XSophe-Sophe-XeprView (R). A computer simulation software suite (v. 1.1.3) for the analysis of continuous wave EPR spectra

The XSophe-Sophe-XeprView((R)) computer simulation software suite enables scientists to easily determine spin Hamiltonian parameters from isotropic, randomly oriented and single crystal continuous wave electron paramagnetic resonance (CW EPR) spectra from radicals and isolated paramagnetic metal ion centers or clusters found in metalloproteins, chemical systems and materials science. XSophe provides an X-windows graphical user interface to the Sophe programme and allows: creation of multiple input files, local and remote execution of Sophe, the display of sophelog (output from Sophe) and input parameters/files. Sophe is a sophisticated computer simulation software programme employing a number of innovative technologies including; the Sydney OPera HousE (SOPHE) partition and interpolation schemes, a field segmentation algorithm, the mosaic misorientation linewidth model, parallelization and spectral optimisation. In conjunction with the SOPHE partition scheme and the field segmentation algorithm, the SOPHE interpolation scheme and the mosaic misorientation linewidth model greatly increase the speed of simulations for most spin systems. Employing brute force matrix diagonalization in the simulation of an EPR spectrum from a high spin Cr(III) complex with the spin Hamiltonian parameters g(e) = 2.00, D = 0.10 cm(-1), E/D = 0.25, A(x) = 120.0, A(y) = 120.0, A(z) = 240.0 x 10(-4) cm(-1) requires a SOPHE grid size of N = 400 (to produce a good signal to noise ratio) and takes 229.47 s. In contrast the use of either the SOPHE interpolation scheme or the mosaic misorientation linewidth model requires a SOPHE grid size of only N = 18 and takes 44.08 and 0.79 s, respectively. Results from Sophe are transferred via the Common Object Request Broker Architecture (CORBA) to XSophe and subsequently to XeprView((R)) where the simulated CW EPR spectra (1D and 2D) can be compared to the experimental spectra. Energy level diagrams, transition roadmaps and transition surfaces aid the interpretation of complicated randomly oriented CW EPR spectra and can be viewed with a web browser and an OpenInventor scene graph viewer.

Evaluation of angle-dependent absorption: Computer simulation and listening test for an objective and subjective evaluation

