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CHNG5602: Cellular Biophysics [not offered in 2019] (2020 - Semester 1)

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Unit: CHNG5602: Cellular Biophysics [not offered in 2019] (6 CP)
Mode: Normal-Day
On Offer: Yes
Level: Postgraduate
Faculty/School: School of Chemical and Biomolecular Engineering
Unit Coordinator/s: Dr Chilcott, Terry
Session options: Semester 1
Versions for this Unit:
Campus: Camperdown/Darlington
Pre-Requisites: None.
Brief Handbook Description: Students will be given a good background in the physics of biological processes. Students will understand the differences between thermodynamically closed and open systems and its relevance to cells and other biological systems. Students will be provided with an introduction to the thermodynamics of irreversible and evolutionary processes of relevance to biology. Students will be introduced to the statistical mechanics of self assembly and equilibrium structures and its relevance to biology at the molecular level.
Assumed Knowledge: None.
Department Permission Department permission is required for enrollment in this session.
Lecturer/s: Professor Coster, Hans
Timetable: CHNG5602 Timetable
Time Commitment:
# Activity Name Hours per Week Sessions per Week Weeks per Semester
1 Lecture 4.00 2 13
2 Independent Study 5.00 13
T&L Activities: Independent Study: Library and Internet research

Attributes listed here represent the key course goals (see Course Map tab) designated for this unit. The list below describes how these attributes are developed through practice in the unit. See Learning Outcomes and Assessment tabs for details of how these attributes are assessed.

Attribute Development Method Attribute Developed
Demonstrations and practice in applying fundamental concepts in Biophysics to the design of processes in the field of biotechnology and related bioengineering areas. Sustainability, Safety & Risk (Core Chemical Engineering Part 4) (Level 5)
Research assignments in thermodynamics, temperature, cytoskeletons, and electrochemical cell and membrane processes Broad-Based Inquiry & Research (Level 5)

For explanation of attributes and levels see Engineering & IT Graduate Outcomes Table 2018.

Learning outcomes are the key abilities and knowledge that will be assessed in this unit. They are listed according to the course goal supported by each. See Assessment Tab for details how each outcome is assessed.

Sustainability, Safety & Risk (Core Chemical Engineering Part 4) (Level 5)
1. Analyse transport (mass transfer) in biological systems and the bioenergetics of such processes.
2. Analyse thermodynamically self-assembly processes, equilibrium/non-equilibrium states and active transport in living systems
3. Be able to deduce basic physical aspects of biological processes in different contexts.
4. Understand and appreciate the rapidly advancing new developments in molecular biology and biotechnology.
Assessment Methods:
# Name Group Weight Due Week Outcomes
1 Regular Assignment No 50.00 Multiple Weeks 1, 2, 3, 4,
2 Take home exam No 50.00 STUVAC (Week 14) 1, 2, 3, 4,
Assessment Description: Assignment: There are 4 assignments. These assignments are individual assignment submissions, hand written except for software programs, tables and graphs generated from software, e.g. spread sheets.

1. Assignment 1 will focus on the thermodynamics for a finite number of entities. This assignment is worth 10% of your overall assessment.

2. Assignment 2 will focus on the temperature of a finite number of entities. This assignment is worth 10% of your overall assessment.

3. Assignment 3 will focus on physicochemical characterisation of cytoskeletons. This assignment is worth 15% of your overall assessment.

4. Assignment 4 will focus on the electrochemical characterisation of cells and membrane potentials. This assignment is worth 15% of your overall assessment.

Take home exam: This will be an open-book exam. A student must get 40% in the final exam to pass the unit, regardless of the sum of his/her individual marks.

Take home exam: The take-home exam will be comprised of several questions covering the course work. Answers will be hand written except for software programs, tables and graphs generated from software, e.g. spread sheets. The exam is worth 40% of your overall assessment. A student must get 40% in the final exam to pass the unit, regardless of the sum of his/her individual marks.

There may be statistically defensible moderation when combining the marks from each component to ensure consistency of marking between markers, and alignment of final grades with unit outcomes.

Final assessment grade will be based on overall performance in assignments and exam as a whole.
Grading:
Grade Type Description
Standards Based Assessment Final grades in this unit are awarded at levels of HD for High Distinction, DI (previously D) for Distinction, CR for Credit, PS (previously P) for Pass and FA (previously F) for Fail as defined by University of Sydney Assessment Policy. Details of the Assessment Policy are available on the Policies website at http://sydney.edu.au/policies . Standards for grades in individual assessment tasks and the summative method for obtaining a final mark in the unit will be set out in a marking guide supplied by the unit coordinator.
Policies & Procedures: See the policies page of the faculty website at http://sydney.edu.au/engineering/student-policies/ for information regarding university policies and local provisions and procedures within the Faculty of Engineering and Information Technologies.
Prescribed Text/s: Note: Students are expected to have a personal copy of all books listed.

