Module CHEM40715.: Soft Matter and Biological Physics

Department: Chemistry

CHEM40715.: Soft Matter and Biological Physics

Prerequisites

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Corequisites

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Excluded Combination of Modules

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Aims

• To introduce some of the key topics in the area of Biological Physics. Specifically biomolecular structure, self-assembly in biological systems, motility and molecular motors.
• To introduce some methods used to investigate biological systems including microrheology, single molecule experiments and advanced microscopy.
• To introduce the topic of soft condensed matter, including the topics polymer structure, dynamics and elasticity, liquid-liquid demixing and phase separation and self-assembly.

Content

• An overview of the building blocks of biology and the forces that dictate their interactions.
• The structure of biomacromolecules from random walk to protein crystal structures.
• An overview of soft matter and the length scales, time scales and forces that are relevant.
• Motility and diffusion in the low Reynolds number limit.
• Aggregating self-assembly in biology including virus assembly, cytoskeletal assembly and disease related assembly.
• Polymer structure, dynamics and elasticity.
• Polymer and block copolymer self-assembly.
• Phase transitions in soft condensed matter.
• Equilibrium phase diagrams and liquid-liquid demixing.
• The kinetics of phase separation.
• Proteins as molecular machines including enzymes and motors.
• Bulk biophysical techniques including static and dynamic scattering techniques and sedimentation.
• Single molecule techniques including AFM, TIRF and fluorescence.
• Advanced microscopy techniques.

Learning Outcomes

• Understanding of the structural features and their associated functional relationship for a range of biomolecules.
• Different examples of biological self-assembly/aggregation, and their disease implications.
• Theoretical and experimental understanding of polymer structure, dynamics and self-assembly in dilute and concentrated solutions.
• Thermodynamics and kinetics of selected examples of soft matter systems.
• Bulk and single molecule techniques used to probe soft matter systems.
• Examples of protein macromolecular machines.

• Specialised mathematical skills in the following areas which can be used with minimal guidance: Modelling and computation.

• Problem solving.
• Self-organisation, self-discipline and self-knowledge.
• Ability to learn actively and reflectively and to develop intuition, the ability to tackle material which is given both unfamiliar and complex.

Modes of Teaching, Learning and Assessment and how these contribute to the learning outcomes of the module

• Lectures will provide the means to give concise, focussed presentation of the relevant subject matter of the module. They will be supported by reference to suitable text books and where appropriate by the distribution of written material or through links on DUO (on-line learning resource).
• Problem sheets will be given regularly in lectures to help students gain an understanding of the concepts presented. These will be assessed formatively.
• Workshops based on the concepts presented will be used as support teaching.
• Practicals in which students use the computer package Maple to implement the numerical methods introduced in the lectures.
• Problem classes and tutorials based on the application of the concepts presented will be used as support teaching.
• Student performance will be assessed summatively through examination and through coursework.
• Formative assessments will provide the means for the student to demonstrate their acquisition of subject knowledge and the development of their problem solving skills. The tests will also provide opportunities for feedback, for students to gauge their progress, and for the Management Committee to monitor progress throughout the duration of the module.

Teaching Methods and Learning Hours

Summative Assessment

Formative Assessment:

Problem sheets distributed in lectures.

■ Attendance at all activities marked with this symbol will be monitored. Students who fail to attend these activities, or to complete the summative or formative assessment specified above, will be subject to the procedures defined in the University's General Regulation V, and may be required to leave the University