PH5016 Biophotonics

Academic year

2023 to 2024 Semester 1

Further information on which modules are specific to your programme.

Key module information

SCOTCAT credits

15

The Scottish Credit Accumulation and Transfer (SCOTCAT) system allows credits gained in Scotland to be transferred between institutions. The number of credits associated with a module gives an indication of the amount of learning effort required by the learner. European Credit Transfer System (ECTS) credits are half the value of SCOTCAT credits.

SCQF level

SCQF level 11

The Scottish Credit and Qualifications Framework (SCQF) provides an indication of the complexity of award qualifications and associated learning and operates on an ascending numeric scale from Levels 1-12 with SCQF Level 10 equating to a Scottish undergraduate Honours degree.

Availability restrictions

Normally only taken in the final year of an MPhys or MSci programme involving the School, or a postgraduate photonics programme.

Module coordinator

Dr G D Bruce

This information is given as indicative. Staff involved in a module may change at short notice depending on availability and circumstances.

Module description

The module will expose students to the exciting opportunities offered by applying photonics methods and technology to biomedical sensing and detection. A rudimentary biological background will be provided where needed. Topics include fluorescence microscopy and assays including time-resolved applications, optical tweezers for cell sorting and DNA manipulation, photodynamic therapy, optogenetics, lab-on-a-chip concepts and bio-MEMS. Two thirds of the module will be taught as lectures, including guest lectures by specialists, with the remaining third consisting of problem-solving exercises, such as writing a specific news piece on a research paper, assessed tutorial sheets and a presentation. A visit to a biomedical research laboratory using various photonics methods will also be arranged.

Relationship to other modules

Pre-requisites

BEFORE TAKING THIS MODULE YOU MUST ( PASS 1 MODULE FROM {PH3081, PH3082} OR PASS 2 MODULES FROM {MT2506, MT2507} ) AND PASS 1 MODULE FROM {PH4034, PH4035},PRE-REQUISITES ARE COMPULSORY UNLESS YOU ARE ON A TAUGHT POSTGRADUATE PROGRAMME.

Assessment pattern

2-hour Written Examination = 80%, Coursework (including presentation)= 20%

Re-assessment

Oral Re-assessment, capped at grade 7

Learning and teaching methods and delivery

Weekly contact

3 lectures or tutorials

Scheduled learning hours

30

The number of compulsory student:staff contact hours over the period of the module.

Guided independent study hours

120

The number of hours that students are expected to invest in independent study over the period of the module.

Additional information from school

Overview

The union of photonics and biotechnology presents some of the most exciting scientific and commercial prospects for the 21st century. Largely due to advances in microscopy and the invention of the laser in the 1960s, photonics has touched all aspects of our lives, ranging from home entertainment to optical telecommunications and data storage. Biophotonics is the fusion of photonics and biology that deals with the interaction between light and biological matter. Light is one of the primary tools in biology, and increasingly sophisticated optical instrumentation is used in biological detection and analysis as well as medical treatment.

 

Learning Outcomes

The key learning outcome is an appreciation for the wide range of photonics technologies that have important roles in the biomedical applications.

The students will therefore gain appreciation of the following:

 

  • Basic biological and biochemical concepts, such as the structure and function of cells, proteins and
  • Methods to investigate biological structures with spatial resolutions from angstroms to millimetres and with temporal resolutions from nanoseconds to seconds and beyond.
  • The nature of the interaction between biological materials (cells, tissue etc.) with light, such as scattering, absorption, fluorescence and Raman.
  • Optical instrumentation used in biomedical practice, especially for imaging.
  • Advanced light- based techniques such as single-molecule fluorescence, super-resolution methods, light-sheet microscopy, OCT and Raman Spectroscopy to provide multi-modal information.
  • Operation of biomedical detection systems such as assays and their detection limits.
  • Advanced optical techniques for mechanical manipulation of proteins and DNA such as optical tweezers and the added functionality and information provided by these methods.
  • An introduction to optogenetics and how to use light to control biological response, mostly in
  • Optical methods to measure forces exerted by cell during the cell life cycle.

 

 

Students will also gain transferable skills by developing some of the material themselves via critical study of research papers and materials, presentations and group work.

 

Synopsis

Imaging at different temporal and spatial scales from molecules to cells including optical coherence tomography, confocal and multiphoton imaging, and imaging beyond the diffraction limit. Overview of Microscopy and relevance for biological inspection. Basics of Cell and Molecular Biology, structure and function of biological structures and samples. Optical scattering, absorption and properties of fluorescent labels including small fluorophores, fluorescence proteins and quantum dots and their use in biological assays and biomedical sensing. New generation imaging methods including super-resolution techniques, light sheet microscopy and single-molecule technologies. Single-molecule DNA sequencing. Force-induced mechanical manipulation of biomolecules and cells using light. Operational principle of optical tweezers and its applications. Different types of beams, how they are generated and their applications. Interaction of light and tissue. Different types of light sources used and their respective advantages and effects, including time-resolved methods/short-pulse lasers. Light as a stimulus in biological samples. Uses of light-sensitive ion channels in optogenetics. Overview of optical methods to measure forces exerted by cells.

 

 

Additional information on continuous assessment etc.

Please note that the definitive comments on continuous assessment will be communicated within the module.  This section is intended to give an indication of the likely breakdown and timing of the continuous assessment. 

 

The coursework includes:

  1. News and Views style paper: a 1200-word essay including one or two figures explaining a research paper and placing the topic and findings into context. A list of research papers to choose from will be provided.
  2. A 15-20 min presentation on the same topic as the News & Views essay.

 

Recommended Books

Please view University online record:

http://resourcelists.st-andrews.ac.uk/modules/ph5016.html

 

General Information

Please also read the general information in the School's Honours handbook that is available via https://www.st-andrews.ac.uk/physics-astronomy/students/ug/timetables-handbooks/.