Course syllabus

Course-PM

TIF315 /  FYM315 Biological and biotechnical physics lp3 VT21 (7.5 hp)

Course is offered by the department of Physics

Contact details

Examiner

FH: Fredrik Höök (fredrik.hook@chalmers.se) 

Teachers:

FH: Fredrik Höök (fredrik.hook@chalmers.se) 

DM: Daniel Midtvedt (dmidtvedt@gmail.com) 

EO: Erik Olsén (olsene@chalmers.se)

Lab and project assistants

EO: Erik Olsén (olsene@chalmers.se)

MS: Mattias Sjöberg (mattias.sjoberg@chalmers.se)

SM: Sara Mohammadi (mohsara@student.chalmers.se)

AG: Adrian Gonzalez Rodriguez (adrian.gonzalez@chalmers.se)

Course purpose

The course is aimed at providing the basic theoretical tools and a basic understanding of central concepts in biological and biotechnical physics. It will also provide an enhanced capability of planning, conducting, analyzing and presenting experimental work with focus on medical diagnostics and drug development.

An important aspect of the course is to utilize the tools and knowledge you have from before in thermodynamics as well as statistical, solid state and soft matter physics (or chemistry, biochemistry, physical chemistry if your background is not physics). Accordingly, the theory part focuses on i) the molecules that are the functional building blocks of living organisms, ii) physical models and principles to describe life processes iii) intermolecular interactions in chemical (non)equilibrium in the living cell, iv) random walks and dynamical molecular machines, v) biological membranes and transport into and out of cells, vi) biological electricity and photosynthesis. Using these basic biophysical concepts, the course is using viruses in general and SARS-CoV-2 as a pedagogic tool to convey biophysical insights. The course also addresses how our senses function, such as sight, hearing, smell etc, and how these relate to man-made sensors utilized in biotechnological applications.

An important aim with the experimental part is that you will get training of working in a wet-chemistry biological laboratory with biological molecules and solvents.* Accordingly, the experimental part of the course consists of i) an introductory experimental part in which you get used to handling buffers and biomolecules in a wet-chemistry laboratory and ii) a larger project focusing on some of the fundamental concepts in the course, such the physical base for the intermolecular interactions that are utilized in e.g. medical diagnostics and how bioanalytical tools and different optical imaging systems are used in biotechnology and diagnostics. The main experimental techniques that will be used are fluorescence microscopy, optical (UV-VIS), fluorescence spectroscopy and surface-sensitive tools such as the quartz crystal microbalance and surface plasmon resonance. You will also gain experience in planning and performing biophysical experiments from the beginning to the end and to analyze and present the results in a written report and in an oral seminar.

*) Due to covid restrictions, the laboratory sessions will most likely be modified for 2021, and partly compensated with theoretical projects. Detailed instructions will follow.

Schedule

TimeEdit (Links to an external site.)

Date	Time	Place	Topic	Lecturer
Tue 19/1	15:15 - 17:00	zoom	Course Introduction and Overview of labs and projects	Fredrik Höök (FH)
			Photosynthesis and Respiration1,2 Ch 18	FH
Thu 21/1	13:15 - 15:00	zoom	The facts of life & biological molecules3.4 Ch 1-3	FH
Thu 21/1	15:15 - 17:00	zoom	Introduction to the Protein Databank:5 www.rcsb.org (Links to an external site.)	FH
Mon 25/1	DEADLINE Lab registration	In Canvas, People
Tue 26/1	13:15 - 15:00	zoom	Life at rest (thermodynamic equilibrium in biology)6 Ch 4-55	FH
Thu 28/1	13:15 - 15:00	zoom	Surface Sensitive techniques & Modern techniques in biophysics	FH
Thu 28/1	15:15 - 17:00	zoom	Optical microscopy7 in biophysics & Introduction to the projects	EO, MS, DM, SM, AG & FH
Fri 29/1	13:15 – 15:00	zoom	Entropy rules and Random walk in biology Ch 6-8	Daniel Midtvedt (DM)
Tue 2/2	8:00 - 12:00	TBA	LAB
Thu 4/2	13:15 - 17:00	TBA	LAB
Fri 5/2	13:15 - 17:00	TBA	LAB
Wed  10/2	DEADLINE homework 1	Mail to FH
Tue 9/2	13:15 - 17:00	TBA	LAB
Mon 15/2	DEADLINE Project registration	In Canvas, People
Fri 12/2	13:15 - 15:00	zoom	Cell membranes and model membrane systems Ch 10-11	FH
Thu 16/2	13:15 - 15:00	zoom	Biophysics of the immune system and COVID-19 infection	FH
Tue 18/2	13:15 - 15:00	zoom	Midterm oral group exam	FH & DM
Tue 18/2	15:00 - 17:15	zoom	Midterm oral group exam	FH & DM
Tue 23/2	15:15 - 17:00	zoom	Biophysics of the immune system and COVID-19 infection cont.	FH
Thu 25/2	13:15 - 15:00	zoom	The biophysics of our senses: hearing8 and tactile sense**	DM
Fri 5/3	DEADLINE homework 2	Mail to FH
Tue 2/3	13:15 - 15:00	zoom	The biophysics of our senses: sight9,**	FH
Thu 4/3	13:15 - 15:00	zoom	The biophysics of our senses: smell and taste** and biophysics in pharma	FH and invited lecturer
Tue 9/3	13:15-17:00	zoom	group teaching	FH
Thu 11/3	13:15-17:00	zoom	Project Presentations	FH, DM, EO, SM and MS
TBA		zoom	Individual oral exam	FH & DM

