Evaluating boundary dependent errors in QM/MM simulations.

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful tool for studying chemical reactions, especially in complex biochemical systems. In most works to date, the quantum region is kept fixed throughout the simulation and is defined in an ad hoc way based on chemical intuition and available computational resources. The simulation errors associated with a given choice of the quantum region are, however, rarely assessed in a systematic manner. Here we study the dependence of two relevant quantities on the QM region size: the force error at the center of the QM region and the free energy of a proton transfer reaction. Taking lysozyme as our model system, we find that in an apolar region the average force error rapidly decreases with increasing QM region size. In contrast, the average force error at the polar active site is considerably higher, exhibits large oscillations and decreases more slowly, and may not fall below acceptable limits even for a quantum region radius of 9.0 A. Although computation of free energies could only be afforded until 6.0 A, results were found to change considerably within these limits. These errors demonstrate that the results of QM/MM calculations are heavily affected by the definition of the QM region (not only its size), and a convergence test is proposed to be a part of setting up QM/MM simulations.

Application of a laminar flamelet model to confined explosion hazards

The majority of computational studies of confined explosion hazards apply simple and inaccurate combustion models, requiring ad hoc corrections to obtain realistic flame shapes and often predicting an order of magnitude error in the overpressures. This work describes the application of a laminar flamelet model to a series of two-dimensional test cases. The model is computationally efficient applying an algebraic expression to calculate the flame surface area, an empirical correlation for the laminar flame speed and a novel unstructured, solution adaptive numerical grid system which allows important features of the solution to be resolved close to the flame. Accurate flame shapes are predicted, the correct burning rate is predicted near the walls, and an improvement in the predicted overpressures is obtained. However, in these fully turbulent calculations the overpressures are still too high and the flame arrival times too low, indicating the need for a model for the early laminar burning phase. Due to the computational expense, it is unrealistic to model a laminar flame in the complex geometries involved and therefore a pragmatic approach is employed which constrains the flame to propagate at the laminar flame speed. Transition to turbulent burning occurs at a specified turbulent Reynolds number. With the laminar phase model included, the predicted flame arrival times increase significantly, but are still too low. However, this has no significant effect on the overpressures, which are predicted accurately for a baffled channel test case where rapid transition occurs once the flame reaches the first pair of baffles. In a channel with obstacles on the centreline, transition is more gradual and the accuracy of the predicted overpressures is reduced. However, although the accuracy is still less than desirable in some cases, it is much better than the order of magnitude error previously expected.

An analysis of the cooperative mechano-sensitive feedback between intracellular signaling, focal adhesion development, and stress fiber contractility

Cells communicate with their external environment via focal adhesions and generate activation signals that in turn trigger the activity of the intracellular contractile machinery. These signals can be triggered by mechanical loading that gives rise to a cooperative feedback loop among signaling, focal adhesion formation, and cytoskeletal contractility, which in turn equilibrates with the applied mechanical loads. We devise a signaling model that couples stress fiber contractility and mechano-sensitive focal adhesion models to complete this above mentioned feedback loop. The signaling model is based on a biochemical pathway where IP3 molecules are generated when focal adhesions grow. These IP3 molecules diffuse through the cytosol leading to the opening of ion channels that disgorge Ca2+ from the endoplasmic reticulum leading to the activation of the actin/myosin contractile machinery. A simple numerical example is presented where a one-dimensional cell adhered to a rigid substrate is pulled at one end, and the evolution of the stress fiber activation signal, stress fiber concentrations, and focal adhesion distributions are investigated. We demonstrate that while it is sufficient to approximate the activation signal as spatially uniform due to the rapid diffusion of the IP3 through the cytosol, the level of the activation signal is sensitive to the rate of application of the mechanical loads. This suggests that ad hoc signaling models may not be able to capture the mechanical response of cells to a wide range of mechanical loading events. © 2011 American Society of Mechanical Engineers.

