Tutorial: Simulating a random walk with NetLogo
The goal of this tutorial is to use the programmable modeling environment NetLogo to
simulate the random walk of a diffusing particle. You will be given a model (the name
for a p
Tutorial #2 - Correction
Tutorial: From Rosalind Franklins x-ray diffraction pattern to
the structure of DNA
1.1 In order to image an object, one needs to use radiations or particles with a
wavelength that is smaller than th
E. coli is a very common type of bacteria
It is a very small (~2 !m) unicellular organism.
Its directed motion can be fast (~25 !m/s).
Electron microscopy image of E.
At these scales:
1) Thermal energy becomes important.
Energy as a function of length scale
The amount of energy necessary to perform certain operations on a system
converges to the value of the thermal energy when we reach the nanometer
Not fortuitously, this scale is exactly that at which biomolecule
What makes a cell a cell?
What are the required elements in order to call yourself a cell?
Definition: An autonomous self-replicating unit that may exist as functional
independent unit of life (as in the case of unicellular organism), or as sub-unit
The medieval frame of mind
Medieval times were very stable from a scientific point of view. Church had a lot
influence on scientific views (and no vested interest in changing them).
Scholastic philosophy: A method of acquiring knowledge by dialectic
Part 2: Experiments
1.1 Light microscopy
1.1.1 The light microscope
This introduction to the functioning and alignment of a light microscope is greatly
inspired by the book Fundamentals of light microscopy and electron imaging by Douglas
Diatoms as a test of a microscope resolution
2.1.1 Objective 1: 0.45; Objective 2: 0.60; Objective 3: 1.30; Objective 4: 0.45
2.1.2 The numerical aperture is at best equal to the index of refraction of the immersion
medium. In principle using an oil objec
History of microscopy
~1000AD Invention of the first vision aid, a glass sphere called the reading stone
used as a magnifier.
Circa 1284 - Invention of the first eye glasses
1590 Zaccharias and Hans Janssen used multiple lenses placed in a t
Tutorial: How does the energy of a system depend on its
1. Electrostatic energy of a thin spherical shell of radius R
A sphere of radius R with surface charge creates an electrostatic potential at r > R:
1 4 R 2 R 2