Course syllabus

Course-PM

TIF315 / FYM315 TIF315 / FYM315 Biological and biotechnical physics lp3 VT24 (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) 

HJ: Hana Jungová (hana.jungova@chalmers.se)

SS: Sviatlana Shashkova (sviatlana.shashkova@physics.gu.se) 

Lab and project assistants

JA: Julia Andersson (julia.andersson@chalmers.se)

SN: Simon Niederkofler (simon.niederkofler@chalmers.se)

Course purpose

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

An important aspect of the course is to utilize the tools and knowledge you have from before in thermodynamics as well as statistical and soft matter physics, although a background in chemistry, biochemistry, physical chemistry is also sufficient to follow and appreciate the course. Accordingly, the theory part focuses on i) the molecules that are the functional building blocks of living organisms, ii) physical and physicochemical 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) photosynthesis, respiration and biological electricity. Using these basic biophysical concepts, the course is using viruses in general and SARS-CoV-2 in particular as a pedagogic tool to convey biophysical insights. The course also addresses how our senses function, including sight, hearing, taste, smell and touch, including how these principles relate to man-made bioanalytical sensors utilized in medical diagnostics and drug discovery.

An important aim with the experimental part of the course 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 life science. The main experimental techniques that will be used are fluorescence microscopy, optical (UV-VIS) and 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.

Schedule

TimeEdit

Date	Time	Place (prel)	Topic	Lecturer
Tue 16/1	13:15 – 15:00	FL52	Course Introduction and Overview of labs and projects 1. Photosynthesis and Respiration1,2 Ch 18	FH
Thu 18/1	13.15 - 15.00	FL51	2. The facts of life & biological molecules3.4 Ch 1-3	FH
Thu 18/1	15:15 – 17:00	FL51	3. Life at rest (thermodynamic equilibrium in biology)6 Ch 4-65	FH
Fri 19/1	13:15 – 15:00	FT4011	4. Introduction to the Protein Databank:5 www.rcsb.org	FH
Fri 20/1	DEADLINE Lab registration	In Canvas, People
Tue 23/1	13.15 - 17:00	F7309	LAB	SN, JA
Thu 25/1	13:15 - 17:00	F7309	LAB	SN, JA
Fri 26/1	08:00 – 11:45	F7309	LAB	SN/JA
Fri 26/1	13:15 - 17:00	F7309	LAB	SN, JA
Tue 30/1	13:15 - 15:00	FL52	5. The living cell	SS
Thu 1/2	13:15 – 15:00	FL51	6. Entropy rules and Random walk in biology Ch 6-8	DM
Thu 1/2	15:15 – 17:00	FL51	7. Life at rest / two state systems Ch 6-7 and Intro to projects	FH/SS
Fri 2/2	13:15 – 15:00	FL52	8. Optical microscopy7 in biophysics	HJ
Wed  7/2	DEADLINE homework 1	Mail to FH
Wed 7/2	DEADLINE Project registration	In Canvas, People
Thu 8/2	13:15 – 15:00	FL52	Midterm oral group exam/lecture	FH & DM
Thu 8/2	15:00 – 17:15	FL52	Midterm oral group exam/lecture	FH & DM
Fri 9/2	13:15 – 15:00	FL52	9. Biophysics of the immune system	SS
Tue 13/2	13:15 – 15:00	FL52	10. Biophysics of the cell membrane, COVID-19 infection.	FH
Fri 16/2	13:15 – 15:00	FL52	11. Vaccine development.9**	FH
Tue 20/2	13:15 - 15:00	FL52	12. The biophysics of our senses: vision, smell and taste**	FH
Thu 22/2	13:15 - 15:00	FL52	13. The biophysics of our senses: hearing8**	DM
Fri 23/2	14:00-15:00	FL52	14. Help with home work tasks	FH
Mon 26/2	DEADLINE homework 2	Mail to FH
Tue 27/2	13:15-15:00	FL52	15. Biophysics in Pharma / Home work solutions	FH
Thu 29/2	13:15-17:00	FL73	Group lectures/questions on projects	FH
Tue 5/3	13:15-15:00	FL52	Project Presentations	FH, DM, EO, JA and NG
TBA		TBA	Individual oral exam (1h times #students)	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 (Links to an external site.)

2) Photosynthesis: https://www.bbc.co.uk/programmes/b0435jyv (Links to an external site.)

3) Enzymes: https://www.bbc.co.uk/programmes/b08rp369 (Links to an external site.)

4) The Cell: https://www.bbc.co.uk/programmes/b01mk8vh (Links to an external site.)

5) Evolution of proteins, viruses and life..: Lex Fridman Podcast #153 (Links to an external site.)

6) Kinetic Theory: https://www.bbc.co.uk/programmes/m00057s5 (Links to an external site.)

7) The Microscope: https://www.bbc.co.uk/programmes/b03jdy3p (Links to an external site.)

8) Echolocation: https://www.bbc.co.uk/programmes/b0b6hrl3 (Links to an external site.)

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 is one homework (homework 1) exercise 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 more 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 homework (homework 2) based on the theoretical part of this module (see schedule for dead-lines), 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).

Home work

The course consists of 2 homework tasks (found in Canvas under Files) to be submitted individually at specific deadlines, as noted in course schedule. Submit your assignments to fredrik.hook@chalmers.se in an e-mail with TIF315 in the heading. The homework is graded and will count for 1/3 of the final grade.

Homework 1 (see Files):

To be uploaded

Homework 2 (see Files):

To be uploaded

Laboratory exercises

The course contains two compulsory labs (Lab-PM found under Files):

LAB 1: Nanoparticle characterization, Supervisor: Simon Niederkofler: simon.niederkofler@chalmers.se

LAB 2: The Spectral Characterization of Myoglobin, Supervisor: Julia Andersson: julia.andersson@chalmers.se 

To register for the labs use Lab groups in Canvas (see People), for deadline see schedule. 

You will 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. 

Deadline to hand in the lab-report to the supervisor with CC to FH: One week after your lab session. The report gets pass or fail, with 3 chances for submission.

Project work

In teams of 3-4 students you will pick a lab project that will run in 3 half-day sessions. The different projects will be presented in the lecture on 2/2. To register for the project use Project groups in Canvas (see People). Deadline registration, see schedule. 

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 supervisor, use TIF315 in subject line), ii) submit a project report (send e-mail to project supervisor, 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 dates).

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

Changes made since the last occasion

Changes made after the course start are marked in yellow in the course syllabus and added as announcements.

Learning objectives and syllabus

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 (>80% presence) 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, Project 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	See schedule
H2	Homework 2	This is an individual homework with tasks that summarizes the remaining chapters of the book covered by the lectures.	Grade 3: >40% Grade 4: >60% Grade 5: >80%  Teacher feedback	See schedule
O1	Oral mid-term 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	See schedule
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	See above
R2	Written project report:	Written group report for the project. Instructions are handed out by the project assistants.	Graded 3, 4 or 5	See above
O2	Oral presentation of project	Oral 15 – 20 min group presentation of the project work	Graded: 3, 4 or 5	See schedule
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.