A simulation conceptual modelling procedure for SCM applications

Purpose – The purpose of this paper is to outline a seven-phase simulation conceptual modelling procedure that incorporates existing practice and embeds a process reference model (i.e. SCOR). Design/methodology/approach – An extensive review of the simulation and SCM literature identifies a set of requirements for a domain-specific conceptual modelling procedure. The associated design issues for each requirement are discussed and the utility of SCOR in the process of conceptual modelling is demonstrated using two development cases. Ten key concepts are synthesised and aligned to a general process for conceptual modelling. Further work is outlined to detail, refine and test the procedure with different process reference models in different industrial contexts. Findings - Simulation conceptual modelling is often regarded as the most important yet least understood aspect of a simulation project (Robinson, 2008a). Even today, there has been little research development into guidelines to aid in the creation of a conceptual model. Design issues are discussed for building an ‘effective’ conceptual model and the domain-specific requirements for modelling supply chains are addressed. The ten key concepts are incorporated to aid in describing the supply chain problem (i.e. components and relationships that need to be included in the model), model content (i.e. rules for determining the simplest model boundary and level of detail to implement the model) and model validation. Originality/value – Paper addresses Robinson (2008a) call for research in defining and developing new approaches for conceptual modelling and Manuj et al., (2009) discussion on improving the rigour of simulation studies in SCM. It is expected that more detailed guidelines will yield benefits to both expert (i.e. avert typical modelling failures) and novice modellers (i.e. guided practice; less reliance on hopeful intuition)

Essays in environmental economic valuation and decision making in the presence of an environmental disaster

The first essay developed a respondent model of Bayesian updating for a double-bound dichotomous choice (DB-DC) contingent valuation methodology. I demonstrated by way of data simulations that current DB-DC identifications of true willingness-to-pay (WTP) may often fail given this respondent Bayesian updating context. Further simulations demonstrated that a simple extension of current DB-DC identifications derived explicitly from the Bayesian updating behavioral model can correct for much of the WTP bias. Additional results provided caution to viewing respondents as acting strategically toward the second bid. Finally, an empirical application confirmed the simulation outcomes. The second essay applied a hedonic property value model to a unique water quality (WQ) dataset for a year-round, urban, and coastal housing market in South Florida, and found evidence that various WQ measures affect waterfront housing prices in this setting. However, the results indicated that this relationship is not consistent across any of the six particular WQ variables used, and is furthermore dependent upon the specific descriptive statistic employed to represent the WQ measure in the empirical analysis. These results continue to underscore the need to better understand both the WQ measure and its statistical form homebuyers use in making their purchase decision. The third essay addressed a limitation to existing hurricane evacuation modeling aspects by developing a dynamic model of hurricane evacuation behavior. A household's evacuation decision was framed as an optimal stopping problem where every potential evacuation time period prior to the actual hurricane landfall, the household's optimal choice is to either evacuate, or to wait one more time period for a revised hurricane forecast. A hypothetical two-period model of evacuation and a realistic multi-period model of evacuation that incorporates actual forecast and evacuation cost data for my designated Gulf of Mexico region were developed for the dynamic analysis. Results from the multi-period model were calibrated with existing evacuation timing data from a number of hurricanes. Given the calibrated dynamic framework, a number of policy questions that plausibly affect the timing of household evacuations were analyzed, and a deeper understanding of existing empirical outcomes in regard to the timing of the evacuation decision was achieved.

Essays in Environmental Economic Valuation and Decision Making in the Presence of an Environmental Disaster

The first essay developed a respondent model of Bayesian updating for a double-bound dichotomous choice (DB-DC) contingent valuation methodology. I demonstrated by way of data simulations that current DB-DC identifications of true willingness-to-pay (WTP) may often fail given this respondent Bayesian updating context. Further simulations demonstrated that a simple extension of current DB-DC identifications derived explicitly from the Bayesian updating behavioral model can correct for much of the WTP bias. Additional results provided caution to viewing respondents as acting strategically toward the second bid. Finally, an empirical application confirmed the simulation outcomes. The second essay applied a hedonic property value model to a unique water quality (WQ) dataset for a year-round, urban, and coastal housing market in South Florida, and found evidence that various WQ measures affect waterfront housing prices in this setting. However, the results indicated that this relationship is not consistent across any of the six particular WQ variables used, and is furthermore dependent upon the specific descriptive statistic employed to represent the WQ measure in the empirical analysis. These results continue to underscore the need to better understand both the WQ measure and its statistical form homebuyers use in making their purchase decision. The third essay addressed a limitation to existing hurricane evacuation modeling aspects by developing a dynamic model of hurricane evacuation behavior. A household’s evacuation decision was framed as an optimal stopping problem where every potential evacuation time period prior to the actual hurricane landfall, the household’s optimal choice is to either evacuate, or to wait one more time period for a revised hurricane forecast. A hypothetical two-period model of evacuation and a realistic multi-period model of evacuation that incorporates actual forecast and evacuation cost data for my designated Gulf of Mexico region were developed for the dynamic analysis. Results from the multi-period model were calibrated with existing evacuation timing data from a number of hurricanes. Given the calibrated dynamic framework, a number of policy questions that plausibly affect the timing of household evacuations were analyzed, and a deeper understanding of existing empirical outcomes in regard to the timing of the evacuation decision was achieved.

