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Biophysics - PHY00033M

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  • Department: Physics
  • Module co-ordinator: Dr. Steven Quinn
  • Credit value: 20 credits
  • Credit level: M
  • Academic year of delivery: 2023-24

Module summary

Interdisciplinary biophysical research is at the forefront of modern science, emerging as a prime area in industry and academia. Key to recent advances has been the development of pioneering experimental techniques and advanced theoretical/modelling approaches capable of assessing the nanoscale dynamics of nature’s biomolecules. This modern armoury of the physicist constitutes a powerful toolbox which can be used to tackle a multitude of open questions related to our understanding of human life and disease. In this module we will cover an exciting array of experimental and theoretical tools from modern biophysics, addressing their purpose, instrumentation, underlying physics, limitations and applications. We will study analysis methods used in research labs around the world, and showcase their application to current research activities

Module will run

Occurrence Teaching period
A Semester 1 2023-24

Module aims

In this module we will review in detail several important modern physical science concepts, models, laws, tools and techniques that can be applied to addressing real biological questions, with a thorough discussion of the underlying physics.

Physical science methods historically have been key to providing enormous breakthroughs in our understanding of fundamental biology - stemming from the early development of optical microscopy in understanding the cellular nature of life, through to complex structural biology techniques to elucidate the shape of vital biomolecules including proteins and DNA.

In the first half of this module we will introduce the key biological macromolecules, the forces that are involved in maintaining their structure and how structure is determined. We will next discuss key physical science developments that have involved methods to study single cells in their native context, single- molecule biophysical methods that permit dynamic and mechanistic information to be extracted with unprecedented precision, and ground-breaking developments in areas of super-resolution imaging and biosensing.

In the second half of the module we will discuss tools and techniques that, broadly, permit the detection and characterization of biological material using non-visible electromagnetic radiation, and methods used to manipulate and quantify biological forces, with particular emphasis throughout placed on real applications. Examples of such tools discussed include electron microscopy, nuclear magnetic resonance spectroscopy and atomic force microscopy. We will also discuss optical and magnetic tweezers for single biological molecule manipulation, ion channel measurements in living cells and core physics concepts of fundamental biological processes which are interrogated using these modern instruments.

Lectures will focus on both the core concepts of biophysics tools and techniques and on real research applications, including ‘guest’ lectures given by expert researchers in several different specific areas of biophysics, in addition to core lectures. Lecture material will be available to download on the VLE, and lectures will include worked-through problem solving and active discussion sessions and so physical attendance at the lectures is strongly encouraged.

Module learning outcomes

The module will focus on a number of concepts, models, laws, tools and techniques of physical science that underpin biophysical methods. It will address a broad range of challenging biological questions. During this module students will:

  • Comprehend the use of physical concepts and laws to produce models of biological systems, and quantitatively analyse these models.
  • Critically analyse the validity of assumptions made in these models and assess their impact on the validity of the results.
  • Understand the physical basis of experimental techniques used to study the biological systems introduced and explain the key results.
  • Assess the key features and biological significance of the systems introduced.
  • Demonstrate an understanding of the key physical principles behind several important biological processes underpinning living matter.
  • Apply modern biophysical tools and techniques to real applications

Module content

The lecture course will discuss the scope of modern biophysics, and introduce students to the fundamentals of chemical bonding, and the structure and function of biological molecules including sugars, lipids, proteins, nucleic acids and molecular machines. Biophysical techniques including optical spectroscopy, dynamic light scattering, fluorescence spectroscopy and the basics of light microscopy will then be discussed in detail. Insights into single-molecule imaging and spectroscopy will then be provided, before a series of lectures on super-resolution approaches. Next, students will encounter techniques which use non-optical waves in their mode of operation, including electron microscopy, X-ray spectroscopy and nuclear magnetic resonance spectroscopy. Experimental techniques which rely on forces, including atomic force microscopy and optical tweezers will then be discussed in detail. Complementary and emerging experimental techniques will also be presented, as well as detailed analysis of molecular dynamics simulations. The lecture course will also include revision of the course material and guest research lectures from specialists in the field. Examples of guest research lectures include, but are not limited to: Digital Holographic Microscopy, Biofilms, Biophotonics and Raman Spectroscopy.

Assessment

Task Length % of module mark
Closed/in-person Exam (Centrally scheduled)
Biophysics		 3 hours 80
Essay/coursework
Assignment		 N/A 20

Special assessment rules

None

Reassessment

Task Length % of module mark
Closed/in-person Exam (Centrally scheduled)
Biophysics		 3 hours 80
Essay/coursework
Assignment		 N/A 20

Module feedback

'Feedback’ at a university level can be understood as any part of the learning process which is designed to guide your progress through your degree programme. We aim to help you reflect on your own learning and help you feel more clear about your progress through clarifying what is expected of you in both formative and summative assessments. A comprehensive guide to feedback and to forms of feedback is available in the Guide to Assessment Standards, Marking and Feedback.

This can be found at: https://www.york.ac.uk/students/studying/assessment-and-examination/guide-to-assessment/

The School of Physics, Engineering & Technology aims to provide some form of feedback on all formative and summative assessments that are carried out during the degree programme. In general, feedback on any written work/assignments undertaken will be sufficient so as to indicate the nature of the changes needed in order to improve the work. Students are provided with their examination results within 25 working days of the end of any given examination period. The School will also endeavour to return all coursework feedback within 25 working days of the submission deadline. The School would normally expect to adhere to the times given, however, it is possible that exceptional circumstances may delay feedback. The School will endeavour to keep such delays to a minimum. Please note that any marks released are subject to ratification by the Board of Examiners and Senate. Meetings at the start/end of each semester provide you with an opportunity to discuss and reflect with your supervisor on your overall performance to date.

Our policy on how you receive feedback for formative and summative purposes is contained in our Physics at York Taught Student Handbook.

Indicative reading

Leake MC: Biophysics: Tools and Techniques for the Physics of Life (CRC Press, 2nd Ed, 2024)

Leake MC: Single-Molecule Cellular Biophysics (CUP, 1st Ed, 2013)

Alberts A et al: Molecular Biology of the Cell (Garland Science, 6th Ed, 2014)


The information on this page is indicative of the module that is currently on offer. The University is constantly exploring ways to enhance and improve its degree programmes and therefore reserves the right to make variations to the content and method of delivery of modules, and to discontinue modules, if such action is reasonably considered to be necessary by the University. Where appropriate, the University will notify and consult with affected students in advance about any changes that are required in line with the University's policy on the Approval of Modifications to Existing Taught Programmes of Study.