Biological Thermodynamics
Spring 2009

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ENGR3699A: Biological Thermodynamics for Engineers

Course Overview

The beauty and depth of this subject cannot be described better than with the words of one of the greatest physicists of the 20th century, Arnold Sommerfeld, “Thermodynamics is a funny subject. The first time you go through it, you don’t understand it at all. The second time you go through it, you think you understand it, except for one or two points. The third time you go through it, you know you don’t understand it, but by that time you are so used to the subject, it doesn’t bother you anymore.” In this course we will venture into the depths of thermodynamics and statistical mechanics, while concentrating on applications of the abstract concepts to biological, biochemical, and biophysical phenomena and drawing from contemporary bioengineering problems. This course provides an introduction to the study of energy transformations in biological systems as well as thermodynamics and kinetics of structure formation and association of biomolecules. Topics covered include energy and its transformation, the First and Second Law of Thermodynamics, Gibbs Free Energy, statistical thermodynamics, binding equilibria and reaction kinetics, and a survey of other interesting areas of biological thermodynamics, particularly the origin of life on Earth. Topics have relevance to numerous pertinent biological/bioengineering applications including diseases based on phase transitions (e.g., cataract of the eye, Alzheimer’s disease, etc.), oxygenation of hemoglobin; protein folding, aggregation, and binding; assembly of everything from the phospholipids bilayer to biomaterials; the macroscopic mechanical properties of biomaterials and even cells; creation and operation of devices at the nano- and micro-scales; understanding the basis of mass transport; osmotic pressure relevant to cells and microvascular filtration; receptor-ligand binding; the melting and annealing of DNA. The concepts employed in this course have relevance to students interested in many disciplines, including Bioengineering, Material Science, and Chemistry.

Course Instructors: Yevgeniya V. Zastavker (Zhenya) and Alisha L. Sieminski (Alisha)
Office: Olin Center, Room 369 and Room 331
Phone: 781-292-2520 and 781-292-2553
Email: zhenya@olin.edu,   alisha.sieminski@olin.edu

Meeting Times: Tuesday, Friday 8:00 pm - 9:50 pm, AC417
Office Hours: Zhenya: TBA OC369
Alisha: by appointment, OC331

Source Material :

We will periodically have readings from Biological Thermodynamics by Donald T. Haynie. We recommend that you purchase this book; it is on reserve in the library.

We will also use primary literature, other texts on reserve, etc.

Course Objectives

  • Students should have gained a working knowledge of the basics of thermodynamics.
  • Students should have an appreciation for the use of thermodynamics in biology, chemistry, and bioengineering.
  • Students should be familiar with the basics of quantitative and qualitative approaches to examining and solving biological thermodynamics problems.

Assessment
We seek informal feedback at all times. In addition, we will distribute a more formal feedback form mid-way through the semester.

Time Commitment
This class meets for 4 hours per week. Attendance is required. Out of class reading, preparation, and research should take a well-prepared, focused student 8 hours per week. We will check in periodically to confirm that the workload is appropriate.

How To Do Well

  1. Attend classes. It is mandatory that you attend ALL classes: course lectures and project classes. Not only will this help you keep on track with the material and skills, but it will also help you learn. Absence from classes may affect your grade. Students must consult with all teaching faculty if they must be absent.
  2. Start your reading and assignments early. We cannot emphasize enough the importance of having enough time to think about the assigned exercise and "digest" the information necessary to solve the problem(s). Starting early will also give you enough time to get help if you encounter difficulties.
  3. Avoid memorization without understanding. As a team, we will be seeking a deep understanding of the material. Memorization of formulae will help you only when you do easy practice problems. The homework problems will challenge you to think, applying your knowledge from various topics. Project assignments will help you develop skills that you will find useful in later projects and courses.
  4. Come See US. Don't be shy! We're here to help you and in most cases nothing beats a face-to-face conversation in helping to clarify difficult issues.
  5. Read the books on reserve. Also, don't be afraid to look at other sources of information (i.e. a quick web search.) To grasp the concepts, you are encouraged to read the materials several times and study the examples presented in the class.
  6. Don't work alone. This is the greatest mistake. People think in different ways: what might be unclear in the classroom can become very easy after your friend explains it to you. Working on assignments together will also help you see how different people approach their tasks differently. You will learn better and faster if you learn in a team-like environment. Remember that you don't know the material until you are able to explain it to your friends.
  7. Strap your seat belts and have fun!!!

Honor Code
Please note that all of your work is subject to the Olin College Honor Code and any violation of this code could result in disciplinary measures from the College.

Disabilities
Students with disabilities who are taking this course and who need disability-related accommodations are encouraged to speak with me about their needs. Rod Crafts, Dean of Student Life, Alison Black and Nick Tatar, Assistant Deans for Student Life, are available to assist students in arranging these accommodations.

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