Course literature

Physical Biology of the Cell, Rob Phillips, Jane Kondev, Julie Theriot and Hernan Garcia, Garland Science 2013.

**) Additional course literature: Handouts at lectures as well as references therein.

Interesting additional material available from BBC In Our Time on (see references in the schedule):

1) The photon: https://www.bbc.co.uk/programmes/b051vlpf

2) Photosynthesis: https://www.bbc.co.uk/programmes/b0435jyv

3) Enzymes: https://www.bbc.co.uk/programmes/b08rp369

4) The Cell: https://www.bbc.co.uk/programmes/b01mk8vh

5) Evolution of proteins, viruses and life..: Lex Fridman Podcast #153

6) Kinetic Theory: https://www.bbc.co.uk/programmes/m00057s5

7) The Microscope: https://www.bbc.co.uk/programmes/b03jdy3p

8) Echolocation: https://www.bbc.co.uk/programmes/b0b6hrl3

9) The Eye: https://www.bbc.co.uk/programmes/b03w2w19

Course design

The course is divided into two modules, each comprising lectures and experimental work of relevance for the respective module.

The first module is focused on theoretical models applicable to Biological and Biotechnical Physics, and how the experimental methods used in the laboratory exercises and projects relate to the theory part, including additional applications of biological physics. It also includes an experimental part consisting of basic experimental training (two half-day laboratory exercises), which are summarized in a written group report. There are two homework exercises assigned for this module (see schedule for dead-lines), which is closed with an oral exam carried out in groups of 3-4 students (see schedule).

The second module is focused on applied aspects of biophysics, with focus on a more challenging experimental project* on sensor technologies used in medical diagnostics and drug discovery to be run at three occasions in groups of 3-4 students. The lectures in this part includes invited lecturers from industry as well lectures on the function of our senses (hearing, sight, smell etc). There is one written group report (see schedule for dead-line) and one oral presentation (see schedule) based on the practical project assigned to this module. The course is closed with an individual oral exam (date TBA).

*) Due to covid-restrictions, this part might in part be replaced by guided theoretical projects. Detailed instructions will follow.

Home work

The course consists of 2 homework tasks to be submitted individually at specific deadlines, as noted in course calendar. Submit your assignments to fredrik.hook@chalmers.se in an e-mail with TIF315 in the heading.

Homework 1:

2.3, 2.4, 2.A*, 2.B*, 3.7, 3.8, 4.1, 4A*

*) Not from the course book,

Homework 2:

5.2, 6.4, 7.5, 8.10, 11.2, and Extra task on random walk*

*) Not from the course book,

Laboratory exercises (due to unknown covid-restrictions, this is preliminary plan)

Overview Labs

The course contains two compulsory labs:

LAB 1: Nanoparticle characterization, Supervisor: Mattias Sjöberg: mattias.sjoberg@chalmers.se

LAB 2: The Spectral Characterization of Myoglobin, Supervisor: Erik Olsén: olsene@chalmers.se

To register for the labs use Lab groups in Canvas (see People). Deadline 25/1.

Before your first lab session (LAB 1 or LAB2), you should watch the following movie about "Safe Handling of Chemicals": https://vimeo.com/84758383 (Links to an external site.). You will also have to do an individual pre-study for each Lab, to be handed in to the lab supervisor the day of the lab session (see lab manual for further information).

