Multiple proton translocation in biomolecular systems: concerted to stepwise transition in a simple model

In this paper we study a simple model potential energy surface (PES) useful for describing multiple proton translocation mechanisms. The approach presented is relevant to the study of more complex biomolecular systems like enzymes. In this model, at low temperatures, proton tunnelling favours a concerted proton transport mechanism, while at higher temperatures there is a crossover from concerted to stepwise mechanisms; the crossover temperature depends on the energetic features of the PES. We illustrate these ideas by calculating the crossover temperature using energies taken from ab initio calculations on specific systems. Interestingly, typical crossover temperatures lie around room temperature; thus both concerted and stepwise reaction mechanisms should play an important role in biological systems, and one can be easily turned into another by external means such as modifying the temperature or the pH, thus establishing a general mechanism for modulation of the biomolecular function by external effectors.

On the reasons for stepwise changes in the tunnelling current across nanogaps

The role of the crystalline orientation of the STM tip in the generation of metal clusters is studied by atom dynamics simulations. When a (111) facet is facing the surface, the process is accompanied by a perturbation of the surface stronger than that observed for more open tip structures. This implies a technological application: the possibility of orienting a nanocrystallite deposited on a tip according to the changes observed in the force on the tip.

A density functional theory study of stepwise addition reactions in ammonia synthesis on Ru(0001)

To shed light on stepwise addition reactions in ammonia synthesis, density functional theory calculations are carried out to investigate NHx (x = 1-3) formation on Ru(0001). The reactions on a flat surface are first examined. Transition states and reaction barriers are determined. It is found that the reaction barriers for these stepwise addition reactions are rather high. For example, the barrier for NH hydrogenation is calculated to be 1.28 eV, which is comparable with that of N-2 dissociation. One of the stepwise addition reactions, NH + H --> NH2, on a stepped surface is also considered. Interestingly, the reaction barrier is found to be significantly lower than that on the flat surface, but is considerably higher than that of N-2 dissociation on the same stepped surface. In addition, the coverage effect on the reaction energetics is also addressed. (C) 2001 Published by Elsevier Science B.V.

Stepwise addition reactions in ammonia synthesis: A first principles study

Catalytic ammonia synthesis is believed to proceed via dissociation of N-2 and H-2 with subsequent stepwise addition reactions from an adsorbed nitrogen atom to NH3. The first step, N-2 dissociation, has been thoroughly studied. However, little is known about the microscopic details of the stepwise addition reactions. To shed light on these stepwise addition reactions, density functional theory calculations with the generalized gradient approximation are employed to investigate NHx (x=1,3) formation on Ru(0001). Transition states and reaction barriers are determined in each elementary step. It is found that the reaction barriers for stepwise addition reactions are rather high, for example, the barrier for NH hydrogenation is calculated to be 1.28 eV, which is comparable with that of N-2 dissociation. In addition, one of the stepwise addition reactions on a stepped surface is also considered. The reaction barrier is found to be much higher than that of N-2 dissociation on the same stepped surface, which indicates the importance of stepwise addition reactions in ammonia synthesis. (C) 2001 American Institute of Physics.

MSC-clustering and forward stepwise regression for virtual metrology in highly correlated input spaces

Increasingly semiconductor manufacturers are exploring opportunities for virtual metrology (VM) enabled process monitoring and control as a means of reducing non-value added metrology and achieving ever more demanding wafer fabrication tolerances. However, developing robust, reliable and interpretable VM models can be very challenging due to the highly correlated input space often associated with the underpinning data sets. A particularly pertinent example is etch rate prediction of plasma etch processes from multichannel optical emission spectroscopy data. This paper proposes a novel input-clustering based forward stepwise regression methodology for VM model building in such highly correlated input spaces. Max Separation Clustering (MSC) is employed as a pre-processing step to identify a reduced srt of well-conditioned, representative variables that can then be used as inputs to state-of-the-art model building techniques such as Forward Selection Regression (FSR), Ridge regression, LASSO and Forward Selection Ridge Regression (FCRR). The methodology is validated on a benchmark semiconductor plasma etch dataset and the results obtained are compared with those achieved when the state-of-art approaches are applied directly to the data without the MSC pre-processing step. Significant performance improvements are observed when MSC is combined with FSR (13%) and FSRR (8.5%), but not with Ridge Regression (-1%) or LASSO (-32%). The optimal VM results are obtained using the MSC-FSR and MSC-FSRR generated models. © 2012 IEEE.

On Variable Selection of a Nonlinear Non-parametric System with a Limited Data Set: A Stepwise Algorithm

his paper considers a problem of identification for a high dimensional nonlinear non-parametric system when only a limited data set is available. The algorithms are proposed for this purpose which exploit the relationship between the input variables and the output and further the inter-dependence of input variables so that the importance of the input variables can be established. A key to these algorithms is the non-parametric two stage input selection algorithm.

A two-stage algorithm for identification of nonlinear dynamic systems

This paper investigates the two-stage stepwise identification for a class of nonlinear dynamic systems that can be described by linear-in-the-parameters models, and the model has to be built from a very large pool of basis functions or model terms. The main objective is to improve the compactness of the model that is obtained by the forward stepwise methods, while retaining the computational efficiency. The proposed algorithm first generates an initial model using a forward stepwise procedure. The significance of each selected term is then reviewed at the second stage and all insignificant ones are replaced, resulting in an optimised compact model with significantly improved performance. The main contribution of this paper is that these two stages are performed within a well-defined regression context, leading to significantly reduced computational complexity. The efficiency of the algorithm is confirmed by the computational complexity analysis, and its effectiveness is demonstrated by the simulation results.