The aim of this thesis is the subjective and objective evaluation of angledependent absorption coefficients. As the assumption of a constant absorption coefficient over the angle of incidence is not always held, a new model acknowledging an angle-dependent reflection must be considered, to get a more accurate prediction in the sound field. The study provides information about the behavior of different materials in several rooms, depending on the reflection modeling of incident sound waves. An objective evaluation was run for an implementation of angle-dependent reflection factors in the image source and ray tracing simulation models. Results obtained were analysed after comparison to diffuse-field averaged data. However, changes in acoustic characteristics of a room do not always mean a variation in the listener’s perception. Thus, additional subjective evaluation allowed a comparison between the different results obtained with the computer simulation and the response from the individuals who participated in the listening test. The listening test was designed following a three-alternative forced-choice (3AFC) paradigm. In each interaction asked to the subjects a sequence of either three pink noise bursts or three natural signals was alternated. These results were supposed to show the influence and perception of the two different ways to implement surface reflection –either with diffuse or angle-dependent absorption properties. Results show slightly audible effects when material properties were exaggerated. El objetivo de este trabajo es la evaluación objetiva y subjetiva del coeficiente de absorción en función del ángulo de incidencia de la onda de sonido. La suposición de un coeficiente de absorción constante con respecto al ángulo de incidencia no siempre se sostiene. Por ello, un nuevo modelo considerando la reflexión dependiente del ángulo se debe tener en cuenta para obtener predicciones más certeras en el campo del sonido. El estudio proporciona información sobre el comportamiento de diferentes materiales en distintos recintos, dependientes del modelo de reflexión de las ondas de sonido incidentes. Debido a las dificultades a la hora de realizar las medidas y, por lo tanto, a la falta de datos, los coeficientes de absorción dependientes del ángulo a menudo no se tienen en cuenta a la hora de realizar las simulaciones. Hoy en día, aún no hay una tendencia de aplicar el coeficiente de absorción dependiente del ángulo para mejorar los modelos de reflexión. Por otra parte, para una medición satisfactoria de la absorción dependiente del ángulo, sólo hay unos pocos métodos. Las técnicas de medición actuales llevan mucho tiempo y hay algunos materiales, condiciones y ángulos que no pueden ser reproducidos y, por lo tanto, no es posible su medición. Sin embargo, en el presente estudio, los ángulos de incidencia de las ondas de sonido son conocidos y almacenados en una de base de datos para cada uno de los materiales, de modo que los coeficientes de absorción para el ángulo dado pueden ser devueltos siempre que sean requeridos por el usuario. Para realizar el estudio se llevó a cabo una evaluación objetiva, por medio de la implementación del factor de reflexión dependiente del ángulo en los modelos de fuentes imagen y trazado de rayos. Los resultados fueron analizados después de ser comparados con el promedio de los datos obtenidos en medidas en el campo difuso. La simulación se hizo una vez se configuraron un número de materiales creados por el autor, a partir de los datos existentes en la literatura y los catálogos de fabricantes. Los modelos de Komatsu y Mechel sirvieron como referencia para los materiales porosos, configurando la resistividad al aire o el grosor, y para los paneles perforados, introduciendo el radio de los orificios y la distancia entre centros, respectivamente. Estos materiales se situaban en la pared opuesta a la que se consideraba que debía alojar a la fuente sonora. El resto de superficies se modelaban con el mismo material, variando su coeficiente de absorción y/o de dispersión. Al mismo tiempo, una serie de recintos fueron modelados para poder reproducir distintos escenarios de los que obtener los resultados. Sin embargo, los cambios en las características acústicas de un recinto no significan variaciones en la percepción por parte del oyente. Por ello, una evaluación subjetiva adicional permitió una comparación entre los diferentes resultados obtenidos mediante la simulación informática y la respuesta de los individuos que participaron en la prueba de escucha. Ésta fue diseñada bajo las pautas del modelo de test three-alternative forced-choice (3AFC), con treinta y dos preguntas diferentes. En cada iteración los sujetos fueron preguntados por una secuencia alterna entre tres señales, siendo dos de ellas iguales. Éstas podían ser tanto ráfagas de ruido rosa como señales naturales, en este test se utilizó un fragmento de una obra clásica interpretada por un piano. Antes de contestar al cuestionario, los bloques de preguntas eran ordenados al azar. Para cada ensayo, la mezcla era diferente, así los sujetos no repetían la misma prueba, evitando un sesgo por efectos de aprendizaje. Los bloques se barajaban recordando siempre el orden inicial, para después almacenar los resultados reordenados. La prueba de escucha fue realizada por veintitrés personas, toda ellas con conocimientos dentro del campo de la acústica. Antes de llevar a cabo la prueba de escucha en un entorno adecuado, una hoja con las instrucciones fue facilitada a cada persona. Los resultados muestran la influencia y percepción de las dos maneras distintas de implementar las reflexiones de una superficie –ya sea con respecto a la propiedad de difusión o de absorción dependiente del ángulo de los materiales. Los resultados objetivos, después de ejecutar las simulaciones, muestran los datos medios obtenidos para comprender el comportamiento de distintos materiales de acuerdo con el modelo de reflexión utilizado en el caso de estudio. En las tablas proporcionadas en la memoria se muestran los valores del tiempo de reverberación, la claridad y el tiempo de caída temprana. Los datos de las características del recinto obtenidos en este análisis tienen una fuerte dependencia respecto al coeficiente de absorción de los diferentes materiales que recubren las superficies del cuarto. En los resultados subjetivos, la media de percepción, a la hora de distinguir las distintas señales, por parte de los sujetos, se situó significativamente por debajo del umbral marcado por el punto de inflexión de la función psicométrica. Sin embargo, es posible concluir que la mayoría de los individuos tienden a ser capaces de detectar alguna diferencia entre los estímulos presentados en el 3AFC test. En conclusión, la hipótesis de que los valores del coeficiente de absorción dependiente del ángulo difieren es contrastada. Pero la respuesta subjetiva de los individuos muestra que únicamente hay ligeras variaciones en la percepción si el coeficiente varía en intervalos pequeños entre los valores manejados en la simulación. Además, si los parámetros de los materiales acústicos no son exagerados, los sujetos no perciben ninguna variación. Los primeros resultados obtenidos, proporcionando información respecto a la dependencia del ángulo, llevan a una nueva consideración en el campo de la acústica, y en la realización de nuevos proyectos en el futuro. Para futuras líneas de investigación, las simulaciones se deberían realizar con distintos tipos de recintos, buscando escenarios con geometrías irregulares. También, la implementación de distintos materiales para obtener resultados más certeros. Otra de las fases de los futuros proyectos puede realizarse teniendo en cuenta el coeficiente de dispersión dependiente del ángulo de incidencia de la onda de sonido. En la parte de la evaluación subjetiva, realizar una serie de pruebas de escucha con distintos individuos, incluyendo personas sin una formación relacionada con la ingeniería acústica.