Decision tree-based context clustering based on cross validation and hierarchical priors

The standard, ad-hoc stopping criteria used in decision tree-based context clustering are known to be sub-optimal and require parameters to be tuned. This paper proposes a new approach for decision tree-based context clustering based on cross validation and hierarchical priors. Combination of cross validation and hierarchical priors within decision tree-based context clustering offers better model selection and more robust parameter estimation than conventional approaches, with no tuning parameters. Experimental results on HMM-based speech synthesis show that the proposed approach achieved significant improvements in naturalness of synthesized speech over the conventional approaches. © 2011 IEEE.

A condition monitoring platform using COTS wireless sensor networks - Lessons and experience

Developments in Micro-Electro-Mechanical Systems (MEMS), wireless communication systems and ad-hoc networking have created new dimensions to improve asset management not only during the operational phase but throughout an asset's lifecycle based on using improved quality of information obtained with respect to two key aspects of an asset: its location and condition. In this paper, we present our experience as well as lessons learnt from building a prototype condition monitoring platform to demonstrate and to evaluate the use of COTS wireless sensor networks to develop a prototype condition monitoring platform with the aim of improving asset management by providing accurate and real-time information. © 2010 IEEE.

Prices need no preferences: social trends determine decisions in experimental markets for pain relief.

OBJECTIVE: A standard view in health economics is that, although there is no market that determines the "prices" for health states, people can nonetheless associate health states with monetary values (or other scales, such as quality adjusted life year [QALYs] and disability adjusted life year [DALYs]). Such valuations can be used to shape health policy, and a major research challenge is to elicit such values from people; creating experimental "markets" for health states is a theoretically attractive way to address this. We explore the possibility that this framework may be fundamentally flawed-because there may not be any stable values to be revealed. Instead, perhaps people construct ad hoc values, influenced by contextual factors, such as the observed decisions of others. METHOD: The participants bid to buy relief from equally painful electrical shocks to the leg and arm in an experimental health market based on an interactive second-price auction. Thirty subjects were randomly assigned to two experimental conditions where the bids by "others" were manipulated to follow increasing or decreasing price trends for one, but not the other, pain. After the auction, a preference test asked the participants to choose which pain they prefer to experience for a longer duration. RESULTS: Players remained indifferent between the two pain-types throughout the auction. However, their bids were differentially attracted toward what others bid for each pain, with overbidding during decreasing prices and underbidding during increasing prices. CONCLUSION: Health preferences are dissociated from market prices, which are strongly referenced to others' choices. This suggests that the price of health care in a free-market has the capacity to become critically detached from people's underlying preferences.

Antiwindup design for induction motor control in the field weakening domain

Operation of induction machines in the high-speed and/or high-torque range requires field-weakening to comply with voltage and current physical limitations. This paper presents an anti-windup approach to this problem: rather than developing an ad-hoc field weakening strategy in the high-speed region, we equip an unconstrained vector-control design with an anti-windup module that automatically adjusts the current and flux set-points so that voltage and current constraints are satisfied at every operating point. The anti-windup module includes a feedforward modification of the set point aimed at maximizing the available torque in steady-state and a feedback modification of the controller based on an internal model-based antiwindup scheme. This paper includes a complete stability analysis of the proposed solution and presents encouraging experimental results on an industrial drive. © 2012 IEEE.

Assessing boost-assist options for turbocharged engines using 1-D engine simulation and model predictive control

Delivering acceptable low end torque and good transient response is a significant challenge for all turbocharged engines. As downsized gasoline engines and Diesel engines make up a larger and larger proportion of the light-duty engines entering the market, the issue takes on greater significance. Several schemes have been proposed to improve torque response in highly boosted engines, including the use of electrical assist turbochargers and compressed air assist. In this paper we examine these methods with respect to their effectiveness in improving transient response and their relative performance along with some of the practical considerations for real world application. Results shown in this paper are from 1-D simulations using the Ricardo WAVE software package. The simulation model is based on a production light-duty Diesel engine modified to allow the introduction of compressed air at various points in the air-path as well as direct torque application to the turbocharger shaft (such as might be available from an electrical assist turbocharger). Whilst the 1-D simulation software provides a suitable environment for investigating the various boost assistance options, the overall air path performance also depends upon the control system. The introduction of boost assistance complicates the control in two significant ways: the system may run into constraints (such as compressor surge) that are not encountered in normal operation and the assistance introduces an additional control input. Production engine controllers are usually based on gain-scheduled PID control and extensive calibration. For this study, the non-linear nature of the engine together with the multiple configurations considered and the slower than real-time execution of 1-D models makes such an approach time consuming. Moreover, an ad-hoc approach would leave some doubt as to the fairness of comparisons between the different boost-assist options. Model Predictive Control has been shown to offer a convenient approach to controlling the 1-D simulations in a close to optimal manner for a typical Diesel VGT-EGR air path configuration. We show that the same technique can be applied to all the considered assistance methods with only modest calibration effort required. Copyright © 2012 SAE International.

