Free energy surface reconstruction from umbrella samples using Gaussian process regression II: Multiple collective variables

We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive allows the concurrent use of histograms and free energy gradients and can easily be extended to include further data. In Part I we review the necessary theory and test the method for one collective variable. We demonstrate improved performance with respect to the weighted histogram analysis method and obtain meaningful error bars without any significant additional computation. In Part II we consider the case of multiple collective variables and compare to a reconstruction using least squares fitting of radial basis functions. We find substantial improvements in the regimes of spatially sparse data or short sampling trajectories. A software implementation is made available on www.libatoms.org.

Computations of turbulent lean premixed combustion using conditional moment closure

Conditional Moment Closure (CMC) is a suitable method for predicting scalars such as carbon monoxide with slow chemical time scales in turbulent combustion. Although this method has been successfully applied to non-premixed combustion, its application to lean premixed combustion is rare. In this study the CMC method is used to compute piloted lean premixed combustion in a distributed combustion regime. The conditional scalar dissipation rate of the conditioning scalar, the progress variable, is closed using an algebraic model and turbulence is modelled using the standard k-e{open} model. The conditional mean reaction rate is closed using a first order CMC closure with the GRI-3.0 chemical mechanism to represent the chemical kinetics of methane oxidation. The PDF of the progress variable is obtained using a presumed shape with the Beta function. The computed results are compared with the experimental measurements and earlier computations using the transported PDF approach. The results show reasonable agreement with the experimental measurements and are consistent with the transported PDF computations. When the compounded effects of shear-turbulence and flame are strong, second order closures may be required for the CMC. © 2013 Copyright Taylor and Francis Group, LLC.

Controlled amine functionality in self-assembled monolayers via the hidden amine route: chemical and electronic tunability.

A synthetic strategy for fabricating a dense amine functionalized self-assembled monolayer (SAM) on hydroxylated surfaces is presented. The assembly steps are monitored by X-ray photoelectron spectroscopy, Fourier transform infrared- attenuated total reflection, atomic force microscopy, variable angle spectroscopic ellipsometry, UV-vis surface spectroscopy, contact angle wettability, and contact potential difference measurements. The method applies alkylbromide-trichlorosilane for the fabrication of the SAM followed by surface transformation of the bromine moiety to amine by a two-step procedure: S(N)2 reaction that introduces the hidden amine, phthalimide, followed by the removal of the protecting group and exposing the free amine. The use of phthalimide moiety in the process enabled monitoring the substitution reaction rate on the surface (by absorption spectroscopy) and showed first-order kinetics. The simplicity of the process, nonharsh reagents, and short reaction time allow the use of such SAMs in molecular nanoelectronics applications, where complete control of the used SAM is needed. The different molecular dipole of each step of the process, which is verified by DFT calculations, supports the use of these SAMs as means to tune the electronic properties of semiconductors and for better synergism between SAMs and standard microelectronics processes and devices.

Efficient parametric uncertainty analysis within the hybrid Finite Element/Statistical Energy Analysis method

This paper is concerned with the development of efficient algorithms for propagating parametric uncertainty within the context of the hybrid Finite Element/Statistical Energy Analysis (FE/SEA) approach to the analysis of complex vibro-acoustic systems. This approach models the system as a combination of SEA subsystems and FE components; it is assumed that the FE components have fully deterministic properties, while the SEA subsystems have a high degree of randomness. The method has been recently generalised by allowing the FE components to possess parametric uncertainty, leading to two ensembles of uncertainty: a non-parametric one (SEA subsystems) and a parametric one (FE components). The SEA subsystems ensemble is dealt with analytically, while the effect of the additional FE components ensemble can be dealt with by Monte Carlo Simulations. However, this approach can be computationally intensive when applied to complex engineering systems having many uncertain parameters. Two different strategies are proposed: (i) the combination of the hybrid FE/SEA method with the First Order Reliability Method which allows the probability of the non-parametric ensemble average of a response variable exceeding a barrier to be calculated and (ii) the combination of the hybrid FE/SEA method with Laplace's method which allows the evaluation of the probability of a response variable exceeding a limit value. The proposed approaches are illustrated using two built-up plate systems with uncertain properties and the results are validated against direct integration, Monte Carlo simulations of the FE and of the hybrid FE/SEA models. © 2013 Elsevier Ltd.

Factorial comparison of working memory models.

Three questions have been prominent in the study of visual working memory limitations: (a) What is the nature of mnemonic precision (e.g., quantized or continuous)? (b) How many items are remembered? (c) To what extent do spatial binding errors account for working memory failures? Modeling studies have typically focused on comparing possible answers to a single one of these questions, even though the result of such a comparison might depend on the assumed answers to both others. Here, we consider every possible combination of previously proposed answers to the individual questions. Each model is then a point in a 3-factor model space containing a total of 32 models, of which only 6 have been tested previously. We compare all models on data from 10 delayed-estimation experiments from 6 laboratories (for a total of 164 subjects and 131,452 trials). Consistently across experiments, we find that (a) mnemonic precision is not quantized but continuous and not equal but variable across items and trials; (b) the number of remembered items is likely to be variable across trials, with a mean of 6.4 in the best model (median across subjects); (c) spatial binding errors occur but explain only a small fraction of responses (16.5% at set size 8 in the best model). We find strong evidence against all 6 documented models. Our results demonstrate the value of factorial model comparison in working memory.

