Course Description (from the University Catalog)

Principles from physics and chemistry are explored in the context of biological processes, especially at the molecular and cellular level. Topics covered include random walks, thermodynamics, molecular recognition, dynamic processes, optics and spectroscopy. Quantitative treatments are emphasized and computer simulation and applications are used extensively.

Course Objectives

This course is designed to help students understand and appreciate the many connections between the physical and biological sciences, and also develop their skills in quantitative problem solving. Many of the most exciting scientific advances now taking place involve the application of principles from chemistry and physics to biological problems, and students who are broadly educated in the sciences will be especially well prepared to participate in these advances. At the end of the course, students will have explored several biophysical concepts in depth and will be able to apply these concepts to new situations, using appropriate quantitative and mathematical tools.

Instructor and Teaching Assistants

Instructor:

David P. Goldenberg
Office: 306 Aline Skaggs Biology Building
Telephone: (801) 581-3885
E-mail:

Office Hours

  • Tuesdays: 9:30 - 11:00 AM
  • Wednesdays: 2:30 - 3:30 PM
The instructor is also available by appointment. The best way to contact him is by e-mail.

Teaching Assistants:

Elom Amematsro

E-mail:

Henry Todd

E-mail:

Class Sessions

Monday, Wednesday, Friday: 9:40 - 10:30 AM
Room 2560 of the new Gardner Commons building.

No classes on: Monday, 4 Sept. (Labor Day), 9-13 October (Fall Break), Friday, 24 Nov. (Thanksgiving Break)

Regular class attendance is expected of all students. The class sessions will have a mixed lecture-discussion format, and engaged participation is essential for learning. Although notes and slides from many of the lectures will be posted on the class web site, these should not be viewed as a substitute for attending class.

Electronic Device Policy

In order to encourage student engagement and create a more effective learning environment for everyone, the use of cell phones, tablet computers or laptop computers will not be allowed during class. Cell phones may be accessed during class only in cases of emergencies. Exceptions to this policy will be made for students who need to use an electronic device as part of an approved accommodation. See the section below on Special Accommodations for information about applying for an accommodation through the Center for Disability Services.

Clickers

The TurningPoint audience response system will be used to facilitate interactive learning during the lectures. The responses will count for 5% of the course grade. Clickers can be purchased from the University Campus Store and can be sold back to the store at the end of the semester.

Any of the following TurningPoint clicker devices should work:
  • ResponseCard NXT
  • ResponseCard RF/LCD and RF
  • QT and QT2
Unfortunately, the Campus Store is only selling the more expensive QT2 model, but the less expensive ResponseCard models can readily be found online.

For this class, you do not need a TurningPoint Cloud account or license, and you should not try to register your clicker through the Turning Point Cloud service, though you may need to do this for other courses. Instead, you will need to register your clicker through an ``assignment'' on Canvas. Registering your clicker by the first lecture (Monday, 20 August) will count for 5 clicker points up front. Registering by the second lecture (Wednesday, 22 August) will count for 2 points.

Although there is a TurningPoint smart-phone app (ResponseWare), it will not be supported for this class. (See the electronic device policy above.)

Discussion Sessions

There will be two scheduled discussion sessions per week, each led by one of the TAs. These sessions will be devoted to working on problems, especially those that are on the quizzes and exams from previous years, which are posted here. You should come to these sessions prepared to work on the problems, not merely to be told the answers!

Text Book

There is no textbook for this course, but a set of detailed lecture notes is provided online here. These notes/text are very much a work in progress, and the chapters will likely be updated during the semester.

Homework Assignments

Problem solving is a major element of this class. Approximately 6 graded problem sets will be assigned during the course of the semester. Each problem set will be graded for a total score of 50 points. Problem sets may be turned in up to 5 days late, but 10 points will be deducted from the score for each day late.

Students are encouraged to work together on the homework assignments and to use outside resources, including the internet. However, the work you turn in must be your own! Any text, graphics or computer files must be clearly distinguishable from that of other students, and other sources must be properly cited. Text from other sources must be clearly identified by quotation marks. Furthermore, extensive quotations, even with proper citation, will not be considered satisfactory answers to questions. Copying and pasting does not demonstrate mastery of the material!

If two or more students turn in work that that is identical, their action will be considered academic misconduct and appropriate sanctions will be imposed. At a minimum, the sanction will include the loss of credit for the copied work, and more severe sanctions may be imposed for more extensive infractions. (See Academic Conduct, below)

Quizzes and Exams

Quizzes

There will be five 25-minute quizzes, given during the lecture sessions on the following dates:
  • Friday, 31 Aug.
  • Friday, 21 Sept.
  • Friday, 2 Nov.
  • Friday, 16 Nov.
  • Monday, 4 Dec.
Each quiz will cover the class material presented since the previous quiz (or mid-term exam). The lowest quiz score will be dropped in calculating the final grade.