To get the lab approved you will need to submit a report (one report per person - report template handed out at the end of the lab session). Send e-mail to lab advisor and use TIF315 in heading. The report gets pass or fail, with 3 chances for submission.

Deadline to hand in the lab-report: One week after the lab session.

Project work (due to unknown covid-restrictions, this is a preliminary plan)

In teams of 3-4 students you will pick a lab project that will run in 3 half-day sessions. The different projects, adjusted to covid restrictions and the size of the class, will be presented in the lecture on 28/1. To register for the project use Project groups in Canvas (see People). Deadline 15/2.

To pass the course you need to i) submit a pre-study at least 2 days before your first half-day. This is an individual assignment (send e-mail to project advisor, use TIF315 in subject line), ii) submit a project report (send e-mail to project advisor, use TIF315 in subject line, deadline two days before final oral exam (TBA) and iii) present your project together with your group members (see course schedule). Each student in the project group is expected to participate in the oral presentation and to listen to other group presentations (see schedule for date(s)).

The projects are graded (participation, report and presentation) and will count for 1/3 of the final grade.

Changes made since the last occasion

A summary of changes made since the last occasion.

Learning objectives and syllabus

Learning objectives:

After taking this course you will be able to:

• Understand and use key vocabulary and physical concepts of relevance for biological systems, and be able to describe the basic physical aspects of biological molecules, such as for example DNA, RNA, proteins, enzymes, cell membranes, viruses and live cells.
• Be familiar with the protein databank and how it can be used to visualize and understand the function of biological molecules.
• Gain new insights about the structural complexity of live cells, exemplified using e.g. photosynthesis, the respiration chain, virus infections and the function of our senses (sight, hearing, smell…).
• Gain knowledge on how to plan and perform experiments in the subject, thereby gaining qualitative insights in some of the main concept of the course, with focus on optical imaging and surface-based bioanalytical sensing.
• Understand the importance of biological and biotechnical physics in medical diagnostics and drug discovery.

Link to the syllabus on Studieportalen (Links to an external site.) (for GU (Links to an external site.))

Examination form

To pass the course, you have to actively participate in the lectures and contribute to the discussions, participate in the laboratory exercises and the project work. You must also hand in sufficiently good lab and project reports, and pass the homework tasks (40% grade 3, 60% grade 4 and 80% grade 5). You must also participate in the project presentation and pass the group and individual oral exams. The Home work and oral exams will each count for 1/3 of the final grade.

A summary of the tasks and (preliminary) dead-lines are listed below, followed by a description of the grading of the course.

The communication with the teachers should be carried using e-mail, starting with TIF315 in the subject line.

 

	Tasks	Short Description	Grading	Due-date
H1	Homework 1	This is an individual homework with tasks that summarizes chapters 1 to 4 of the course book plus the protein databank and basic concepts with respect to the use of surface-sensitive techniques to probe reversible intermolecular interactions.	Grade 3: >40% Grade 4: >60% Grade 5: >80%  Teacher feedback	Wed  10/2
H2	Homework 2	This is an individual homework with tasks that summarizes chapters 5 to 8 of the course book	Grade 3: >40% Grade 4: >60% Grade 5: >80%  Teacher feedback	Fri, 5/3
O1	Oral group exam	30 to 45 minutes oral group presentation in which we go through the basic concepts that have been discussed in the course thus far.	Pass or fail   Teacher feedback	Thu, 18/2, zoom
R1	Laboratory reports	Written group reports for the two first laboratory exercises. Instructions are handed out by the lab assistants.	Pass or fail   Teacher feedback	TBA
R2	Written project report:	Written group report for the project. Instructions are handed out by the project assistants.	Graded 3, 4 or 5	TBA
O2	Oral presentation of project	Oral 15 – 20 min group presentation of the project work	Graded: 3, 4 or 5	Tue 9/3, zoom Thu 11/3, zoom
O3	Oral individual exam	Individual 30 min oral exam in which questions that relate both to the theoretical and experimental parts of the course are discussed.	Graded: 3, 4 or 5	TBA

Grading

Your grade will be formed from:

• grade on the individual homework tasks
• grade (for the group) on the project report and presentation
• grade on the individual oral exam

The grades on the homework and project sets the base for the level of difficulty on the oral exam, at which the final grade of the course will be decided.