XSophe, a computer simulation software suite for the analysis of electron paramagnetic resonance spectra

The XSophe computer simulation software suite consisting of a daemon, the XSophe interface and the computational program Sophe is a state of the art package for the simulation of electron paramagnetic resonance spectra. The Sophe program performs the computer simulation and includes a number of new technologies including; the SOPHE partition and interpolation schemes, a field segmentation algorithm, homotopy, parallelisation and spectral optimisation. The SOPHE partition and interpolation scheme along with a field segmentation algorithm greatly increases the speed of simulations for most systems. Multidimensional homotopy provides an efficient method for accurately tracing energy levels and hence tracing transitions in the presence of energy level anticrossings and looping transitions and allowing computer simulations in frequency space. Recent enhancements to Sophe include the generalised treatment of distributions of orientational parameters, termed the mosaic misorientation linewidth model and a faster more efficient algorithm for the calculation of resonant field positions and transition probabilities. For complex systems the parallelisation enables the simulation of these systems on a parallel computer and the optimisation algorithms in the suite provide the experimentalist with the possibility of finding the spin Hamiltonian parameters in a systematic manner rather than a trial-and-error process. The XSophe software suite has been used to simulate multifrequency EPR spectra (200 MHz to 6 00 GHz) from isolated spin systems (S > ~½) and coupled centres (Si, Sj _> I/2). Griffin, M.; Muys, A.; Noble, C.; Wang, D.; Eldershaw, C.; Gates, K.E.; Burrage, K.; Hanson, G.R."XSophe, a Computer Simulation Software Suite for the Analysis of Electron Paramagnetic Resonance Spectra", 1999, Mol. Phys. Rep., 26, 60-84.

Xsophe, A computer simulation software suite (v 1.1) and its application to the analysis of EPR spectra from the molbydoenzyme dimethylsulfide dehydrogenase

Proceedings of the 44th Rocky Mountain conference on analytical chemistry

Ecological validity in neuropsychological assessment: A case for greater consideration in research with neurologically intact populations

The focus of the discipline of neuropsychology is shifting towards a greater emphasis on understanding the relationship between assessment results and performance of everyday tasks (ecological validity). To date, the literature has highlighted the importance of this concept in the assessment of patients with brain injury or disease (e.g. in rehabilitation and forensic settings). This paper presents the argument that there is another important area in which the ecological validity of neuropsychological assessments should be considered: in clinical outcomes studies using neurologically intact participants. For example, determining the extent to which a medical procedure or intervention affects performance of everyday cognitive tasks can provide useful information that can potentially guide decision-making regarding treatment options. It is argued that tests designed with ecological validity in mind (the verisimilitude approach), as opposed to traditional tests, may be most effective at predicting everyday functioning. Explanations are proposed as to why researchers may be reluctant to use tests with verisimilitude in favor of more traditional measures. (c) 2006 National Academy of Neuropsychology. Published by Elsevier Ltd. All rights reserved.

Simulation of Brugada syndrome using cellular and three-dimensional whole-heart modeling approaches

Brugada syndrome (BS) is a genetic disease identified by an abnormal electrocardiogram ( ECG) ( mainly abnormal ECGs associated with right bundle branch block and ST-elevation in right precordial leads). BS can lead to increased risk of sudden cardiac death. Experimental studies on human ventricular myocardium with BS have been limited due to difficulties in obtaining data. Thus, the use of computer simulation is an important alternative. Most previous BS simulations were based on animal heart cell models. However, due to species differences, the use of human heart cell models, especially a model with three-dimensional whole-heart anatomical structure, is needed. In this study, we developed a model of the human ventricular action potential (AP) based on refining the ten Tusscher et al (2004 Am. J. Physiol. Heart Circ. Physiol. 286 H1573 - 89) model to incorporate newly available experimental data of some major ionic currents of human ventricular myocytes. These modified channels include the L-type calcium current (ICaL), fast sodium current (I-Na), transient outward potassium current (I-to), rapidly and slowly delayed rectifier potassium currents (I-Kr and I-Ks) and inward rectifier potassium current (I-Ki). Transmural heterogeneity of APs for epicardial, endocardial and mid-myocardial (M) cells was simulated by varying the maximum conductance of IKs and Ito. The modified AP models were then used to simulate the effects of BS on cellular AP and body surface potentials using a three-dimensional dynamic heart - torso model. Our main findings are as follows. (1) BS has little effect on the AP of endocardial or mid-myocardial cells, but has a large impact on the AP of epicardial cells. (2) A likely region of BS with abnormal cell AP is near the right ventricular outflow track, and the resulting ST-segment elevation is located in the median precordium area. These simulation results are consistent with experimental findings reported in the literature. The model can reproduce a variety of electrophysiological behaviors and provides a good basis for understanding the genesis of abnormal ECG under the condition of BS disease.

