SOFT MATTER AND BIOLOGICAL PHYSICS - 2017/8

Module code: PHY3040

Module provider

Physics

Module Leader

KEDDIE JL Prof (Physics)

Number of Credits

15

ECT Credits

15

Framework

FHEQ Level 6

JACs code

F900

Module cap (Maximum number of students)

N/A

Module Availability

Semester 1

Overall student workload

Independent Study Hours: 117

Lecture Hours: 33

Tutorial Hours: 5

Assessment pattern

Assessment type Unit of assessment Weighting
Coursework COURSEWORK ASSIGNMENT 30%
Examination END OF SEMESTER 1.5HR EXAMINATION 70%

Alternative Assessment

Alternative assessment: Examination and Coursework submitted during the Late Summer Assessment period.

Prerequisites / Co-requisites

None.

Module overview

The module will cover two closely related and rapidly growing fields of contemporary physics: soft matter and biological physics. Soft matter is the field of physics that concerns the structure and properties of substances in which weak molecular interactions, self-assembly, and thermal motion are all important characteristics. Examples of soft matter include polymers, colloids, gels and liquid crystals. Most soft matter is soft in the sense that it is either a liquid or an easily deformable solid. Living organisms, ranging from humans to bacteria, are largely composed of soft matter. For example, both DNA and proteins are polymers, and a living cell is a solid but is rather soft.  Weak interactions and self-assembly are characteristic of soft matter, and are found in many biological systems, such as cells and folded proteins.  This module introduces the linked subjects of soft matter and biological physics in a co-ordinated way.  There is emphasis on how the structure and interactions between molecules, such as DNA, control properties such as viscosity and elasticity. The module builds upon previous study of solid state physics (in which strong covalent bonds are dominant), thermodynamics and statistical physics.

Module aims

To describe and to classify the various types of intermolecular forces in soft condensed matter with emphasis on van der Waals' interactions.

To explain the relevance of time scales in soft matter and their relation to the glass transition and viscoelasticity.

To define colloids and to explain what determines their stability and shear response.

To define and classify polymers according to structure (e.g. copolymers, biopolymers) and properties (e.g. glasses and elastomers) and to describe their properties with emphasis on their mechanical response.

To show how principles of thermodynamics can explain self-assembly and ordering in soft matter systems.

To introduce some of the constituents of human bodies and show how soft matter physics explains how they function, including the transport of oxygen by both flow and diffusion.

To show how by consuming energy, molecular motors of order 10 nm across, can convert random diffusion into directional transport.

To show how a switch can be built from a set of dynamically interacting molecules, and to discuss how such switches are essential to the development of a body from a fertilised egg and how a malfunctioning switch can result in cancer.

To cover current topics in modern biological physics, such as statistical models of cancer and evolution.

Learning outcomes

Attributes Developed
Know the common distinguishing features of the main types of soft matter, e.g. liquid crystals, colloids, and polymers (glasses, elastomers, solutions, and melts), which separate soft matter from covalent solids studied at FHEQ Level 5 in Solid State Physics (PHY2068).  K
Apply advanced skills in problem-solving and creative thinking by using statistical physics to predict and explain phenomena such as the phase separation of liquids and the random walks of Brownian particles. P
Consolidate their skills in making order of magnitude estimates for relevant energies and length scales. ( T
Extend their analytical skills to encompass the use of dimensionless ratios, e.g., Peclet and Reynolds' numbers, in physics, at the level of diagnosing which quantities are needed to determine a ratio, and then critically evaluating it.  
Extend their knowledge of physics to living organisms as an example of complex machines made of soft matter. K
Develop critical skills in making order-of-magnitude estimates for the rates of processes inside cells. KT
Address the soft-matter constituents of cells, e.g., energy consumption of molecular motors by drawing on physics concepts. KT
Exercise judgement to determine what limits the laws of physics impose on how living organisms function, and to justify why genetic switches are essential in all cells. T
Present data analysis and logical arguments clearly and concisely in written format P
Extend their knowledge of thermodynamics obtained in the PHY2063 module to explain analytically the observed structures of soft matter (e.g. random coils, micelles, and lamellae) and the mechanisms of self-assembly. K

Attributes Developed

C - Cognitive/analytical

K - Subject knowledge

T - Transferable skills

P - Professional/Practical skills

Module content

Indicative content includes:

22 hours of lectures will introduce the fundamental concepts of soft matter and 11 hours of lectures will introduce biological physics.

Soft matter topics will include:

· Characteristics of soft matter; interaction potentials;

· Polar molecules; polarisability; van der Waals interactions;

· Cohesive energy; molecular crystals; response to mechanical stress;

· Time scales in soft matter; rheology; the glass transition

· Structure of glasses, liquids and liquid crystals

       · Colloids; Stokes’ drag force; Brownian diffusion; viscosity of colloids, shear thinning; Peclet number

· Van der Waals' interactions; Hamaker constant;

· Types of polymers (glassy, crystalline) and chain conformation of polymers;

· Phase separation in polymers (applying statistical physics); self-assembly of copolymers;

       · Rubber elasticity; reptation theory, polymer viscosity and diffusion.

Biological Physics topics will include:

· Demonstration that cells and living organisms are made of soft matter, and applications of physics concepts such as diffusion and flow to understanding how they function.

· A simple model of molecular motors;

· A simple model of a switch made from molecules, and applications of switches in cells;

       · Modern biological physics topics, including evolution.

Methods of Teaching / Learning

The learning and teaching strategy is designed to:



Inspire students to want to learn more about the subject by presenting videos, animations, photographs, and demonstrations of relevant phenomena and principles.


Engage students in discussions on the topic of soft matter and biological physics.


Guide student reading and independent study.


Develop problem-solving skills by showing worked examples and challenging students to attempt problem-solving on their own.


Apply knowledge and develop skills by completion of coursework assignments.



 

The learning and teaching methods include:



Lectures (three hours per week: two hours on soft matter physics and one hour on biological physics)


Tutorials (five one-hour tutorials in total, spread throughout the semester)


Coursework and problem sets that build on the material presented in lectures


Assessment Strategy

The assessment strategy is designed to provide students with the opportunity to demonstrate their knowledge of soft matter and biological physics, their ability to apply concepts, and their skills in problem-solving.

Thus, the summative assessment for this module consists of:


Coursework submitted in Week 9, weighted at 30%. It will consist of questions testing the student’s understanding of soft matter and biological physics, questions testing problem-solving skills (including estimating quantities from limited information), and questions testing the ability to interpret the predictions of simple models. Students will be assigned a unique set of questions to complete on their own.
1.5-hour examination at the end of the semester with two questions from three to be attempted, weighted at 70%.


Formative assessment

Problem sets are provided weekly on topics of soft matter and biological physics, which allow the students to test their understanding of course material.

 

Feedback

Verbal feedback is provided at hour-long tutorial sessions throughout the semester. Model solutions are provided for the questions on the problem sets to provide students with feedback on their problem-solving ability.

Reading list

Reading list for SOFT MATTER AND BIOLOGICAL PHYSICS : http://aspire.surrey.ac.uk/modules/phy3040

Please note that the information detailed within this record is accurate at the time of publishing and may be subject to change. This record contains information for the most up to date version of the programme / module for the 2017/8 academic year.