- Oct 22
- Second set is assigned, and due November 3.
- Oct 8
- First problem set is assigned, due Oct 22 at the start of class.
- Sept 29
- First lecture for ChE/BE 163.
- Sept 16
- Lecture 1 reading for ChE/BE 163 is posted. Please make sure to do
the reading BEFORE class.
Professor Frances H. Arnold
228 Spalding Lab, x4162
Office hours: TBD
Professor Niles Pierce
165 Broad, x8086
Rusty Lewis (Directed Evolution)
335 Spalding Lab, x4664
Office hours: Wednesday 4-5:30pm Spalding 335 (102 for large groups)
Mark Fornace (Rational Design)
173 Broad, x8844
Cell: 301 641 1890
Office hours: Wednesday 4-5:30pm Spalding 102
The course introduces rational design and evolutionary methods for
engineering functional protein and nucleic acid systems. Rational
design topics include molecular modeling, positive and negative design
paradigms, simulation and optimization of equilibrium and kinetic
properties, design of catalysts, sensors, motors, and circuits.
Evolutionary design topics include evolutionary mechanisms and
tradeoffs, fitness landscapes, directed evolution of proteins, and
metabolic pathways. Some assignments require programming (MATLAB or
You can download
the syllabus here.
60% problem sets, quizzes, and reading
40% final project
Lecture attendance and required readings are mandatory for this course
- Lecture 1 - September 29 - Arnold
- Lecture 2 - October 1 - Pierce
- Lecture 3 - October 6 - Pierce
- Lecture 4 - October 8 - Pierce
- Lecture 5 - October 13 - Pierce
- Lecture 6 - October 15 - Pierce
- Lecture 7 - October 20 - Arnold
- Lecture 8 - October 22 - Arnold
- Lecture 9 - October 27 - Arnold
- Lecture 10 - October 29 - Arnold
- Lecture 11 - November 3 - Pierce
- Lecture 12 - November 5 - Pierce
- Lecture 13 - November 10 - Pierce
- Lecture 14 - November 12 - Pierce
- Lecture 15 - November 17 - Arnold
- Lecture 16 - November 19 - Tirrell
- Lecture 17 - November 24 - Arnold
- Lecture 18 - December 1 - Arnold
- Lecture 19 - December 3 - TBD
- PS1: October 8 - October 22 (rational design).
- PS2: October 22 - November 3 (directed evolution).
- Pre-proposal due Tuesday, November 10
- Suggested reading for coming up with project ideas
- PS3: November 10 - November 24 (rational design).
- PS4: November 24 - Thursday December 3 (directed evolution).
- Final proposal due Friday, December 11.
assignments are due at 1pm on the stated dates (i.e. before class
starts). Work can be turned in to the appropriate TA up to three days
late, with a 10% deduction taken per day (e.g., for a problem set that
is two days late, the maximum score will be 80%). Each student is also
permitted a total of four late days (no deduction) to be allocated
across the four problem sets as the student sees fit. These late days
provide flexibility to deal with other course deadlines,
extracurricular activities, off-campus interviews, etc.
Final Project Instructions
A pre-proposal outlining a research project
inspired by material presented in the course
2 pages total (including figures and
NIH guidelines (0.5 inch margins, 11pt
We should be able to assess the main idea, direction, and feasibility of
your ideas from the pre-proposal. The pre-proposal is meant to
help use give you guidance as you prepare your final proposal.
A research proposal inspired by material
presented in the course
5 pages total (including figures and
NIH guidelines (0.5 inch margins, 11pt
handout for more guideline information
- Specific Aims (brief unreferenced overview of
motivation and goals followed by 2 or 3 bulleted specific aims)
- Significance (explain the importance of the
problem, barrier, or concept that the project will address)
- Innovation (describe the novelty of the proposed
- Approach (describe the research plan for each
Specific Aim, address potential problems and alternative strategies)
Unless otherwise noted on a particular problem set, you may discuss
assignments with other students. The work, however, should be
substantially your own. It is a violation of the Honor Code to copy
solutions from classmates or to use course materials from previous