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 Mechanics for Fall 2022

Barring any changes due to a resurgence of COVID-19, this course will taught in person. The audio and slides of class sessions will be recorded and posted on Canvas, but the sessions will not be live-streamed. Accommodations will be made for those unable to attend classes because of COVID-19 or other unavoidable absences. Further details are provided in the sections below.

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: 9:00 - 10:00 AM (via Zoom)
  • Thursdays: 1:00 - 2:00 PM (in-person)
The instructor is also available by appointment. The best way to contact him is by e-mail.

Teaching Assistant:

Juli Kim,

Class Sessions

Monday, Wednesday, Friday: 9:40 - 10:30 AM, Room 203 Business Classroom Building
No classes on:
  • Monday, 5 Sept. (Labor Day)
  • Week of Monday, 10 October (Fall Break)
  • Friday, 25 Nov. (Thanksgiving Break)

Attendance and Excused Absences

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. The class sessions will be recorded, with only the audio and slides, and these recordings, along with the slides, will be posted on Canvas. But the recordings and slides should not be viewed as a substitute for attending class. They are intended primarily for review and for those who are unable to attend because of illness, family emergency or an official University of Utah activity.
If you need to seek an ADA accommodation to request an exception to this attendance policy due to a disability, please contact the Center for Disability and Access (CDA). CDA will work with us to determine what, if any, ADA accommodations are reasonable and appropriate.
To accomodate absences, the five lowest clicker scores will be dropped from the final average. If you must miss more than five classes because of illness, family emergency or an official University of Utah activity, please contact the instructor.

COVID-19 Precautions and Information

Given the current rates of COVID-19 infections in Utah, wearing a face mask in class is strongly encouraged. According to the CDC, wearing a mask remains an effective means of preventing infection for both unvaccinated and vaccinated people. Regardless of what someone chooses (mask or no mask), the university seeks to foster a sense of community and asks everyone on campus to be respectful of individual decisions on mask wearing.
Current university COVID information can be found at these sites:
  • General COVID-19 information and guidelines: https://coronavirus.utah.edu
  • On-campus vaccination information: https://alert.utah.edu/covid/vaccine/
  • COVID testing information: https://alert.utah.edu/covid-19-testing/
  • Self reporting forms: In order to help monitor the spread of COVID-19 and respond appropriately, the university requires that all students, faculty and staff complete a reporting form if they have been exposed to, are being tested for or have been diagnosed with COVID-19, using this form.
  • Exposure guidelines: If you have been exposed to COVID-19, you should read and follow these guidelines.

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 iClicker audience response system will be used to facilitate interactive learning during the class sessions. The responses will be graded and will count for 5% of the course grade. For some questions, credit will be given for any answer, but for others points will only be given for correct answers.
For each class session in which clickers are used, the scores will be normalized to a total of five points. The five lowest scores will be dropped when calculating the final average.
Although there is an iClicker app for mobile devices, it will not be supported in this class. (See the electronic device policy above.) You will thus need to purchase or rent one of the following two remote devices: The Campus Store will have the less-expensive iClicker+ available for sale for $44.99 and will buy back the device at the end of the term, though the amount to paid has not yet been determined. . Alternatively, the links above provide information for purchasing or renting the devices directly.
To use the device with this class, the following steps are required:
  1. If you do not already have an iClicker account, you will need to create one before classes begin, following the instructions at:
    How-to-Create-an-iClicker-Student-Account
  2. Register your iClicker remote device so that it is linked to your account:
    How-to-Register-an-iClicker-Remote
    Follow the instructions under the heading "My instructor is using iClicker Cloud"
  3. Add Biol 3550/3551 to your account, as described here:
    Add-Your-Instructor-s-Course-in-the-iClicker-Student-App
    The course should be listed with the title, ``Physical Principles in Biology'', and the course ID, ``Biol 3550/3551''.
  4. Use of the iClicker system requires a license. If your clicker was purchased new, it will come with a five-year license, and there will be no additional charges. If, however, you buy a second-hand clicker that was previously registered to another account, you will need to purchase a license. Similarly, rented clickers do not include a license.
    When you create a new iClicker account, you will receive a free two-week trial license. At the end of this period, however, you will need to purchase a license (if you don't already have one). A license for six months costs $15.99, and other pricing options are listed here:
    https://www.iclicker.com/pricing

Other ways to earn points

  • Group problem solving sessions. Every two weeks or so, part of the lecture time will be devoted to problem solving, with students working in groups of two or three. Points for these activities will be recorded and combined with those from the clicker responses.
  • Special homework assignments. There will be one or a few short homework assignments, in addition to the bigger ones described below. Points for these assignments will be added to the clicker points.
  • Catch out the prof! Extra clicker points will be given for finding errors in the lecture notes or the slides used class, with the number of points determined by the significance of the error (as judged by the instructor). To count for points, errors on the lecture slide have to be caught before the instructor catches them in class!

Discussion Sessions

There will be at least one scheduled discussion sessions per week, led by the teaching assistant and held via Zoom. These sessions will be devoted to working on problems, especially those that are on the quizzes and exams from previous years, which are posted on the web site and on Canvas. You should come to these sessions prepared to work on the problems, not merely to be told the answers!
The discussion sessions will be scheduled, based on polling of the class, during the first week of classes

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, 2 Sept.
  • Friday, 23 Sept.
  • Friday, 28 Oct.
  • Friday, 11 Nov.
  • Friday, 2 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, 7 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--10:00 AM, Tuesday, 13 December. This exam will cover everything covered in class.

Grades

The final numerical grade for the class will be based on the homework, quiz and exam scores, weighted as follows:
  • Clicker responses and other activities: 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 and practical skills in:
  • 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.

Important Dates

  • First day of classes: Monday, 22 August
  • Last day to add, drop (delete), elect CR/NC, or audit classes: Friday, 2 September
  • Last day to withdraw from classes: Friday, 21 October (No tuition refund, "W" appears on transcript.)
  • Last day to reverse CR/NC option: Friday, 2 December
  • Last day of classes: Thursday, 8 December
  • Final exam: Tuesday, 13 December, 8:00-10:00 AM

University Policies

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, in 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 the class, reasonable prior notice needs to be given to the Center for Disability and Access. CDA will work with you and the instructor to make arrangements for accommodations.

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.

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).

University Safety Statement

The University of Utah values the safety of all campus community members. To report suspicious activity or to request a courtesy escort, call campus police at 801-585-COPS (801-585-2677). You will receive important emergency alerts and safety messages regarding campus safety via text message. For more information regarding safety and to view available training resources, including helpful videos, visit safeu.utah.edu.

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.