Decision making in childhood asthma exacerbation – a clinical judgement analysis

Background: Clinical decisions which impact directly on patient safety and quality of care are made during acute asthma attacks by individual doctors on the basis of their knowledge and experience. These include administration of systemic corticosteroids (CS), oral antibiotics, and admission to hospital. Clinical judgement analysis provides a methodology for comparing decisions between practitioners with different training and experience, and improving decision making. Methods: Stepwise linear regression was used to select clinical cues based on visual analogue scale assessments of the propensity of 62 clinicians to prescribe a short course of oral CS (decision 1), a course of antibiotics (decision 2), and/or admit to hospital (decision 3) for 60 â??paperâ?? patients. Results:When compared by specialty, paediatriciansâ?? models for decision 1 were more likely to include as a cue level of alertness (54% v. 16%); for decision 2 presence of crepitations (49% v. 16%), and less likely to include inhaled CS (8% v. 40%), respiratory rate (0% v. 24%), and air entry (70% v. 100%). When compared to other grades, the models derived for decision 3 by consultants/general practitioners were more likely to include wheeze severity as a cue (39% v. 6%). Conclusions: Clinicians differed in their use of individual cues and the number included in their models. Patient safety and quality of care will benefit from clarification of decision making strategies as general learning points during medical training, in the development of guidelines and care pathways, and by clinicians developing self-awareness of their own preferences.

Savory peptides present in Moromi obtained from soy sauce fermentation of yellow soybean

The presence of savory peptides in moromi has been investigated. Moromi was prepared by fermenting yellow soybean using Aspergillus oryzae as the starter at the first step (mold fermentation) and 20% brine solution at the next step (brine fermentation). The moromi was then ultrafiltered stepwise using membranes with MW cut-offs of 10,000, 3,000, and 500 Da, respectively. The fraction with MW <500 Da was chromatographed using Sephadex G-25 SF to yield four fractions, 1-4. Analysis of soluble peptides, NaCl content, alpha-amino nitrogen, amino acid composition, peptide profile using CE coupled with DAD, taste profile and free glutamic acid content, were performed for each fraction. Fraction 2 contained a relatively high total glutamic acid content, but a relatively low free glutamic acid content and had the highest umami taste. This fraction also had more peptides containing non-aromatic amino acids than the other fractions. The peptides present in fraction 2 may play a role, at least in part, in its intense umami taste.

A modular approach to luminescent dinuclear ruthenium(II) and rhenium(I) complexes

A series of dinuclear (bipyridine)tricarbonylrhenium(I) and tris(bipyridine)ruthenium(II) complexes have been isolated and characterised, bridged by a flexible diamido ethylene glycol chain. A new stepwise synthetic pathway has been investigated to heterometallic complexes, with the rhenium(I) complexes exhibiting an unusual configuration and inequivalence of the metal centres potentially arising from a surprising hydrogen-bonding interaction between an Re–CO group and an amide proton in low-polarity solvents. This interaction appears to be broken by competing hydrogen-bonding species such as dihydrogen phosphate. This effect was not observed in the corresponding ruthenium(II) complexes, which showed very little interaction with anions. The photophysical characterisation shows that the inclusion of two ester/amide groups to the rhenium centre effectively quenches the fluorescence at room temperature. The ruthenium(II) complexes have considerably stronger fluorescence than the rhenium species, and are less affected by theinclusion of ester and amide groups to the 2,2'-bipyridine chelating group.

Health status of children with cerebral palsy living in Europe: a multi-centre study

Aim The aim of this report is to describe the health status of 8–12-year-old children with cerebral palsy (CP) of all severities in Europe using the Child Health Questionnaire (CHQ).

Method A total of 818 children with CP from nine centres in defined geographical areas participated. CP type, gross and fine motor function, additional impairments were classified and family data were obtained. The CHQ was used to measure the parent's perception of their child's physical (PHY) and psychosocial (PSY) health.

Results PHY scores were lower than the reference samples with a median of 46. The severity of gross motor function influenced the CHQ scores significantly in the PHY scale with the lowest scores for children with least gross motor function. There were significant differences between the CP types in PHY with the higher scores for children with unilateral spastic and the lowest scores for children with bilateral spastic and dyskinetic CP type. Fine motor function severity significantly affected both the PHY and PSY scales. The severity of intellectual impairment was significantly associated with CHQ scores in most dimensions with higher scores for higher IQ level in PHY and PSY. Children with seizures during the last year had a significantly lower health compared with children without seizures. The results of the multivariate regression analyses (forward stepwise regression) of CHQ scores on CP subtype, gross and fine motor function, cognitive function, additional impairments, seizures, parental education and employment revealed gross motor function, cognitive level and type of school attended were significant prognostic factors.

Conclusion This report is based on the largest sample to date of children with CP. Health status as measured using the CHQ was affected in all children and was highly variable. Gross motor function level correlates with health from the PHY well-being perspective but the PSY and emotional aspects do not appear to follow the same pattern.