BioJADE: A Design and Simulation Tool for Synthetic Biological Systems

The next generations of both biological engineering and computer engineering demand that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems may provide us with the ability to build cells that are capable of a plethora of activities, from computation to synthesizing nanostructures. To develop these systems, we must have a set of tools not only for synthesizing systems, but also designing and simulating them. The BioJADE project provides a comprehensive, extensible design and simulation platform for synthetic biology. BioJADE is a graphical design tool built in Java, utilizing a database back end, and supports a range of simulations using an XML communication protocol. BioJADE currently supports a library of over 100 parts with which it can compile designs into actual DNA, and then generate synthesis instructions to build the physical parts. The BioJADE project contributes several tools to Synthetic Biology. BioJADE in itself is a powerful tool for synthetic biology designers. Additionally, we developed and now make use of a centralized BioBricks repository, which enables the sharing of BioBrick components between researchers, and vastly reduces the barriers to entry for aspiring Synthetic Biologists.

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.

Towards Grid-Wide Modeling and Simulation

Modeling and simulation permeate all areas of business, science and engineering. With the increase in the scale and complexity of simulations, large amounts of computational resources are required, and collaborative model development is needed, as multiple parties could be involved in the development process. The Grid provides a platform for coordinated resource sharing and application development and execution. In this paper, we survey existing technologies in modeling and simulation, and we focus on interoperability and composability of simulation components for both simulation development and execution. We also present our recent work on an HLA-based simulation framework on the Grid, and discuss the issues to achieve composability.

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.

Modeling and Analysis of Two-Part Type Manufacturing Systems

This paper presents a model and analysis of a synchronous tandem flow line that produces different part types on unreliable machines. The machines operate according to a static priority rule, operating on the highest priority part whenever possible, and operating on lower priority parts only when unable to produce those with higher priorities. We develop a new decomposition method to analyze the behavior of the manufacturing system by decomposing the long production line into small analytically tractable components. As a first step in modeling a production line with more than one part type, we restrict ourselves to the case where there are two part types. Detailed modeling and derivations are presented with a small two-part-type production line that consists of two processing machines and two demand machines. Then, a generalized longer flow line is analyzed. Furthermore, estimates for performance measures, such as average buffer levels and production rates, are presented and compared to extensive discrete event simulation. The quantitative behavior of the two-part type processing line under different demand scenarios is also provided.

Peeling, healing and bursting in a lubricated elastic sheet

We consider the dynamics of an elastic sheet lubricated by the flow of a thin layer of fluid that separates it from a rigid wall. By considering long wavelength deformations of the sheet, we derive an evolution equation for its motion, accounting for the effects of elastic bending, viscous lubrication and body forces. We then analyze various steady and unsteady problems for the sheet such as peeling, healing, levitating and bursting using a combination of numerical simulation and dimensional analysis. On the macro-scale, we corroborate our theory with a simple experiment, and on the micro-scale, we analyze an oscillatory valve that can transform a continuous stream of fluid into a series of discrete pulses.

Discrete and continuous compositions

This paper examines a dataset which is modeled well by the Poisson-Log Normal process and by this process mixed with Log Normal data, which are both turned into compositions. This generates compositional data that has zeros without any need for conditional models or assuming that there is missing or censored data that needs adjustment. It also enables us to model dependence on covariates and within the composition

Compositional analysis of bivariate discrete probabilities

A joint distribution of two discrete random variables with finite support can be displayed as a two way table of probabilities adding to one. Assume that this table has n rows and m columns and all probabilities are non-null. This kind of table can be seen as an element in the simplex of n · m parts. In this context, the marginals are identified as compositional amalgams, conditionals (rows or columns) as subcompositions. Also, simplicial perturbation appears as Bayes theorem. However, the Euclidean elements of the Aitchison geometry of the simplex can also be translated into the table of probabilities: subspaces, orthogonal projections, distances. Two important questions are addressed: a) given a table of probabilities, which is the nearest independent table to the initial one? b) which is the largest orthogonal projection of a row onto a column? or, equivalently, which is the information in a row explained by a column, thus explaining the interaction? To answer these questions three orthogonal decompositions are presented: (1) by columns and a row-wise geometric marginal, (2) by rows and a columnwise geometric marginal, (3) by independent two-way tables and fully dependent tables representing row-column interaction. An important result is that the nearest independent table is the product of the two (row and column)-wise geometric marginal tables. A corollary is that, in an independent table, the geometric marginals conform with the traditional (arithmetic) marginals. These decompositions can be compared with standard log-linear models. Key words: balance, compositional data, simplex, Aitchison geometry, composition, orthonormal basis, arithmetic and geometric marginals, amalgam, dependence measure, contingency table

Modeling of hybrid systems by piecewise decomposition

Piecewise linear models systems arise as mathematical models of systems in many practical applications, often from linearization for nonlinear systems. There are two main approaches of dealing with these systems according to their continuous or discrete-time aspects. We propose an approach which is based on the state transformation, more particularly the partition of the phase portrait in different regions where each subregion is modeled as a two-dimensional linear time invariant system. Then the Takagi-Sugeno model, which is a combination of local model is calculated. The simulation results show that the Alpha partition is well-suited for dealing with such a system

Lecture on Carrier Communications Simulation

Discusses the influence of Nyquist sampling theory on carrier communication simulations.

Assignment on Carrier Communications Simulation

Simulation of AM, QAM, complex QAM, 4QAM and 16QAM carrier communication schemes in Matlab.

Discrete Dynamical Systems

Exercises and solutions for a third or fourth year maths course. Diagrams for the questions are all together in the support.zip file, as .eps files

Evaluation of the effectiveness of an organization in the field of brand perception using a computer agent-based simulation system

Este proyecto de investigación busca usar un sistema de cómputo basado en modelación por agentes para medir la percepción de marca de una organización en una población heterogénea. Se espera proporcionar información que permita dar soluciones a una organización acerca del comportamiento de sus consumidores y la asociada percepción de marca. El propósito de este sistema es el de modelar el proceso de percepción-razonamiento-acción para simular un proceso de razonamiento como el resultado de una acumulación de percepciones que resultan en las acciones del consumidor. Este resultado definirá la aceptación de marca o el rechazo del consumidor hacia la empresa. Se realizó un proceso de recolección información acerca de una organización específica en el campo de marketing. Después de compilar y procesar la información obtenida de la empresa, el análisis de la percepción de marca es aplicado mediante procesos de simulación. Los resultados del experimento son emitidos a la organización mediante un informe basado en conclusiones y recomendaciones a nivel de marketing para mejorar la percepción de marca por parte de los consumidores.

Análisis del modelo de Internacionalización de e-Tech Simulation según la teoría de redes

La teoría de redes de Johanson y Mattson (1988) explica como las pequeñas empresas, también conocidas como PyMes, utilizan las redes de negocio para desarrollar sus procesos de internacionalización. Es así que a través de las redes pueden superar sus limitaciones de tamaño para encontrar cierto tipo de fluidez y dinamismo en su gestión, con el fin de aprovechar los beneficios de la internacionalización. A partir del desarrollo y fortalecimiento de las relaciones dentro de la red la organización puede posicionarse en una instancia competitiva cada vez más fuerte (Jarillo, 1988). Según Forsgren y Johanson (1992), para los gerentes es importante coordinar la interacción entre los diferentes actores de la red, ya que a través de estas su posición dentro de la red mejora y así mismo el flujo de recursos será mayor. El propósito de este trabajo es analizar el modelo de internacionalización según la teoría de redes, desde una perspectiva cultural, de e-Tech Simulation una PyME “Born to be global” norteamericana. Esta empresa ha minimizado su riesgo de internacionalización, a través del desarrollo de acuerdos entre los diferentes actores. Al mejorar su posición dentro de la red, es decir al fortalecer aún más los lazos existentes y crear nuevas relaciones, la empresa ha obtenido mayores beneficios de la misma y ha logrado ser aún más flexible con sus clientes. Es por esto que a partir de este análisis se planteó una serie de recomendaciones para mejorar los procesos de negociación dentro de la red, bajo un contexto cultural. De igual forma se evidencio la importancia del papel del emprendimiento del gerente en los procesos de internacionalización, así como su habilidad para mezclar los recursos obtenidos de diferentes mercados internacionales para satisfacer las necesidades de los clientes.