Integrating runtime assertions with dynamic types: Structuring a derivation from an incomputable specification

An inherent incomputability in the specification of a functional language extension that combines assertions with dynamic type checking is isolated in an explicit derivation from mathematical specifications. The combination of types and assertions (into "dynamic assertion-types" - DATs) is a significant issue since, because the two are congruent means for program correctness, benefit arises from their better integration in contrast to the harm resulting from their unnecessary separation. However, projecting the "set membership" view of assertion-checking into dynamic types results in some incomputable combinations. Refinement of the specification of DAT checking into an implementation by rigorous application of mathematical identities becomes feasible through the addition of a "best-approximate" pseudo-equality that isolates the incomputable component of the specification. This formal treatment leads to an improved, more maintainable outcome with further development potential.

Computer simulations of coupled problems in geological and geochemical systems

The finite element method is used to simulate coupled problems, which describe the related physical and chemical processes of ore body formation and mineralization, in geological and geochemical systems. The main purpose of this paper is to illustrate some simulation results for different types of modelling problems in pore-fluid saturated rock masses. The aims of the simulation results presented in this paper are: (1) getting a better understanding of the processes and mechanisms of ore body formation and mineralization in the upper crust of the Earth; (2) demonstrating the usefulness and applicability of the finite element method in dealing with a wide range of coupled problems in geological and geochemical systems; (3) qualitatively establishing a set of showcase problems, against which any numerical method and computer package can be reasonably validated. (C) 2002 Published by Elsevier Science B.V.

Ecosystem process models at multiple scales for mapping tropical forest productivity

Quantifying mass and energy exchanges within tropical forests is essential for understanding their role in the global carbon budget and how they will respond to perturbations in climate. This study reviews ecosystem process models designed to predict the growth and productivity of temperate and tropical forest ecosystems. Temperate forest models were included because of the minimal number of tropical forest models. The review provides a multiscale assessment enabling potential users to select a model suited to the scale and type of information they require in tropical forests. Process models are reviewed in relation to their input and output parameters, minimum spatial and temporal units of operation, maximum spatial extent and time period of application for each organization level of modelling. Organizational levels included leaf-tree, plot-stand, regional and ecosystem levels, with model complexity decreasing as the time-step and spatial extent of model operation increases. All ecosystem models are simplified versions of reality and are typically aspatial. Remotely sensed data sets and derived products may be used to initialize, drive and validate ecosystem process models. At the simplest level, remotely sensed data are used to delimit location, extent and changes over time of vegetation communities. At a more advanced level, remotely sensed data products have been used to estimate key structural and biophysical properties associated with ecosystem processes in tropical and temperate forests. Combining ecological models and image data enables the development of carbon accounting systems that will contribute to understanding greenhouse gas budgets at biome and global scales.

An atomistic simulation of solid state sintering using Monte Carlo methods

This paper presents results on the simulation of the solid state sintering of copper wires using Monte Carlo techniques based on elements of lattice theory and cellular automata. The initial structure is superimposed onto a triangular, two-dimensional lattice, where each lattice site corresponds to either an atom or vacancy. The number of vacancies varies with the simulation temperature, while a cluster of vacancies is a pore. To simulate sintering, lattice sites are picked at random and reoriented in terms of an atomistic model governing mass transport. The probability that an atom has sufficient energy to jump to a vacant lattice site is related to the jump frequency, and hence the diffusion coefficient, while the probability that an atomic jump will be accepted is related to the change in energy of the system as a result of the jump, as determined by the change in the number of nearest neighbours. The jump frequency is also used to relate model time, measured in Monte Carlo Steps, to the actual sintering time. The model incorporates bulk, grain boundary and surface diffusion terms and includes vacancy annihilation on the grain boundaries. The predictions of the model were found to be consistent with experimental data, both in terms of the microstructural evolution and in terms of the sintering time. (C) 2002 Elsevier Science B.V. All rights reserved.

Hormone replacement therapy and everyday memory in mid-aged New Zealand women

While empirical research to date has generally supported positive effects of estrogen on verbal memory performance in women, the literature examining specific effects of Hormone Replacement Therapy (HRT) on cognitive functioning in mid-life women is more equivocal. The Rivermead Behavioural Memory Test-Extended Version (RBMT-E), a measure of everyday memory functioning in adults within an average range of cognitive functioning, was administered to a sample of 104 New Zealand women aged 40 to 60 years who had self-selected to either use or not use HRT (53 HRT users and 51 non-users). Self-report. measures of mood, stress, general health and menopausal symptoms were also administered. These variables, along with age and education level, were used in analyses of group differences on the everyday memory measures. Results showed significant differences between the groups for three sub-tests of the RBMT-E:'Story Immediate', 'Story Delayed', and 'Message Delayed'. Women who use HRT scored higher on these subtests than those who do not use HRT. After calculation of a total profile score (adjusting for age and IQ), HRT users score higher than HRT non-users on the RBMT-E overall measure of Everyday Memory. These pilot results suggest that HRT use in this sample-is related to enhanced verbal memory in everyday memory tasks and that the RBMT-E may be a useful tool for further work in this area of research.