Note that the "Weeks" referred to in this Schedule are those of the official university semester calendar https://web.timetable.usyd.edu.au/calendar.jsp

Week Description
Week 1 Lecture/Tutorial: Introduction to cellular physiology, thermodynamics and functionality
Week 2 Lecture/Tutorial: Probability theory, disorder and entropy for a finite number of entities
Week 3 Lecture/Tutorial: Thermodynamic relationship between Entropy and Temperature
Week 4 Lecture/Tutorial: Thermodynamic relationships between Entropy, Work and Chemical mixtures
Week 5 Lecture/Tutorial: Maxwell identities, osmosis and application to red blood cells
Week 6 Lecture/Tutorial: Application of statistical mechanics to self-assembly of molecular structures
Week 7 Lecture/Tutorial: Molecular self-assembly of bilayers and proteins into bilayers
Week 8 Lecture/Tutorial: Electrostatic properties of charged molecules in cells and cell membranes (Dielectric exclusion and ion partitioning)
Week 9 Lecture/Tutorial: Drift and diffusion of ions in membrane systems (Donnan Equilibrium, Goldmann Katz Equation)
Week 10 Lecture/Tutorial: Action potential (Hodgkin and Huxley Equations)
Week 11 Lecture/Tutorial: Active transport (vectorial chemistry)and proton transporting ATP synthase protein (reversible molecular-engine)
Week 12 Lecture/Tutorial: Revision based on requests from students
Week 13 Take home exam
STUVAC (Week 14) Assessment Due: Take home exam

Course Relations

The following is a list of courses which have added this Unit to their structure.

Course Year(s) Offered
Chemical & Biomolecular 2018, 2019, 2020, 2015, 2016, 2017
Biomedical Engineering / Law 2013, 2014
Biomedical Engineering / Arts 2013, 2014
Biomedical Engineering / Commerce 2013, 2014
Biomedical Engineering / Medical Science 2013, 2014
Biomedical Engineering / Project Management 2013, 2014
Biomedical Engineering / Science 2013, 2014
Biomedical - Chemical and Biomolecular Major 2013, 2014, 2015
Biomedical - Electrical Major 2013, 2014
Biomedical - Information Technology Major 2013, 2014, 2015
Biomedical - Mechanical Major 2013, 2014, 2015
Biomedical - Mechatronics Major 2013, 2014, 2015
Chemical & Biomolecular (till 2014) 2010, 2011, 2012, 2013, 2014
Chemical & Biomolecular Engineering / Arts 2011, 2012, 2013, 2014
Chemical & Biomolecular Engineering / Commerce 2010, 2011, 2012, 2013, 2014
Chemical & Biomolecular Engineering / Medical Science 2011, 2012, 2013, 2014
Chemical & Biomolecular Engineering / Science 2011, 2012, 2013, 2014
Chemical & Biomolecular Engineering / Law 2012, 2013, 2014
Chemical & Biomolecular Engineering / Project Management 2012, 2013, 2014
Biomedical Mid-Year 2016, 2017, 2018, 2019, 2020
Biomedical/ Project Management 2019, 2020
Biomedical 2016, 2017, 2018, 2019, 2020
Biomedical / Arts 2015, 2016, 2017, 2018, 2019, 2020
Biomedical / Commerce 2015, 2016, 2017, 2018, 2019, 2020
Biomedical / Medical Science 2015, 2016, 2017
Biomedical / Music Studies 2016, 2017
Biomedical / Project Management 2015, 2016, 2017, 2018
Biomedical /Science 2015, 2016, 2017, 2018, 2019, 2020
Biomedical/Science (Health) 2018, 2019, 2020
Biomedical - Electrical Major 2015
Biomedical / Law 2015, 2016, 2017, 2018, 2019, 2020
Chemical & Biomolecular / Arts 2015, 2016, 2017
Chemical & Biomolecular / Commerce 2015
Chemical & Biomolecular / Medical Science 2015, 2016, 2017
Chemical & Biomolecular / Project Management 2015, 2016, 2017, 2018
Chemical & Biomolecular / Science 2015, 2016, 2017, 2018, 2019, 2020
Chemical & Biomolecular/Science (Health) 2018, 2019, 2020
Chemical & Biomolecular / Law 2015
Chemical & Biomolecular Mid-Year 2016, 2017, 2018, 2019, 2020
Chemical & Biomolecular/ Project Management 2019, 2020
Biomedical/Science (Medical Science Stream) 2018, 2019, 2020
Chemical & Biomolecular/Science (Medical Science Stream) 2018, 2019, 2020
Master of Engineering 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020
Master of Engineering (Biophysical Processes) 2012
Master of Engineering (Chemical and Biomolecular) 2012
Master of Professional Engineering (Accelerated) (Biomedical) 2019, 2020
Master of Professional Engineering (Accelerated) (Chemical & Biomolecular) 2019, 2020
Master of Professional Engineering (Biomedical) 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020
Master of Professional Engineering (Chemical & Biomolecular) 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020

Course Goals

This unit contributes to the achievement of the following course goals:

Attribute Practiced Assessed
Professional Communication (Level 5) No 0%
Creative Team Culture (Level 5) No 0%
Broad-Based Inquiry & Research (Level 5) Yes 0%
Solution Development and Testing (Level 5) No 0%
Problem Identification and Analysis (Level 5) No 0%
Sustainability, Safety & Risk (Core Chemical Engineering Part 4) (Level 5) Yes 100%

These goals are selected from Engineering & IT Graduate Outcomes Table 2018 which defines overall goals for courses where this unit is primarily offered. See Engineering & IT Graduate Outcomes Table 2018 for details of the attributes and levels to be developed in the course as a whole. Percentage figures alongside each course goal provide a rough indication of their relative weighting in assessment for this unit. Note that not all goals are necessarily part of assessment. Some may be more about practice activity. See Learning outcomes for details of what is assessed in relation to each goal and Assessment for details of how the outcome is assessed. See Attributes for details of practice provided for each goal.