Numerical Modelling of Eddy Current Probes for CANDU® Fuel Channel Inspection

Multi-frequency Eddy Current (EC) inspection with a transmit-receive probe (two horizontally offset coils) is used to monitor the Pressure Tube (PT) to Calandria Tube (CT) gap of CANDU® fuel channels. Accurate gap measurements are crucial to ensure fitness of service; however, variations in probe liftoff, PT electrical resistivity, and PT wall thickness can generate systematic measurement errors. Validated mathematical models of the EC probe are very useful for data interpretation, and may improve the gap measurement under inspection conditions where these parameters vary. As a first step, exact solutions for the electromagnetic response of a transmit-receive coil pair situated above two parallel plates separated by an air gap were developed. This model was validated against experimental data with flat-plate samples. Finite element method models revealed that this geometrical approximation could not accurately match experimental data with real tubes, so analytical solutions for the probe in a double-walled pipe (the CANDU® fuel channel geometry) were generated using the Second-Order Vector Potential (SOVP) formalism. All electromagnetic coupling coefficients arising from the probe, and the layered conductors were determined and substituted into Kirchhoff’s circuit equations for the calculation of the pickup coil signal. The flat-plate model was used as a basis for an Inverse Algorithm (IA) to simultaneously extract the relevant experimental parameters from EC data. The IA was validated over a large range of second layer plate resistivities (1.7 to 174 µΩ∙cm), plate wall thickness (~1 to 4.9 mm), probe liftoff (~2 mm to 8 mm), and plate-to plate gap (~0 mm to 13 mm). The IA achieved a relative error of less than 6% for the extracted FP resistivity and an accuracy of ±0.1 mm for the LO measurement. The IA was able to achieve a plate gap measurement with an accuracy of less than ±0.7 mm error over a ~2.4 mm to 7.5 mm probe liftoff and ±0.3 mm at nominal liftoff (2.42±0.05 mm), providing confidence in the general validity of the algorithm. This demonstrates the potential of using an analytical model to extract variable parameters that may affect the gap measurement accuracy.

Spatio-temporal characteristics of Agulhas leakage: a model inter-comparison study

Investigating the variability of Agulhas leakage, the volume transport of water from the Indian Ocean to the South Atlantic Ocean, is highly relevant due to its potential contribution to the Atlantic Meridional Overturning Circulation as well as the global circulation of heat and salt and hence global climate. Quantifying Agulhas leakage is challenging due to the non-linear nature of this process; current observations are insufficient to estimate its variability and ocean models all have biases in this region, even at high resolution . An Eulerian threshold integration method is developed to examine the mechanisms of Agulhas leakage variability in six ocean model simulations of varying resolution. This intercomparison, based on the circulation and thermo- haline structure at the Good Hope line, a transect to the south west of the southern tip of Africa, is used to identify features that are robust regardless of the model used and takes into account the thermohaline biases of each model. When determined by a passive tracer method, 60 % of the magnitude of Agulhas leakage is captured and more than 80 % of its temporal fluctuations, suggesting that the method is appropriate for investigating the variability of Agulhas leakage. In all simulations but one, the major driver of variability is associated with mesoscale features passing through the section. High resolution (<1/10 deg.) hindcast models agree on the temporal (2–4 cycles per year) and spatial (300–500 km) scales of these features corresponding to observed Agulhas Rings. Coarser resolution models (<1/4 deg.) reproduce similar time scale of variability of Agulhas leakage in spite of their difficulties in representing the Agulhas rings properties. A coarser resolution climate model (2 deg.) does not resolve the spatio-temporal mechanism of variability of Agulhas leakage. Hence it is expected to underestimate the contribution of Agulhas Current System to climate variability.