Dynamic high-resolution computer simulation of electrophoretic enantiomer separations with neutral cyclodextrins as chiral selectors.

GENTRANS, a comprehensive one-dimensional dynamic simulator for electrophoretic separations and transport, was extended for handling electrokinetic chiral separations with a neutral ligand. The code can be employed to study the 1:1 interaction of monovalent weak and strong acids and bases with a single monovalent weak or strong acid or base additive, including a neutral cyclodextrin, under real experimental conditions. It is a tool to investigate the dynamics of chiral separations and to provide insight into the buffer systems used in chiral capillary zone electrophoresis (CZE) and chiral isotachophoresis. Analyte stacking across conductivity and buffer additive gradients, changes of additive concentration, buffer component concentration, pH, and conductivity across migrating sample zones and peaks, and the formation and migration of system peaks can thereby be investigated in a hitherto inaccessible way. For model systems with charged weak bases and neutral modified ��-cyclodextrins at acidic pH, for which complexation constants, ionic mobilities, and mobilities of selector-analyte complexes have been determined by CZE, simulated and experimentally determined electropherograms and isotachopherograms are shown to be in good agreement. Simulation data reveal that CZE separations of cationic enantiomers performed in phosphate buffers at low pH occur behind a fast cationic migrating system peak that has a small impact on the buffer composition under which enantiomeric separation takes place.

Dynamic computer simulation of electrophoretic enantiomer migration order and separation in presence of a neutral cyclodextrin

One-dimensional dynamic computer simulation was employed to investigate the separation and migration order change of ketoconazole enantiomers at low pH in presence of increasing amounts of (2-hydroxypropyl)-��-cyclodextrin (OHP-��-CD). The 1:1 interaction of ketoconazole with the neutral cyclodextrin was simulated under real experimental conditions and by varying input parameters for complex mobilities and complexation constants. Simulation results obtained with experimentally determined apparent ionic mobilities, complex mobilities, and complexation constants were found to compare well with the calculated separation selectivity and experimental data. Simulation data revealed that the migration order of the ketoconazole enantiomers at low (OHP-��-CD) concentrations (i.e. below migration order inversion) is essentially determined by the difference in complexation constants and at high (OHP-��-CD) concentrations (i.e. above migration order inversion) by the difference in complex mobilities. Furthermore, simulations with complex mobilities set to zero provided data that mimic migration order and separation with the chiral selector being immobilized. For the studied CEC configuration, no migration order inversion is predicted and separations are shown to be quicker and electrophoretic transport reduced in comparison to migration in free solution. The presented data illustrate that dynamic computer simulation is a valuable tool to study electrokinetic migration and separations of enantiomers in presence of a complexing agent.

Computer simulation of electrophoretic aspects of enantiomer migration and separation in capillary electrochromatography with a neutral selector.

A computer simulation study describing the electrophoretic separation and migration of methadone enantiomers in presence of free and immobilized (2-hydroxypropyl)-��-CD is presented. The 1:1 interaction of methadone with the neutral CD was simulated by using experimentally determined mobilities and complexation constants for the complexes in a low-pH BGE comprising phosphoric acid and KOH. The use of complex mobilities represents free solution conditions with the chiral selector being a buffer additive, whereas complex mobilities set to zero provide data that mimic migration and separation with the chiral selector being immobilized, that is CEC conditions in absence of unspecific interaction between analytes and the chiral stationary phase. Simulation data reveal that separations are quicker, electrophoretic displacement rates are reduced, and sensitivity is enhanced in CEC with on-column detection in comparison to free solution conditions. Simulation is used to study electrophoretic analyte behavior at the interface between sample and the CEC column with the chiral selector (analyte stacking) and at the rear end when analytes leave the environment with complexation (analyte destacking). The latter aspect is relevant for off-column analyte detection in CEC and is described here for the first time via the dynamics of migrating analyte zones. Simulation provides insight into means to counteract analyte dilution at the column end via use of a BGE with higher conductivity. Furthermore, the impact of EOF on analyte migration, separation, and detection for configurations with the selector zone being displaced or remaining immobilized under buffer flow is simulated. In all cases, the data reveal that detection should occur within or immediately after the selector zone.