Model based control for closed loop testing of 1-D engine simulation models

1-D engine simulation models are widely used for the analysis and verification of air-path design concepts and prediction of the resulting engine transient response. The latter often requires closed loop control over the model to ensure operation within physical limits and tracking of reference signals. For this purpose, a particular implementation of Model Predictive Control (MPC) based on a corresponding Mean Value Engine Model (MVEM) is reported here. The MVEM is linearised on-line at each operating point to allow for the formulation of quadratic programming (QP) problems, which are solved as the part of the proposed MPC algorithm. The MPC output is used to control a 1-D engine model. The closed loop performance of such a system is benchmarked against the solution of a related optimal control problem (OCP). As an example this study is focused on the transient response of a light-duty car Diesel engine. For the cases examined the proposed controller implementation gives a more systematic procedure than other ad-hoc approaches that require considerable tuning effort. © 2012 IFAC.

Climb-enabled discrete dislocation plasticity

A small strain two-dimensional discrete dislocation plasticity framework coupled to vacancy diffusion is developed wherein the motion of edge dislocations is by a combination of glide and climb. The dislocations are modelled as line defects in a linear elastic medium and the mechanical boundary value problem is solved by the superposition of the infinite medium elastic fields of the dislocations and a complimentary non-singular solution that enforces the boundary conditions. Similarly, the climbing dislocations are modelled as line sources/sinks of vacancies and the vacancy diffusion boundary value problem is also solved by a superposition of the fields of the line sources/sinks in an infinite medium and a complementary non-singular solution that enforces the boundary conditions. The vacancy concentration field along with the stress field provides the climb rate of the dislocations. Other short-range interactions of the dislocations are incorporated via a set of constitutive rules. We first employ this formulation to investigate the climb of a single edge dislocation in an infinite medium and illustrate the existence of diffusion-limited and sink-limited climb regimes. Next, results are presented for the pure bending and uniaxial tension of single crystals oriented for single slip. These calculations show that plasticity size effects are reduced when dislocation climb is permitted. Finally, we contrast predictions of this coupled framework with an ad hoc model in which dislocation climb is modelled by a drag-type relation based on a quasi steady-state solution. © 2013 Elsevier Ltd. All rights reserved.

Gaussian processes for POMDP-based dialogue manager optimization

A partially observable Markov decision process (POMDP) has been proposed as a dialog model that enables automatic optimization of the dialog policy and provides robustness to speech understanding errors. Various approximations allow such a model to be used for building real-world dialog systems. However, they require a large number of dialogs to train the dialog policy and hence they typically rely on the availability of a user simulator. They also require significant designer effort to hand-craft the policy representation. We investigate the use of Gaussian processes (GPs) in policy modeling to overcome these problems. We show that GP policy optimization can be implemented for a real world POMDP dialog manager, and in particular: 1) we examine different formulations of a GP policy to minimize variability in the learning process; 2) we find that the use of GP increases the learning rate by an order of magnitude thereby allowing learning by direct interaction with human users; and 3) we demonstrate that designer effort can be substantially reduced by basing the policy directly on the full belief space thereby avoiding ad hoc feature space modeling. Overall, the GP approach represents an important step forward towards fully automatic dialog policy optimization in real world systems. © 2013 IEEE.