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Silicon Biology MAS.962

Fall 2001
Instructors
Professors Scott Manalis, Joseph Jacobson, and Shuguang Zhang

Fall 2001: MAS 962 Silicon Biology

Student Directory

Course Description

Class Schedule: Part I | Part II | Part III

Part I: Sensing

Instructor: Scott Manalis

Guest Lecturers: Juergen Fritz and Steffen Nock
Sept 6
Sept 13
Mechanical biosensors
- Cantilever design and deflection sensors
- Fundamental limits of force resolution
- Applications: forces (pulling on biomolecules), mass (cells), bimetallic (microcalorimetry and photospectroscopy), surface stress (nose and label free biosensor)
Sept 20 Field-Effect Sensors
- Semiconductor fundamentals
- Description of metal-oxide-semiconductor (MOS) devices and field-effect-transistors (FET)
- Single electron transistor and Coulomb blockade
- Applications
Sept 27

The Solid - Liquid Interface
- Liquid properties: buffers, conductivity, and the double layer
- Biochemical reactions: functionalization, kinetics, and detection
- Case study: DNA biochips

Oct 4
Surface Analysis and patterning
- Scanning probe microscopy
- Spectroscopic methods (electrons, XPS, UPS, Auger, and IR)
- Structuring surfaces (spotting, lithography, microcontact printing)
- Mass spectrometry, ellipsometry
Oct 11 Protein microarrays: Combining the world of materials science with protein biochemistry

Part II - Molecular Machines

Instructors: Joseph Jacobson and Shuguang Zhang

Guest Lecturers: Kim Hamad, Peter Carr
Oct 18 Nanochemistry: State of the art for synthetic systems. Synthetic Techniques for Creating Nanostructures. Molecular Electronics. Supermolecular Complexes.
Oct 25 New Understandings in Molecular Biology: Structure Function Relationships in Proteins and Peptides. Ab-initio design. RNAi. Inteins. Aptomers, Ribozymes. Self Assembly in Biology: cytoskelat, Viral Capsid. Amyloid. Hoogstein and Holliday Junctions.
Nov 1 BioAssemblers and Bio-Molecular Machines: Molecular Motors. BioMolecular Assembly Lines and Fabricators. Biomolecular Electronics. Molecular Control
Nov 8 The Genetic Switch: Transcriptional Translational Logic. Designing and Programming Cellular Computers
Nov 15 The Immune System: An Iterated Design System with Feedback. Combinatoric carbohydrates.
Nov 29 Strategies Against Disease: Putting it all together: AIDS as a test case for biomolecular computers.
Dec 6 Nueronal Logic: Constructing Logic Circuits from Neurons. Towards optimal design strategies for logic
Part III
Dec 11 Final Project