Impact of Taylor-Aris diffusivity on analyte and system zone dispersion in CZE assessed by computer simulation and experimental validation.

Application of pressure-driven laminar flow has an impact on zone and boundary dispersion in open tubular CE. The GENTRANS dynamic simulator for electrophoresis was extended with Taylor-Aris diffusivity which accounts for dispersion due to the parabolic flow profile associated with pressure-driven flow. Effective diffusivity of analyte and system zones as functions of the capillary diameter and the amount of flow in comparison to molecular diffusion alone were studied for configurations with concomitant action of imposed hydrodynamic flow and electroosmosis. For selected examples under realistic experimental conditions, simulation data are compared with those monitored experimentally using modular CE setups featuring both capacitively coupled contactless conductivity and UV absorbance detection along a 50 ��m id fused-silica capillary of 90 cm total length. The data presented indicate that inclusion of flow profile based Taylor-Aris diffusivity provides realistic simulation data for analyte and system peaks, particularly those monitored in CE with conductivity detection.

Cerebellar mechanisms for motor learning: Testing predictions from a large-scale computer simulation

The cerebellum is the major brain structure that contributes to our ability to improve movements through learning and experience. We have combined computer simulations with behavioral and lesion studies to investigate how modification of synaptic strength at two different sites within the cerebellum contributes to a simple form of motor learning���Pavlovian conditioning of the eyelid response. These studies are based on the wealth of knowledge about the intrinsic circuitry and physiology of the cerebellum and the straightforward manner in which this circuitry is engaged during eyelid conditioning. Thus, our simulations are constrained by the well-characterized synaptic organization of the cerebellum and further, the activity of cerebellar inputs during simulated eyelid conditioning is based on existing recording data. These simulations have allowed us to make two important predictions regarding the mechanisms underlying cerebellar function, which we have tested and confirmed with behavioral studies. The first prediction describes the mechanisms by which one of the sites of synaptic modification, the granule to Purkinje cell synapses (gr ��� Pkj) of the cerebellar cortex, could generate two time-dependent properties of eyelid conditioning���response timing and the ISI function. An empirical test of this prediction using small, electrolytic lesions of the cerebellar cortex revealed the pattern of results predicted by the simulations. The second prediction made by the simulations is that modification of synaptic strength at the other site of plasticity, the mossy fiber to deep nuclei synapses (mf ��� nuc), is under the control of Purkinje cell activity. The analysis predicts that this property should confer mf ��� nuc synapses with resistance to extinction. Thus, while extinction processes erase plasticity at the first site, residual plasticity at mf ��� nuc synapses remains. The residual plasticity at the mf ��� nuc site confers the cerebellum with the capability for rapid relearning long after the learned behavior has been extinguished. We confirmed this prediction using a lesion technique that reversibly disconnected the cerebellar cortex at various stages during extinction and reacquisition of eyelid responses. The results of these studies represent significant progress toward a complete understanding of how the cerebellum contributes to motor learning. ^

Computer Simulation of Crowd Dynamics and Destructive Crowd Behavior

The social processes that lead to destructive behavior in celebratory crowds can be studied through an agent-based computer simulation. Riots are an increasingly common outcome of sports celebrations, and pose the potential for harm to participants, bystanders, property, and the reputation of the groups with whom participants are associated. Rioting cannot necessarily be attributed to the negative emotions of individuals, such as anger, rage, frustration and despair. For instance, the celebratory behavior (e.g., chanting, cheering, singing) during UConn���s ���Spring Weekend��� and after the 2004 NCAA Championships resulted in several small fires and overturned cars. Further, not every individual in the area of a riot engages in violence, and those who do, do not do so continuously. Instead, small groups carry out the majority of violent acts in relatively short-lived episodes. Agent-based computer simulations are an ideal method for modeling complex group-level social phenomena, such as celebratory gatherings and riots, which emerge from the interaction of relatively ���simple��� individuals. By making simple assumptions about individuals��� decision-making and behaviors and allowing actors to affect one another, behavioral patterns emerge that cannot be predicted by the characteristics of individuals. The computer simulation developed here models celebratory riot behavior by repeatedly evaluating a single algorithm for each individual, the inputs of which are affected by the characteristics of nearby actors. Specifically, the simulation assumes that (a) actors possess 1 of 5 distinct social identities (group memberships), (b) actors will congregate with actors who possess the same identity, (c) the degree of social cohesion generated in the social context determines the stability of relationships within groups, and (d) actors��� level of aggression is affected by the aggression of other group members. Not only does this simulation provide a systematic investigation of the effects of the initial distribution of aggression, social identification, and cohesiveness on riot outcomes, but also an analytic tool others may use to investigate, visualize and predict how various individual characteristics affect emergent crowd behavior.