Distinct conformational properties determined by implicit and explicit representation of protein-solvent interactions. An analytical and computer simulation study

In the protein folding problem, solvent-mediated forces are commonly represented by intra-chain pairwise contact energy. Although this approximation has proven to be useful in several circumstances, it is limited in some other aspects of the problem. Here we show that it is possible to achieve two models to represent the chain-solvent system. one of them with implicit and other with explicit solvent, such that both reproduce the same thermodynamic results. Firstly, lattice models treated by analytical methods, were used to show that the implicit and explicitly representation of solvent effects can be energetically equivalent only if local solvent properties are time and spatially invariant. Following, applying the same reasoning Used for the lattice models, two inter-consistent Monte Carlo off-lattice models for implicit and explicit solvent are constructed, being that now in the latter the solvent properties are allowed to fluctuate. Then, it is shown that the chain configurational evolution as well as the globule equilibrium conformation are significantly distinct for implicit and explicit solvent systems. Actually, strongly contrasting with the implicit solvent version, the explicit solvent model predicts: (i) a malleable globule, in agreement with the estimated large protein-volume fluctuations; (ii) thermal conformational stability, resembling the conformational hear resistance of globular proteins, in which radii of gyration are practically insensitive to thermal effects over a relatively wide range of temperatures; and (iii) smaller radii of gyration at higher temperatures, indicating that the chain conformational entropy in the unfolded state is significantly smaller than that estimated from random coil configurations. Finally, we comment on the meaning of these results with respect to the understanding of the folding process. (C) 2009 Elsevier B.V. All rights reserved.

Speech recognition in noise for cochlear implant listeners: Benefits of residual hearing

The purpose of this study was to explore the potential advantages, both theoretical and applied, of preserving low-frequency acoustic hearing in cochlear implant patients. Several hypotheses are presented that predict that residual low-frequency acoustic hearing along with electric stimulation for high frequencies will provide an advantage over traditional long-electrode cochlear implants for the recognition of speech in competing backgrounds. A simulation experiment in normal-hearing subjects demonstrated a clear advantage for preserving low-frequency residual acoustic hearing for speech recognition in a background of other talkers, but not in steady noise. Three subjects with an implanted "short-electrode" cochlear implant and preserved low-frequency acoustic hearing were also tested on speech recognition in the same competing backgrounds and compared to a larger group of traditional cochlear implant users. Each of the three short-electrode subjects performed better than any of the traditional long-electrode implant subjects for speech recognition in a background of other talkers, but not in steady noise, in general agreement with the simulation studies. When compared to a subgroup of traditional implant users matched according to speech recognition ability in quiet, the short-electrode patients showed a 9-dB advantage in the multitalker background. These experiments provide strong preliminary support for retaining residual low-frequency acoustic hearing in cochlear implant patients. The results are consistent with the idea that better perception of voice pitch, which can aid in separating voices in a background of other talkers, was responsible for this advantage.

RWMODEL II: Computer simulation of the Rescorla-Wagner model of Pavlovian conditioning

RWMODEL II simulates the Rescorla-Wagner model of Pavlovian conditioning. It is written in Delphi and runs under Windows 3.1 and Windows 95. The program was designed for novice and expert users and can be employed in teaching, as well as in research. It is user friendly and requires a minimal level of computer literacy but is sufficiently flexible to permit a wide range of simulations. It allows the display of empirical data, against which predictions from the model can be validated.

Molecular dynamics computer simulation of scratch resistance testing of polymers: visualization

Experimental scratch resistance testing provides two numbers: the penetration depth Rp and the healing depth Rh. In molecular dynamics computer simulations, we create a material consisting of N statistical chain segments by polymerization; a reinforcing phase can be included. Then we simulate the movement of an indenter and response of the segments during X time steps. Each segment at each time step has three Cartesian coordinates of position and three of momentum. We describe methods of visualization of results based on a record of 6NX coordinates. We obtain a continuous dependence on time t of positions of each of the segments on the path of the indenter. Scratch resistance at a given location can be connected to spatial structures of individual polymeric chains.

