Numerical simulation of ion transport through ion channels and solid-state nanopores

Ion channels are pore-forming proteins that regulate the flow of ions across biological cell membranes. Ion channels are fundamental in generating and regulating the electrical activity of cells in the nervous system and the contraction of muscolar cells. Solid-state nanopores are nanometer-scale pores located in electrically insulating membranes. They can be adopted as detectors of specific molecules in electrolytic solutions. Permeation of ions from one electrolytic solution to another, through a protein channel or a synthetic pore is a process of considerable importance and realistic analysis of the main dependencies of ion current on the geometrical and compositional characteristics of these structures are highly required. The project described by this thesis is an effort to improve the understanding of ion channels by devising methods for computer simulation that can predict channel conductance from channel structure. This project describes theory, algorithms and implementation techniques used to develop a novel 3-D numerical simulator of ion channels and synthetic nanopores based on the Brownian Dynamics technique. This numerical simulator could represent a valid tool for the study of protein ion channel and synthetic nanopores, allowing to investigate at the atomic-level the complex electrostatic interactions that determine channel conductance and ion selectivity. Moreover it will provide insights on how parameters like temperature, applied voltage, and pore shape could influence ion translocation dynamics. Furthermore it will help making predictions of conductance of given channel structures and it will add information like electrostatic potential or ionic concentrations throughout the simulation domain helping the understanding of ion flow through membrane pores.

Cluster identification and characterization in the riser of a circulating fluidized bed from numerical simulation results

A methodology of identification and characterization of coherent structures mostly known as clusters is applied to hydrodynamic results of numerical simulation generated for the riser of a circulating fluidized bed. The numerical simulation is performed using the MICEFLOW code, which includes the two-fluids IIT`s hydrodynamic model B. The methodology for cluster characterization that is used is based in the determination of four characteristics, related to average life time, average volumetric fraction of solid, existing time fraction and frequency of occurrence. The identification of clusters is performed by applying a criterion related to the time average value of the volumetric solid fraction. A qualitative rather than quantitative analysis is performed mainly owing to the unavailability of operational data used in the considered experiments. Concerning qualitative analysis, the simulation results are in good agreement with literature. Some quantitative comparisons between predictions and experiment were also presented to emphasize the capability of the modeling procedure regarding the analysis of macroscopic scale coherent structures. (c) 2007 Elsevier Inc. All rights reserved.

Acoustic Simulation of a Special Switched Reluctance Drive by Means of Field-Circuit Coupling and Multiphysics Simulation

The approach presented in this paper consists of an energy-based field-circuit coupling in combination with multi-physics simulation of the acoustic radiation of electrical machines. The proposed method is applied to a special switched reluctance motor with asymmetric pole geometry to improve the start-up torque. The pole shape has been optimized, subject to low torque ripple, in a previous study. The proposed approach here is used to analyze the impact of the optimization on the overall acoustic behavior. The field-circuit coupling is based on a temporary lumped-parameter model of the magnetic part incorporated into a circuit simulation based on the modified nodal analysis. The harmonic force excitation is calculated by means of stress tensor computation, and it is transformed to a mechanical mesh by mapping techniques. The structural dynamic problem is solved in the frequency domain using a finite-element modal analysis and superposition. The radiation characteristic is obtained from boundary element acoustic simulation. Simulation results of both rotor types are compared, and measurements of the drive are presented.

Numerical simulation of double-diffusion driven convective flow and rock alteration in three-dimensional fluid-saturated geological fault zones

Numerical methods are used to simulate the double-diffusion driven convective pore-fluid flow and rock alteration in three-dimensional fluid-saturated geological fault zones. The double diffusion is caused by a combination of both the positive upward temperature gradient and the positive downward salinity concentration gradient within a three-dimensional fluid-saturated geological fault zone, which is assumed to be more permeable than its surrounding rocks. In order to ensure the physical meaningfulness of the obtained numerical solutions, the numerical method used in this study is validated by a benchmark problem, for which the analytical solution to the critical Rayleigh number of the system is available. The theoretical value of the critical Rayleigh number of a three-dimensional fluid-saturated geological fault zone system can be used to judge whether or not the double-diffusion driven convective pore-fluid flow can take place within the system. After the possibility of triggering the double-diffusion driven convective pore-fluid flow is theoretically validated for the numerical model of a three-dimensional fluid-saturated geological fault zone system, the corresponding numerical solutions for the convective flow and temperature are directly coupled with a geochemical system. Through the numerical simulation of the coupled system between the convective fluid flow, heat transfer, mass transport and chemical reactions, we have investigated the effect of the double-diffusion driven convective pore-fluid flow on the rock alteration, which is the direct consequence of mineral redistribution due to its dissolution, transportation and precipitation, within the three-dimensional fluid-saturated geological fault zone system. (c) 2005 Elsevier B.V. All rights reserved.

Numerical simulation of plasmonic effects in amorphous silicon induced by embedded aluminium nanoparticles

This work reports a theoretical study aimed to identify the plasmonic resonance condition for a system formed by metallic nanoparticles embedded in an a-Si: H matrix. The study is based on a Tauc-Lorentz model for the electrical permittivity of a-Si: H and a Drude model for the metallic nanoparticles. It is calculated the The polarizability of an sphere and ellipsoidal shaped metal nanoparticles with radius of 20 nm. We also performed FDTD simulations of light propagation inside this structure reporting a comparison among the effects caused by a single nanoparticles of Aluminium, Silver and, as a comparison, an ideally perfectly conductor. The simulation results shows that is possible to obtain a plasmonic resonance in the red part of the spectrum (600-700 nm) when 20-30 nm radius Aluminium ellipsoids are embedded into a-Si: H.

A spectrum-driven damage Identification technique : application and validation through the numerical simulation of the Z24 Bridge

The present paper focuses on a damage identification method based on the use of the second order spectral properties of the nodal response processes. The explicit dependence on the frequency content of the outputs power spectral densities makes them suitable for damage detection and localization. The well-known case study of the Z24 Bridge in Switzerland is chosen to apply and further investigate this technique with the aim of validating its reliability. Numerical simulations of the dynamic response of the structure subjected to different types of excitation are carried out to assess the variability of the spectrum-driven method with respect to both type and position of the excitation sources. The simulated data obtained from random vibrations, impulse, ramp and shaking forces, allowed to build the power spectrum matrix from which the main eigenparameters of reference and damage scenarios are extracted. Afterwards, complex eigenvectors and real eigenvalues are properly weighed and combined and a damage index based on the difference between spectral modes is computed to pinpoint the damage. Finally, a group of vibration-based damage identification methods are selected from the literature to compare the results obtained and to evaluate the performance of the spectral index.

Numerical simulation of combined heat transfer phenomena (conduction, convection, and radiation). Application to he optimisation of thermal systems

Thermal systems interchanging heat and mass by conduction, convection, radiation (solar and thermal ) occur in many engineering applications like energy storage by solar collectors, window glazing in buildings, refrigeration of plastic moulds, air handling units etc. Often these thermal systems are composed of various elements for example a building with wall, windows, rooms, etc. It would be of particular interest to have a modular thermal system which is formed by connecting different modules for the elements, flexibility to use and change models for individual elements, add or remove elements without changing the entire code. A numerical approach to handle the heat transfer and fluid flow in such systems helps in saving the full scale experiment time, cost and also aids optimisation of parameters of the system. In subsequent sections are presented a short summary of the work done until now on the orientation of the thesis in the field of numerical methods for heat transfer and fluid flow applications, the work in process and the future work.

Numerical simulation of left ventricular assist device implantations: comparing the ascending and the descending aorta cannulations.

In this work we present numerical simulations of continuous flow left ventricle assist device implantation with the aim of comparing difference in flow rates and pressure patterns depending on the location of the anastomosis and the rotational speed of the device. Despite the fact that the descending aorta anastomosis approach is less invasive, since it does not require a sternotomy and a cardiopulmonary bypass, its benefits are still controversial. Moreover, the device rotational speed should be correctly chosen to avoid anomalous flow rates and pressure distribution in specific location of the cardiovascular tree. With the aim of assessing the differences between these two approaches and device rotational speed in terms of flow rate and pressure waveforms, we set up numerical simulations of network of one-dimensional models where we account for the presence of an outflow cannula anastomosed to different locations of the aorta. Then, we use the resulting network to compare the results of the two different cannulations for several stages of heart failure and different rotational speed of the device. The inflow boundary data for the heart and the cannulas are obtained from a lumped parameters model of the entire circulatory system with an assist device, which is validated with clinical data. The results show that ascending and descending aorta cannulations lead to similar waveforms and mean flow rate in all the considered cases. Moreover, regardless of the anastomosis region, the rotational speed of the device has an important impact on wave profiles; this effect is more pronounced at high RPM.

Numerical simulation of gel electrophoresis of DNA knots in weak and strong electric fields.

Gel electrophoresis allows one to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots, being more compact, drift faster than simpler knots. Recent experiments have shown that the drift velocity dependence on the knot type is inverted when changing from low to high electric fields. We present a computer simulation on a lattice of a closed, knotted, charged DNA chain drifting in an external electric field in a topologically restricted medium. Using a Monte Carlo algorithm, the dependence of the electrophoretic migration of the DNA molecules on the knot type and on the electric field intensity is investigated. The results are in qualitative and quantitative agreement with electrophoretic experiments done under conditions of low and high electric fields.

Numerical simulation of rotor-stator interaction and tip clearance flow in centrifugal compressors

The effect of the tip clearance and vaneless diffuser width on the stage performance and flow fields of a centrifugal compressor were studied numerically and results were compared to the experimental measurements. The diffuser width was changed by moving the shroud side of the diffuser axially and six tip clearances size from 0.5 to 3 mm were studied. Moreover, the effects of rotor-stator interaction on the diffuser and impeller flow fields and performance were studied. Also transient simulations were carried out in order to investigate the influence of the interaction on the impeller and diffuser performance parameters. It was seen that pinch could improve the performance and it help to get more uniform flow at exit and less back flow from diffuser to the impeller.

The Kineticist's Workbench: Combining Symbolic and Numerical Methods in the Simulation of Chemical Reaction Mechanisms

The Kineticist's Workbench is a program that simulates chemical reaction mechanisms by predicting, generating, and interpreting numerical data. Prior to simulation, it analyzes a given mechanism to predict that mechanism's behavior; it then simulates the mechanism numerically; and afterward, it interprets and summarizes the data it has generated. In performing these tasks, the Workbench uses a variety of techniques: graph- theoretic algorithms (for analyzing mechanisms), traditional numerical simulation methods, and algorithms that examine simulation results and reinterpret them in qualitative terms. The Workbench thus serves as a prototype for a new class of scientific computational tools---tools that provide symbiotic collaborations between qualitative and quantitative methods.

Numerical Simulation of Electroosmotic Flow with Step Change in Zeta Potential

Electroosmotic flow is a convenient mechanism for transporting polar fluid in a microfluidic device. The flow is generated through the application of an external electric field that acts on the free charges that exists in a thin Debye layer at the channel walls. The charge on the wall is due to the chemistry of the solid-fluid interface, and it can vary along the channel, e.g. due to modification of the wall. This investigation focuses on the simulation of the electroosmotic flow (EOF) profile in a cylindrical microchannel with step change in zeta potential. The modified Navier-Stoke equation governing the velocity field and a non-linear two-dimensional Poisson-Boltzmann equation governing the electrical double-layer (EDL) field distribution are solved numerically using finite control-volume method. Continuities of flow rate and electric current are enforced resulting in a non-uniform electrical field and pressure gradient distribution along the channel. The resulting parabolic velocity distribution at the junction of the step change in zeta potential, which is more typical of a pressure-driven velocity flow profile, is obtained.

Numerical simulation of tephra transport and deposition of the 1982 El Chichón eruption and implications for hazard assessment

El Chichón volcano, Chiapas, Mexico, erupted explosively on March 29th, 1982, after a repose period of about 550 years. Amongst ten eruptive episodes documented between March 29th and April 4th, only the three that occurred on March 29th and April 4th produced significant pyroclastic tephra deposits. Here we use analytical (HAZMAP) and numerical (FALL3D) tephra transport models to reconstruct the deposits and the atmospheric plume dispersal associated with the three main fallout units of the 1982 eruption. On the basis of such a reconstruction, we produce hazard maps of tephra fallout associated to a Plinian eruption and discuss the implications of such a severe eruption scenario.

Numerical Simulation Of Sediment Transport And Bedmorphology Around A Hydraulic Structure On A River

Scour around hydraulic structures is a critical problem in hydraulic engineering. Under prediction of scour depth may lead to costly failures of the structure, while over prediction might result in unnecessary costs. Unfortunately, up-to-date empirical scour prediction formulas are based on laboratory experiments that are not always able to reproduce field conditions due to complicated geometry of rivers and temporal and spatial scales of a physical model. However, computational fluid dynamics (CFD) tools can perform using real field dimensions and operating conditions to predict sediment scour around hydraulic structures. In Korea, after completing the Four Major Rivers Restoration Project, several new weirs have been built across Han, Nakdong, Geum and Yeongsan Rivers. Consequently, sediment deposition and bed erosion around such structures have became a major issue in these four rivers. In this study, an application of an open source CFD software package, the TELEMAC-MASCARET, to simulate sediment transport and bed morphology around Gangjeong weir, which is the largest multipurpose weir built on Nakdong River. A real bathymetry of the river and a geometry of the weir have been implemented into the numerical model. The numerical simulation is carried out with a real hydrograph at the upstream boundary. The bedmorphology obtained from the numerical results has been validated against field observation data, and a maximum of simulated scour depth is compared with the results obtained by empirical formulas of Hoffmans. Agreement between numerical computations, observed data and empirical formulas is judged to be satisfactory on all major comparisons. The outcome of this study does not only point out the locations where deposition and erosion might take place depending on the weir gate operation, but also analyzes the mechanism of formation and evolution of scour holes after the weir gates.

Numerical simulation of drop impact and jet buckling problems using the eXtended Pom-Pom model

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)