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 evaluaci��n objetiva y subjetiva del coeficiente de absorci��n en funci��n del ��ngulo de incidencia de la onda de sonido. La suposici��n de un coeficiente de absorci��n constante con respecto al ��ngulo de incidencia no siempre se sostiene. Por ello, un nuevo modelo considerando la reflexi��n dependiente del ��ngulo se debe tener en cuenta para obtener predicciones m��s certeras en el campo del sonido. El estudio proporciona informaci��n sobre el comportamiento de diferentes materiales en distintos recintos, dependientes del modelo de reflexi��n 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 absorci��n dependientes del ��ngulo a menudo no se tienen en cuenta a la hora de realizar las simulaciones. Hoy en d��a, a��n no hay una tendencia de aplicar el coeficiente de absorci��n dependiente del ��ngulo para mejorar los modelos de reflexi��n. Por otra parte, para una medici��n satisfactoria de la absorci��n dependiente del ��ngulo, s��lo hay unos pocos m��todos. Las t��cnicas de medici��n actuales llevan mucho tiempo y hay algunos materiales, condiciones y ��ngulos que no pueden ser reproducidos y, por lo tanto, no es posible su medici��n. Sin embargo, en el presente estudio, los ��ngulos 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 absorci��n para el ��ngulo dado pueden ser devueltos siempre que sean requeridos por el usuario. Para realizar el estudio se llev�� a cabo una evaluaci��n objetiva, por medio de la implementaci��n del factor de reflexi��n dependiente del ��ngulo en los modelos de fuentes imagen y trazado de rayos. Los resultados fueron analizados despu��s de ser comparados con el promedio de los datos obtenidos en medidas en el campo difuso. La simulaci��n se hizo una vez se configuraron un n��mero de materiales creados por el autor, a partir de los datos existentes en la literatura y los cat��logos 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 deb��a alojar a la fuente sonora. El resto de superficies se modelaban con el mismo material, variando su coeficiente de absorci��n y/o de dispersi��n. 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 caracter��sticas ac��sticas de un recinto no significan variaciones en la percepci��n por parte del oyente. Por ello, una evaluaci��n subjetiva adicional permiti�� una comparaci��n entre los diferentes resultados obtenidos mediante la simulaci��n inform��tica y la respuesta de los individuos que participaron en la prueba de escucha. ��sta fue dise��ada bajo las pautas del modelo de test three-alternative forced-choice (3AFC), con treinta y dos preguntas diferentes. En cada iteraci��n los sujetos fueron preguntados por una secuencia alterna entre tres se��ales, siendo dos de ellas iguales. ��stas pod��an ser tanto r��fagas de ruido rosa como se��ales naturales, en este test se utiliz�� un fragmento de una obra cl��sica interpretada por un piano. Antes de contestar al cuestionario, los bloques de preguntas eran ordenados al azar. Para cada ensayo, la mezcla era diferente, as�� los sujetos no repet��an la misma prueba, evitando un sesgo por efectos de aprendizaje. Los bloques se barajaban recordando siempre el orden inicial, para despu��s almacenar los resultados reordenados. La prueba de escucha fue realizada por veintitr��s personas, toda ellas con conocimientos dentro del campo de la ac��stica. 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 percepci��n de las dos maneras distintas de implementar las reflexiones de una superficie ���ya sea con respecto a la propiedad de difusi��n o de absorci��n dependiente del ��ngulo de los materiales. Los resultados objetivos, despu��s de ejecutar las simulaciones, muestran los datos medios obtenidos para comprender el comportamiento de distintos materiales de acuerdo con el modelo de reflexi��n utilizado en el caso de estudio. En las tablas proporcionadas en la memoria se muestran los valores del tiempo de reverberaci��n, la claridad y el tiempo de ca��da temprana. Los datos de las caracter��sticas del recinto obtenidos en este an��lisis tienen una fuerte dependencia respecto al coeficiente de absorci��n de los diferentes materiales que recubren las superficies del cuarto. En los resultados subjetivos, la media de percepci��n, a la hora de distinguir las distintas se��ales, por parte de los sujetos, se situ�� significativamente por debajo del umbral marcado por el punto de inflexi��n de la funci��n psicom��trica. Sin embargo, es posible concluir que la mayor��a de los individuos tienden a ser capaces de detectar alguna diferencia entre los est��mulos presentados en el 3AFC test. En conclusi��n, la hip��tesis de que los valores del coeficiente de absorci��n dependiente del ��ngulo difieren es contrastada. Pero la respuesta subjetiva de los individuos muestra que ��nicamente hay ligeras variaciones en la percepci��n si el coeficiente var��a en intervalos peque��os entre los valores manejados en la simulaci��n. Adem��s, si los par��metros de los materiales ac��sticos no son exagerados, los sujetos no perciben ninguna variaci��n. Los primeros resultados obtenidos, proporcionando informaci��n respecto a la dependencia del ��ngulo, llevan a una nueva consideraci��n en el campo de la ac��stica, y en la realizaci��n de nuevos proyectos en el futuro. Para futuras l��neas de investigaci��n, las simulaciones se deber��an realizar con distintos tipos de recintos, buscando escenarios con geometr��as irregulares. Tambi��n, la implementaci��n de distintos materiales para obtener resultados m��s certeros. Otra de las fases de los futuros proyectos puede realizarse teniendo en cuenta el coeficiente de dispersi��n dependiente del ��ngulo de incidencia de la onda de sonido. En la parte de la evaluaci��n subjetiva, realizar una serie de pruebas de escucha con distintos individuos, incluyendo personas sin una formaci��n relacionada con la ingenier��a ac��stica.

