PHYS 429 A: Biophysics

Welcome to PHYS 429. My name is Armita Nourmohammad (pronouns she/her), and I will be your instructor. 

In this class everyone is welcome, regardless of other identities you hold in addition to that of physics student.  I expect everyone in this class to treat each other with respect.

Overview

The advent of high-throughput techniques is transforming biology into a fully quantitative and theory-rich science. For example, recent advancements in genetic sequencing has opened new avenues to study cellular processes at short time scales at the level of individual organisms, and on longer evolutionary time scales at the level of species and populations. Statistical physics is the right language to describe complex biological systems with many degrees of freedom, and is being used to uncover principles of molecular motions, protein folding, evolution of populations, or to interpret biological data. The main focus of this course is to explore how physics can shed light on complex biological processes. By highlighting examples from a broad range of biological phenomena, the course will cover topics on biological numeracy and estimation, principles of gene regulation, cellular processes, and evolutionary dynamics. Through a few programming bootcamps, students will familiarize themselves with analysis and probabilistic treatment of biological data,  and  will numerically investigate complex questions for which arriving at an exact analytical solution may be difficult. Inspired by these topics, students will work in groups on small projects and will present their work at the end of the quarter.

Getting started

• The class will be hybrid, with lectures broadcasted over panopto or zoom.
• Slack will be the primary space where you can communicate with your TA and the rest of the class. To get started with this space, please:
  
  • Use your UW email to join our Slack workspace with this link.
  • Get Slack running on your device. Here are useful tips and features for using Slack. I highly recommend downloading the mobile or desktop app, and turning notifications on so that you don't miss messages.

Lecture Materials and Assignments

• Go to the Modules tab (on the left) and review each week's notes and recorded videos on the week's material.
• Each week's assignments and the suggested reading can be found in the week's Module
• Textbooks:
  • required:
    • Physical Biology of the Cell (PBoC); R. Philips et al. 2nd ed, ISBN-10: 9780815344506
      since the book is currently unavailable at the University bookstore, you can access the electronic copy of the book here.
      

• • recommended:
    • Street fighting mathematics; S. Mahajan, ISBN: 9780262514293
    • Cell biology by numbers; R. Milo, et al. download link

Lectures and Office Hours

• Lectures take place at PAA A110 on Tuesdays and Thursdays at 11:30 am - 12:50 pm, or on zoom. The link to video recordings can be accessed through modules (on the left).
  • The direct link to the lecture zoom meetings: https://washington.zoom.us/j/96540286183
  • Recorded lectures can be accessed under the "cloud recording" in the canvas zoom page or through the module page.
• Office hours (on zoom):
  • Prof. Nourmohammad: Tuesdays 1:00 - 2:00 pm, zoom link: https://washington.zoom.us/j/96540286183
  • TA Zachary Montague: Thursdays 1:00 - 2:00 pm, zoom link: https://washington.zoom.us/j/94894109076
  • TA Eli Lilleskov:  Fridays 2:30 - 3:30 pm, zoom link: https://washington.zoom.us/j/99286031266
    
    

Credits

To get credits in this class it is expected that you:

• hand in the homework assignments (40%)
• participate in class discussions (20%)
• final project essay and presentation (40%)
  
  

Protocols for in-person attendance:

• If you are symptomatic with COVID, flu, or another illness, please do not attend in person.  Lectures will be available as zoom recordings.
• If you arrive early, please fill to the center of the rows to reduce the need for others to climb over you. Please wait for the previous class to exit rather than crowd the entrances.
• It is highly recommended you join the Husky Coronavirus Testing program and sign up for WANotify if you have not done so already.  If you test positive for COVID or are in close contact with someone who does, notify covidehc@uw.edu.  Please get a Vaccine Booster (3rd shot) as soon as you are eligible.
  
  

Rules and Courtesies for remote classes:

• If we are remote, please use the "Raise Hand" feature in Zoom and wait until you are called on to ask a question.  You may also use the "Chat" feature in Zoom to ask a question.
• Please remain Muted unless you are expressly asking or answering a question designed to be heard by the entire class.
• Please be understanding of connectivity issues - should the speaker's internet go out during class, please stand by for 10 minutes before logging out.
• You may not share video or audio of this class.

FERPA, Zoom, and Privacy

When class is remote, class will be held via Zoom. These Zoom class sessions will be recorded. The recording will capture the presenter’s audio, video and computer screen. Student audio and video will be recorded if they share their computer audio and video during the recorded session.

When class is in person, class will be recorded via Panopto.  The recording will capture the projector feed, room microphone audio, and a video of the room taken from the projector booth.  The back of students' heads are visible; audio is typically not well recorded unless someone speaks directly into the microphone.  If you do not wish to appear on the video, sit near the back on the sides of the room.

In both cases, the recordings will only be accessible to students enrolled in the course.  These recordings will not be shared with or accessible to the public.

The University and Zoom have FERPA-compliant agreements in place to protect the security and privacy of UW Zoom accounts.

Students who do not wish to be recorded when class is on Zoom should:

• Change their Zoom screen name to hide any personal identifying information like their name or UW Net ID
• Not share their computer audio or video during their Zoom sessions
  
  

Access and accommodation

Your experience in this class is important to me, so if you have a temporary health condition or permanent disability that requires accommodations (conditions include but are not limited to: mental health, attention-related, learning, vision, hearing, physical), please contact DRS to arrange accommodations.

Safe campus

I am committed to ensuring a safe environment on campus.  I encourage you to check out the resources available here.

Religious Accommodations

Washington state law requires that UW develop a policy for accommodation of student absences or significant hardship due to reasons of faith or conscience, or for organized religious activities. The UW’s policy, including more information about how to request an accommodation, is available at Religious Accommodations Policy (https://registrar.washington.edu/staffandfaculty/religious-accommodations-policy/). Accommodations must be requested within the first two weeks of this course using the Religious Accommodations Request form (https://registrar.washington.edu/students/religious-accommodations-request/).

Academic integrity and student conduct

The University takes academic integrity and student conduct very seriously.  Behaving with integrity and respect is part of our responsibility to our shared learning community.  Acts of academic misconduct may include, but are not limited to, cheating by working with others or sharing answers on exams.

Please note that screenshots or recordings of instructors, other students, and course materials during active video (Zoom) participation sessions are strictly forbidden.  Streaming or posting inappropriate materials on any course platform is also not allowed. 

All the course materials including lecture notes, lecture videos are intellectual properties of the instructor and the University of Washington. Distributing them in any form without permission is forbidden.  

The University of Washington Student Conduct Code (WAC 478-121) defines prohibited academic and behavioral conduct and describes how the University holds students accountable as they pursue their academic goals.  Allegations of misconduct by students may be referred to the appropriate campus office for investigation and resolution.  More information can be found online at https://www.washington.edu/studentconduct/.

If you’re uncertain about if something is academic or behavioral misconduct, ask me.  I am willing to discuss questions you might have.

Course Summary*:

* a more detailed information on the material, notes, and the recordings can be found at the linked pages.