Static analysis of Euler-Bernoulli beams with multiple unilateral cracks under combined axial and transverse loads

The paper deals with the static analysis of pre-damaged Euler-Bernoulli beams with any number of unilateral cracks and subjected to tensile or compression forces combined with arbitrary transverse loads. The mathematical representation of cracks with a bilateral behaviour (i.e. always open) via Dirac delta functions is extended by introducing a convenient switching variable, which allows each crack to be open or closed depending on the sign of the axial strain at the crack centre. The proposed model leads to analytical solutions, which depend on four integration constants (to be computed by enforcing the boundary conditions) along with the Boolean switching variables associated with the cracks (whose role is to turn on and off the additional flexibility due to the presence of the cracks). An efficient computational procedure is also presented and numerically validated. For this purpose, the proposed approach is applied to two pre-damaged beams, with different damage and loading conditions, and the results so obtained are compared against those given by a standard finite element code (in which the correct opening of the cracks is pre-assigned), always showing a perfect agreement. © 2013 Elsevier Ltd. All rights reserved.

Exploring the use of sensors to measure behavioral interactions: an experimental evaluation of using hand trajectories.

Humans appear to be sensitive to relative small changes in their surroundings. These changes are often initially perceived as irrelevant, but they can cause significant changes in behavior. However, how exactly people's behavior changes is often hard to quantify. A reliable and valid tool is needed in order to address such a question, ideally measuring an important point of interaction, such as the hand. Wearable-body-sensor systems can be used to obtain valuable, behavioral information. These systems are particularly useful for assessing functional interactions that occur between the endpoints of the upper limbs and our surroundings. A new method is explored that consists of computing hand position using a wearable sensor system and validating it against a gold standard reference measurement (optical tracking device). Initial outcomes related well to the gold standard measurements (r = 0.81) showing an acceptable average root mean square error of 0.09 meters. Subsequently, the use of this approach was further investigated by measuring differences in motor behavior, in response to a changing environment. Three subjects were asked to perform a water pouring task with three slightly different containers. Wavelet analysis was introduced to assess how motor consistency was affected by these small environmental changes. Results showed that the behavioral motor adjustments to a variable environment could be assessed by applying wavelet coherence techniques. Applying these procedures in everyday life, combined with correct research methodologies, can assist in quantifying how environmental changes can cause alterations in our motor behavior.

Predictive control for spacecraft rendezvous in an elliptical orbit using an FPGA

A field programmable gate array (FPGA)-based predictive controller for a spacecraft rendezvous manoeuvre is presented. A linear time varying prediction model is used to accommodate elliptical orbits, and a variable prediction horizon is used to facilitate finite time completion of manoeuvres. The resulting constrained optimisation problems are solved using a primal dual interior point algorithm. The majority of the computational demand is in solving a set of linear equations at each iteration of this algorithm. To accelerate this operation, a custom circuit is implemented, using a combination of Mathworks HDL Coder and Xilinx System Generator for DSP, and used as a peripheral to a MicroBlaze soft core processor. The system is demonstrated in closed loop by linking the FPGA with a simulation of the plant dynamics running in Simulink on a PC, using Ethernet. © 2013 EUCA.

Efficient decoding with generative score-spaces using the expectation semiring

State-of-the-art speech recognisers are usually based on hidden Markov models (HMMs). They model a hidden symbol sequence with a Markov process, with the observations independent given that sequence. These assumptions yield efficient algorithms, but limit the power of the model. An alternative model that allows a wide range of features, including word- and phone-level features, is a log-linear model. To handle, for example, word-level variable-length features, the original feature vectors must be segmented into words. Thus, decoding must find the optimal combination of segmentation of the utterance into words and word sequence. Features must therefore be extracted for each possible segment of audio. For many types of features, this becomes slow. In this paper, long-span features are derived from the likelihoods of word HMMs. Derivatives of the log-likelihoods, which break the Markov assumption, are appended. Previously, decoding with this model took cubic time in the length of the sequence, and longer for higher-order derivatives. This paper shows how to decode in quadratic time. © 2013 IEEE.

Low voltage ride-through of DFIG and brushless DFIG: Similarities and differences

The brushless doubly fed induction generator (BDFIG) has been proposed as a viable alternative in wind turbines to the commonly used doubly fed induction generator (DFIG). The BDFIG retains the benefits of the DFIG, i.e. variable speed operation with a partially rated converter, but without the use of brush gear and slip rings, thereby conferring enhanced reliability. As low voltage ride-through (LVRT) performance of the DFIG-based wind turbine is well understood, this paper aims to analyze LVRT behavior of the BDFIG-based wind turbine in a similar way. In order to achieve this goal, the equivalence between their two-axis model parameters is investigated. The variation of flux linkages, back-EMFs and currents of both types of generator are elaborated during three phase voltage dips. Moreover, the structural differences between the two generators, which lead to different equivalent parameters and hence different LVRT capabilities, are investigated. The analytical results are verified via time-domain simulations for medium size wind turbine generators as well as experimental results of a voltage dip on a prototype 250 kVA BDFIG. © 2014 Elsevier B.V.