Computer simulation of the interplay between fractal structures and surrounding heterogeneous multifractal distributions. Applications

In a large number of physical, biological and environmental processes interfaces with high irregular geometry appear separating media (phases) in which the heterogeneity of constituents is present. In this work the quantification of the interplay between irregular structures and surrounding heterogeneous distributions in the plane is made For a geometric set image and a mass distribution (measure) image supported in image, being image, the mass image gives account of the interplay between the geometric structure and the surrounding distribution. A computation method is developed for the estimation and corresponding scaling analysis of image, being image a fractal plane set of Minkowski dimension image and image a multifractal measure produced by random multiplicative cascades. The method is applied to natural and mathematical fractal structures in order to study the influence of both, the irregularity of the geometric structure and the heterogeneity of the distribution, in the scaling of image. Applications to the analysis and modeling of interplay of phases in environmental scenarios are given.

Computer simulation of random parckings for self-similar particle size distributions in soil and granular materials: porosity and pore size distribution

A 2D computer simulation method of random packings is applied to sets of particles generated by a self-similar uniparametric model for particle size distributions (PSDs) in granular media. The parameter p which controls the model is the proportion of mass of particles corresponding to the left half of the normalized size interval [0,1]. First the influence on the total porosity of the parameter p is analyzed and interpreted. It is shown that such parameter, and the fractal exponent of the associated power scaling, are efficient packing parameters, but this last one is not in the way predicted in a former published work addressing an analogous research in artificial granular materials. The total porosity reaches the minimum value for p = 0.6. Limited information on the pore size distribution is obtained from the packing simulations and by means of morphological analysis methods. Results show that the range of pore sizes increases for decreasing values of p showing also different shape in the volume pore size distribution. Further research including simulations with a greater number of particles and image resolution are required to obtain finer results on the hierarchical structure of pore space.

Computer Simulation of Packing of Particles with Size Distributions Produced by Fragmentation Processes

Fragmentation schemes inspired by theoretical results and conjectures of Kolmogorov are applied to produce particle size distributions of different natures, depending on fragmentation parameters. A two-dimensional computer simulation method of packing is applied to the resulting distributions and the void fraction is evaluated. The relationship between the void fraction and characteristic parameters of the fragmentation process is studied.

Computer simulation of packing of particles with size distributions produced by fragmentation processes

Fragmentation schemes inspired by theoretical results and conjectures of Kolmogorov are applied to produce particle size distributions of different natures, depending on fragmentation parameters. A two-dimensional computer simulation method of packing is applied to the resulting distributions and the void fraction is evaluated. The relationship between the void fraction and characteristic parameters of the fragmentation process is studied.

Analysis of the role of the Spitzenk��rper in fungal morphogenesis by computer simulation of apical branching in Aspergillus���niger

High-resolution video microscopy, image analysis, and computer simulation were used to study the role of the Spitzenk��rper (Spk) in apical branching of ramosa-1, a temperature-sensitive mutant of Aspergillus niger. A shift to the restrictive temperature led to a cytoplasmic contraction that destabilized the Spk, causing its disappearance. After a short transition period, new Spk appeared where the two incipient apical branches emerged. Changes in cell shape, growth rate, and Spk position were recorded and transferred to the fungus simulator program to test the hypothesis that the Spk functions as a vesicle supply center (VSC). The simulation faithfully duplicated the elongation of the main hypha and the two apical branches. Elongating hyphae exhibited the growth pattern described by the hyphoid equation. During the transition phase, when no Spk was visible, the growth pattern was nonhyphoid, with consecutive periods of isometric and asymmetric expansion; the apex became enlarged and blunt before the apical branches emerged. Video microscopy images suggested that the branch Spk were formed anew by gradual condensation of vesicle clouds. Simulation exercises where the VSC was split into two new VSCs failed to produce realistic shapes, thus supporting the notion that the branch Spk did not originate by division of the original Spk. The best computer simulation of apical branching morphogenesis included simulations of the ontogeny of branch Spk via condensation of vesicle clouds. This study supports the hypothesis that the Spk plays a major role in hyphal morphogenesis by operating as a VSC���i.e., by regulating the traffic of wall-building vesicles in the manner predicted by the hyphoid model.

Cost effectiveness of shortening screening interval or extending age range of NHS breast screening programme: computer simulation study

Objective: To compare the cost effectiveness of two possible modifications to the current UK screening programme: shortening the screening interval from three to two years and extending the age of invitation to a final screen from 64 to 69.

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

We describe a procedure for the generation of chemically accurate computer-simulation models to study chemical reactions in the condensed phase. The process involves (i) the use of a coupled semiempirical quantum and classical molecular mechanics method to represent solutes and solvent, respectively; (ii) the optimization of semiempirical quantum mechanics (QM) parameters to produce a computationally efficient and chemically accurate QM model; (iii) the calibration of a quantum/classical microsolvation model using ab initio quantum theory; and (iv) the use of statistical mechanical principles and methods to simulate, on massively parallel computers, the thermodynamic properties of chemical reactions in aqueous solution. The utility of this process is demonstrated by the calculation of the enthalpy of reaction in vacuum and free energy change in aqueous solution for a proton transfer involving methanol, methoxide, imidazole, and imidazolium, which are functional groups involved with proton transfers in many biochemical systems. An optimized semiempirical QM model is produced, which results in the calculation of heats of formation of the above chemical species to within 1.0 kcal/mol (1 kcal = 4.18 kJ) of experimental values. The use of the calibrated QM and microsolvation QM/MM (molecular mechanics) models for the simulation of a proton transfer in aqueous solution gives a calculated free energy that is within 1.0 kcal/mol (12.2 calculated vs. 12.8 experimental) of a value estimated from experimental pKa values of the reacting species.

Analytical pedestrian accident reconstruction using computer simulation. Final report.

Mode of access: Internet.