CPS 296.2: Computational Biology and Biomolecular Computation


Professor John H. Reif

Rm. D223, L.S.R.C.

Office Phone: 660-6568

e-mail: reif@cs.duke.edu

Asst. to Dr. Reif

Denita Thomas, Rm. D211, L.S.R.C.
Office Phone: 660-6534

e-mail: denita@cs.duke.edu

Meeting Times:

Monday, Wends, Friday 1:10 pm-2:00pm during the Fall Term 2000 semester in room D243 of the Levine Science Research Center(LSRC Building).


Section A Introduction: to Biopolymer Structures

& Recombinant DNA Techniques

Section B Nanosystems: Atomic Force Microscope,

Molecular Probes, DNA NanoAssembly & Molecular Electronics

Section C: Introduction to DNA Computing

Section D: Surface Based Chemistry:

DNA Chips & Surface Based DNA Computation

Section E: Bioinformatics, Sequencing, and Tagging

This is a graduate level course without prerequisites.

Required Textbooks (at Duke Bookstore)

 Introduction to Computational Molecular Biology

Setubal and Meidanis ISBN: 0-534-95262-3

Introduction to Computational Biology,

Waterman ISBN: 0-412-99391-0


Assignments will be made available on-line from this site as the semester progresses.


There will be no Midterm or Final Exam


There will be due a project paper on a topic of your choice. Potential projects should be discussed with me before a final topic is chosen.

Class Lecture Notes

Some of the Class lecture notes are in PostScript and are on-line and those will be made available on-line from this site as the semester progresses. Hard copies of the other lecture note will also be made available.

Detailed Course Outline

Section A Introduction:

to Biopolymer Structure & Recombinant DNA Techniques

Lecture 1:Overview of Course Material

-DNA & Protein Structure

-Overview of Bioinformatics Topics

-Recombinant DNA Operations

-DNA Computation: Adeleman's Experiment

Lecture 2:Introduction to DNA structure

Lecture 3: Intro to Recombinant DNA Techniques, Part I: Cutting and Joining DNA Operations

Lecture 4: Intro to Recombinant DNA Techniques, Part II: Separation and Amplification Techniques

Lecture 5: Duke Laboratory on

Recombinant DNA Techniques

Lecture 6: Mathematical Models & Simulation Software for Recombinant DNA


-reaction models

-hybridization models

-error resiliency in word design

Lecture 7: Introduction to Protein Structure

Lecture 8: Molecular Simulation Algorithms & Software for Protein Structure Prediction

Lecture 9: Introduction to RNA Structure & Directed Evolutionary Techniques


Section B Nanosystems:

Lecture 10:Intro to DNA NanoAssembly

Lecture 11:DNA Comp. by Self-Assembly

-Tiling Theory

-Computations by Self-Assembly

Lecture 12: Mathematical Models and Software Simulations of DNA Self-Assembly

Lecture 13: DNA Self-Assembly Experiments

Lecture 14: Atomic Force Microscope Lab

-Duke Lab: Atomic Force Microscope

-Imaging of DNA NanoAssemblies

Lecture 15: DNA and Protein Motors


Section B Nanosystems, continued

Lecture 16:Carbon Nano-Tubes

structure & assembly

Lecture 17:Molecular Electronic Components Using Organic Compounds

Lecture 18: UNC Laboratory:

Molecular Force Feedback Systems & Molecular Probe Systems for Molecular Electronics


Section C: Introduction to DNA Computing

Lecture 18: Theoretical Models & Algorithms

in DNA Computing:

-Test Tube Models

-Splicing Models

-Associative Matching Models

Lecture 19: Experiments in DNA Computing

-details of Adelman's experiment

-Experiments based on

Primer Extension

-Whip-Lash DNA Computations


Section D: Surface Based Chemistry:

DNA Chips & Surface Based DNA Computation

Lecture 20:Intro to Surface Based Chemistry

Lecture 21:Intro to DNA Chips

& Applications

Lecture 22: DNA Computation Using

Surface Based Chemistry


Section E: Sequencing, Tagging, and Bioinformatics

Lecture 23:DNA Sequencing Techniques

-Traditional DNA Sequencing Techniques

-Sequence reconstruction by fragment


-Shotgun Sequencing Techniques

Lecture 24: DNA Tagging Techniques

Lecture 25: Databases for storage of

DNA Sequence Information

Lecture 26: Algorithms & Software for

DNA Sequence Alignment

Lecture 27: Statistical Processing of Sequence Information

Lecture 28:

Phylogenetic tree construction

-Phylogenetic tree construction

-Comparative analysis

-RNA evolution