Sub-kHz RF electrical linewidth from a 10GHz passively mode-locked quantum-dot laser diode

A packaged 10GHz monolithic two-section quantum-dot mode-locked laser is presented, with record narrow 500Hz RF electrical linewidth for passive mode-locking. Single sideband noise spectra show 147fs integrated timing jitter over the 4MHz-80MHz frequency range. © 2009 Optical Society of America.

Daily timing of emersion and elevated atmospheric CO2 concentration affect photosynthetic performance of the intertidal macroalga Ulva lactuca (Chlorophyta) in sunlight

The lunar day differs in length from the solar day so that times of low tide vary from day to day. Thus, aerial exposure of intertidal seaweeds may be during the day or during the night. We measured photosynthetic CO, assimilation rates of the intertidal green macroalga Ulva lactuca during exposures of varied daily timings during sunny days of summer to establish how photosynthetic performance responds to emersion timing under varied CO2 levels [at ambient (360 ppmv) and 2x ambient (720 ppmv) atmospheric CO2 concentrations]. There was an increase in net photosynthetic rates following some duration of exposure when the initial timing of exposure occurred during early morning (06.30 h) and late afternoon (17.15 h). In contrast, net rates exhibited a sharp decline with exposure duration when the initial timing of exposure occurred at 09.30 h, 15.30 h and especially at noon (12.30 h), implying the occurrence of a severe photoinhibition resulting from mid-day insolation. Doubled atmospheric CO2 concentration significantly enhanced the emersed photosynthetic rates, indicating that the emersed photosynthesis is CO2-limited at ambient CO2 levels. However, increasing CO2 barely stimulates the emersed photosynthetic rates during mid-day insolation.

An improved method for the extraction of low molecular weight organic acids in variable charge soils

Due to specific adsorption to variable charge soils, low molecular weight organic acids (LMWOAs) have not been sufficiently extracted, even if common extractants, such as water and 0.1 M sodium hydroxide (NaOH), were employed. In this work, the method for extracting LMWOAs in soils with 0.1 M NaOH was improved for variable charge soils; e.g. 1.0 M potassium fluoride (KF) with pH 4.0 was applied as an extractant jointed with 0.1 M NaOH based on its stronger ability to change the electrochemical properties of variable charge soils by specific adsorption. With the proposed method, the recoveries of oxalic, tartaric, malic, citric and fumaric acids were increased from 83 4, 93 1, 22 2, 63 +/- 5 and 84 +/- 3% to 98 +/- 2, 100 +/- 2, 85 +/- 2, 90 +/- 2 and 89 +/- 2%, respectively, compared with NaOH alone. Simultaneously, the LMWOAs in Agri-Udic Ferrosol with field moisture were measured with a satisfactory result.

Characterizing the class of local metal sheet thickening processes

The need to create high-value products for specialist applications, and the search for efficient forming routes that obviate the need for some machining steps, is driving Interest In a novel class of forming processes aiming to create locally thickened features within sheet work- pieces. A number of novel forming processes have been proposed to meet this need, but it is as yet unclear which processes will be most effective in creating local thickening of various geometries, and many process configurations have yet to be tried. This paper aims to provide some basic principles for designing and characterising process behaviour. A simplified generic description of sheet thickening processes is provided, with two tools of variable operating on a sheet workpiece in plane strain, with different tool separations and motions parameterised. A comprehensive numerical study of the behaviour of this class of processes is conducted in Abaqus to predict the main characteristics of the material flow in each configuration. The results are used to classify the different basic behaviours that can be achieved by the sheet-bulk thickening processes and to give guidance on future process development, capability and applicability. © 2011 Wiley-VCH Verlag GmbH & Co. KGaA. Weinheim.

Local strain rate and curvature dependences of scalar dissipation rate transport in turbulent premixed flames: A direct numerical simulation analysis

The statistical behaviours of the instantaneous scalar dissipation rate Nc of reaction progress variable c in turbulent premixed flames have been analysed based on three-dimensional direct numerical simulation data of freely propagating statistically planar flame and V-flame configurations with different turbulent Reynolds number Ret. The statistical behaviours of N c and different terms of its transport equation for planar and V-flames are found to be qualitatively similar. The mean contribution of the density-variation term T1 is positive, whereas the molecular dissipation term (-D2) acts as a leading order sink. The mean contribution of the strain rate term T2 is predominantly negative for the cases considered here. The mean reaction rate contribution T3 is positive (negative) towards the unburned (burned) gas side of the flame, whereas the mean contribution of the diffusivity gradient term (D) assumes negative (positive) values towards the unburned (burned) gas side. The local statistical behaviours of Nc, T1, T2, T 3, (-D2), and f(D) have been analysed in terms of their marginal probability density functions (pdfs) and their joint pdfs with local tangential strain rate aT and curvature km. Detailed physical explanations have been provided for the observed behaviour. © 2014 Y. Gao et al.