|Course coordinator(s)||dr. JA Dijksman|
|dr. B Bera|
|Lecturer(s)||dr. JA Dijksman|
|Examiner(s)||dr. JA Dijksman|
Language of instruction:
Assumed knowledge on:
PCC-21802 Introductory Thermodynamics or PCC-22306 Driving Forces in Chemistry, Physics and Biology; PCC-20806 Soft Matter.
The course connects relevant concepts from thermodynamics and physical chemistry with processes in different kind of systems in physics, chemistry and biology. It involves linear non-equilibrium thermodynamics to describe coupled processes. Focus is on transport and rate processes such as diffusion and convection, migration in electric fields, adsorption, (bio)chemical reactions, and mechanical deformation. