Filippo Menolascina/Thesis

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Contents

My Masters Thesis Open Notebook

This is the open notebook of my thesis project. I will collect here all the ideas and notes I will come across in this period; I hope you will find them useful (however, don't take them too seriously!) for your research too!


Modelling Life: a Systems Biology Approach

Brief Introduction to Molecular Cell Biology

DNA, Genes and RNA

Proteins as Sensors and Actuators

Measurement Approaches

Model Organisms

Cells from a Control System-Theoretic Perspective

Dimerizations

Bifurcations

Activation and Inhibition as Control Mechanisms

Species Interaction and Modelling Formalisms

Phase Space and Step Response

Systems Properties and Modelling Formalisms

Biological Systems Properties

Challenges to Control Systems Theory in Molecular Biology

Realization and Identification Issues

Consistent Graphs and Monotone Systems

Manipulating Life: Engineering Cellular Logic Gates

Biochemical Reaction Systems and Models

Kinetic Models

Detailed Kinetic Models

Simplified Kinetic Models

Example: Modelling a Signal Trasduction System

Ordinary Differential Equation based Representation

-calculus and Stochastic -calculus

Stochastic Differential Equation Representation

Hybrid Networks

Representations

Deterministic and Probabilistic Boolean Networks

Petri Networks

Bayesian Networks

The EGFR model

Kholodeko's Model

Oda's Model

Systems Structural and Dynamic Properties Investigation in Systems Biology

Connectivity

Cohesive Subgroups

N-Clicque

K-Plex

K-Core

λ-sets

Radius of a Graph

Jacobian

Elasticity and Plasticity

Sensitivity

Eigenvalues

Stability

Oscillations

Systems Identification Theory in Systems Biology

General Framework for System Identification Experiments

Transfer Function Identification

Spectral Identification

State Space Models Identification

Box-Jenkins and Derived Models

AR/ARX Models

ARMA/ARMAX Models

I/O Error

ARAR/ARXAR

NARMA

Model Sets, Model Structures and Identifiability

Asymptotic Distribution of Parameter Estimates in Fitness Function Design

Prediction Error

Final Prediction Error
Akaike Information Criterion
Minimum Description Length

Asymptotic Variance

Frequency Domani Expression of the Asymptotic Variance

Algorithms for System Identification

Prediction Error Minimization

Linear Regressions, Least Squares Method and Maximum Likelihood Method

Heuristic Approaches in System Identification

Genetic Algorithms
Pattern Search Methods
Hybrid Algorithms

Characterizing Spectral Properties for Optimal Experimental Design in Systems Biology

Fisher Information Matrix

Cramer-Rao Inequality and Cramer-Rao Bound

A, D, E, L Optimality Methods

Specific pathway properties elicitation via time varying driving inputs

Informative Dataset

Convergence and Consistency

Covariance Matrix and Identifiability

Persistence of excitation

Experimental Design

Open loop identification

Closed loop identification

Algorithms for System Identification

Developing and Constraining Input Signals

Micropumps and Micropumping Systems

Technological Constraints to Systems Perturbations in Bioreactors

Microfluidics Systems for Cell Stimulation

Model Simulations in Integrated Environments

Systems Biology Toolbox (MATLAB)

SimBio Toolbox (MATLAB)

Potterswheel Toolbox (MATLAB)

Systems Biology Workbench

Jarnac

Jacobian Viewer

Structural Analysis GUI

Bifurcation Discovery

Oscill8

Microfluidics and Optoelectronics for System Identification in Systems Biology

Theoretical Introduction to Microfluidics and Optoelectronics

Fluids and Mechanical Equilibrium

Hydraulic Resistance

Diffusion

Micropumps and Micro-pumping Systems

Opto-spectroscopy

Developing Application Specific Microfluidics Chips: Modules and Systems

Modulating Signals in Microfluidics Channels

Droplet based Approaches

Controllig Diffusion Phenomena

T-Shape Micromixer
Magnetically Driven Micro-Mixing
Ferrofluid Based Mixing

Physical Phenomena based Signal Modulation: Controlling Flow and Instability

Proportional Flow Controller
Rayleigh-Taylor Instability
Kelvin-Helmholtz Instability
von Karman Vortex Streets

Evaluating Bio-Compatibility of Optofluidic Devices

Integrating Microfluidics and Optoelectronics towards Optofluidics: Labrys

Labrys web page on OWW

Design Principles

Fluid Dynamics Simulations

Implementation Details and PDMS Technology

Numerical Simulations

Model Discrimination via Constrained/Time-Varying Input Stimuli: a Conceptual Framework with Applications

Conclusions