Computer simulation study of liquid lithium at 470 and 843 K

Both structural and dynamical properties of 7Li at 470 and 843 K are studied by molecular dynamics simulation and the results are comapred with the available experimental data. Two effective interatomic potentials are used, i.e., a potential derived from the Ashcroft pseudopotential [Phys. Lett. 23, 48 (1966)] and a recently proposed potential deduced from the neutral pseudoatom method [J. Phys.: Condens. Matter 5, 4283 (1993)]. Although the shape of the two potential functions is very different, the majority of the properties calculated from them are very similar. The differences among the results using the two interaction models are carefully discussed.

Diffusive transport properties in monovalent and divalent metal-ion halide melts: A computer simulation study

Self- and cross-velocity correlation functions and related transport coefficients of molten salts are studied by molecular-dynamics simulation. Six representative systems are considered, i.e., NaCl and KCl alkali halides, CuCl and CuBr noble-metal halides, and SrCl2 and ZnCl2 divalent metal-ion halides. Computer simulation results are compared with experimental self-diffusion coefficients and electrical conductivities. Special attention is paid to dynamic cross correlations and their dependence on the Coulomb interactions as well as on the size and mass differences between anions and cations.

Computer-simulation study of magnetic relaxation in anisotropic magnetic systems

We present a computer-simulation study of the effect of the distribution of energy barriers in an anisotropic magnetic system on the relaxation behavior of the magnetization. While the relaxation law for the magnetization can be approximated in all cases by a time logarithmic decay, the law for the dependence of the magnetic viscosity with temperature is found to be quite sensitive to the shape of the distribution of barriers. The low-temperature region for the magnetic viscosity never extrapolates to a positive no-null value. Moreover our computer simulation results agree reasonably well with some recent relaxation experiments on highly anisotropic single-domain particles.

Comblike poly(a-alkyl g glutamate)s: computer simulation studies of an intermediate thermal phase.

Monte Carlo (MC) simulations have been used to study the structure of an intermediate thermal phase of poly(R-octadecyl ç,D-glutamate). This is a comblike poly(ç-peptide) able to adopt a biphasic structure that has been described as a layered arrangement of backbone helical rods immersed in a paraffinic pool of polymethylene side chains. Simulations were performed at two different temperatures (348 and 363 K), both of them above the melting point of the paraffinic phase, using the configurational bias MC algorithm. Results indicate that layers are constituted by a side-by-side packing of 17/5 helices. The organization of the interlayer paraffinic region is described in atomistic terms by examining the torsional angles and the end-to-end distances for the octadecyl side chains. Comparison with previously reported comblike poly(â-peptide)s revealed significant differences in the organization of the alkyl side chains.

Studies Using Computer Simulation Models to Solve Problems Related to Logistics Terminals

This thesis deals with the use of simulation as a problem-solving tool to solve a few logistic system related problems. More specifically it relates to studies on transport terminals. Transport terminals are key elements in the supply chains of industrial systems. One of the problems related to use of simulation is that of the multiplicity of models needed to study different problems. There is a need for development of methodologies related to conceptual modelling which will help reduce the number of models needed. Three different logistic terminal systems Viz. a railway yard, container terminal of apart and airport terminal were selected as cases for this study. The standard methodology for simulation development consisting of system study and data collection, conceptual model design, detailed model design and development, model verification and validation, experimentation, and analysis of results, reporting of finding were carried out. We found that models could be classified into tightly pre-scheduled, moderately pre-scheduled and unscheduled systems. Three types simulation models( called TYPE 1, TYPE 2 and TYPE 3) of various terminal operations were developed in the simulation package Extend. All models were of the type discrete-event simulation. Simulation models were successfully used to help solve strategic, tactical and operational problems related to three important logistic terminals as set in our objectives. From the point of contribution to conceptual modelling we have demonstrated that clubbing problems into operational, tactical and strategic and matching them with tightly pre-scheduled, moderately pre-scheduled and unscheduled systems is a good workable approach which reduces the number of models needed to study different terminal related problems.

Diffusive transport properties in monovalent and divalent metal-ion halide melts: A computer simulation study

Self- and cross-velocity correlation functions and related transport coefficients of molten salts are studied by molecular-dynamics simulation. Six representative systems are considered, i.e., NaCl and KCl alkali halides, CuCl and CuBr noble-metal halides, and SrCl2 and ZnCl2 divalent metal-ion halides. Computer simulation results are compared with experimental self-diffusion coefficients and electrical conductivities. Special attention is paid to dynamic cross correlations and their dependence on the Coulomb interactions as well as on the size and mass differences between anions and cations.