Mid-term exam

There will be one mid-term exam, on Friday, 5 October. This exam will cover all of the material previously presented in class.

Final exam

A final exam will be given during the regularly-scheduled 2-hour exam period: 8:00 AM, Wednesday, 12 December. This exam will be cumulative, covering everything from the semester.

The schedule for quizzes and the mid-term exam is subject to change. The date of the final exam is not!

Grades

The final numerical grade for the class will be based on the homework, quiz and exam scores, weighted as follows:
  • Clicker responses: 5%
  • Homework: 30%
  • Quizzes: 30%
  • Mid-term exam: 15%
  • Final exam:20%
The following represent maximum cutoffs for determining class letter grades:
  • A: 92-100% (including A-)
  • B: 82-91% (including B- and B+)
  • C: 70-81% (including C- and C+)
  • D: 60-69%
  • E: < 60%
Depending on how things go, the grade cutoffs may be revised downwards, i.e. to make the grading more generous. The cutoffs will not be moved upwards to make the grading less generous.

Expected Learning Outcomes

What you learn from this class will depend greatly on your preparation and efforts. Students who are well prepared and who put a conscientious effort into all of the class components can expect to gain an appreciation for the connections among mathematics, the physical sciences and biology and should leave with a good understanding of:
  • Quantitative problem solving.
  • Probability and the nature of random processes.
  • Computer simulations of random processes.
  • Diffusion and its role in biological processes
  • Principles of thermodynamics and their applications in biology
  • Mechanisms of molecular motors and methods for studying them.

University Policies

Important Dates

  • First day of classes: Monday, 20 August
  • Last day to add classes, elect CR/NC or audit classes: Friday, 1 September
  • Last day to drop (delete) classes: Friday, 31 August (No tuition penalty; class does not appear on record.)
  • Last day to withdraw from classes: Friday, 19 October (No tuition refund, "W" appears on transcript.)
  • Last day to reverse CR/NC option: Friday 30 November
  • Last day of classes: Thursday, 6 December
  • Final exam: Wednesday, 12 December, 8:00 AM

Faculty and Student Responsibilities

All students are expected to maintain professional behavior in the classroom setting, according to the Student Code. Students have specific rights in the classroom as detailed in Section II of the Code. The Code also specifies expectations of student behavior (Section III). Students should read the Code carefully and know they are responsible for the content. According to Faculty Rules and Regulations, it is the faculty responsibility to enforce responsible classroom behaviors, beginning with verbal warnings and progressing to dismissal from class and a failing grade. Students have the right to appeal such action to the Student Behavior Committee.

Special Accommodations

The University of Utah seeks to provide equal access to its programs, services, and activities for people with disabilities. If you will need accommodations in this class, reasonable prior notice needs to be given to the Center for Disability Services, 162 Olpin Union Building, (801) 581-5020. CDS will work with you and the instructor to make arrangements for accommodations. All written information in this course can be made available in an alternative format with prior notification to the Center for Disability Services.

Title IX: Addressing Sexual Misconduct

Title IX makes it clear that violence and harassment based on sex and gender (which Includes sexual orientation and gender identity/expression) is a civil rights offense subject to the same kinds of accountability and the same kinds of support applied to offenses against other protected categories such as race, national origin, color, religion, age, status as a person with a disability, veteran's status or genetic information. If you or someone you know has been harassed or assaulted, you are encouraged to report it to the Title IX Coordinator in the Office of Equal Opportunity and Affirmative Action, 135 Park Building, 801-581-8365, or the Office of the Dean of Students, 270 Union Building, 801-581-7066. For support and confidential consultation, contact the Center for Student Wellness, 426 SSB, 801-581-7776. To report to the police, contact the Department of Public Safety, 801-585-2677(COPS).

Academic Conduct

In order to ensure that the highest standards of academic conduct are promoted and supported at the University, students must adhere to generally accepted standards of academic honesty. Acts of academic misconduct include cheating, plagiarizing, research misconduct, misrepresenting one's work, and inappropriately collaborating. Suspected cases of academic misconduct will be dealt with according to the rules found in the Student Code, University Policy 6-400(V) . Instances of academic misconduct will be recorded in a database that may be made available to other University of Utah Departments and Colleges.

Disclaimer

The information provided here and in the syllabus does not represent a binding legal contract. It may be modified by the instructor when students are given reasonable notice of the change.