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 Python).

You can download the syllabus here.


60% problem sets, quizzes, and reading
40% final project

Please note Lecture attendance and required readings are mandatory for this course

Course Reading

Problem Sets

Due dates

All 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

Pre-proposal Guidelines

Content: A pre-proposal outlining a research project inspired by material presented in the course
Length: 2 pages total (including figures and references)
Format: NIH guidelines (0.5 inch margins, 11pt Helvetica)
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.

Proposal Guidelines

Content: A research proposal inspired by material presented in the course
Length: 5 pages total (including figures and references)
Format: NIH guidelines (0.5 inch margins, 11pt Helvetica)
See this handout for more guideline information

Honor Code

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 years.