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: 2:00 - 3:00 PM

Teaching Assistants:

Reid Bohanon

E-mail:
Office Hours -Thursdays: 11:00 AM to noon, Room 103, South Biology Building

Bibhash Neupane

E-mail:
Office Hours - Mondays: 2:00 - 3:00 PM, Room 103, South Biology Building

Office hours by appointment

The instructor and TAs are also happy to meet with you by appointment. The best way to contact any of them is by e-mail.

Class Sessions

Monday, Wednesday, Friday: 9:40 - 10:30 AM
Room 105, Building 73 (The old Law School 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. Some responses will be graded and 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.

Either the older NXT or newer QT/QT2 devices should work. For this class, you do not need a TurningPoint account or license, and you should not try to register your clicker for this course through the Turning Point Cloud service, though you may need to do this for other courses. You will need to register your clicker through an ``assignment'' on Canvas. If at all possible, please have your clicker registered by the first lecture.

Although there is a TurningPoint smart-phone app (ResponseWare) that can, in principle, be used instead of a clicker, my experience with it has not been good, and it will not be supported for this class.

Text book

There is no assigned textbook for this class. Readings and handouts will be posted on this web site.

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. Many of these will include computer exercises. The lowest homework score will be dropped in calculating final grades.

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, 1 Sept.
  • Friday, 22 Sept.
  • Friday, 3 Nov.
  • Friday, 17 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, 6 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, Tuesday, 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

Students completing this course will gain an appreciation for the connections among mathematics, the physical sciences and biology and enhanced 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, 21 August
  • Last day to add classes, elect CR/NC or audit classes: Friday, 1 September
  • Last day to drop (delete) classes: Friday, 1 September (No tuition penalty; class does not appear on record.)
  • Last day to withdraw from classes: Friday, 20 October (No tuition refund, "W" appears on transcript.)
  • Last day to reverse CR/NC option: Friday 1 December
  • Last day of classes: Thursday, 7 December
  • Final exam: Tuesday, 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 the student is given reasonable notice of the modification.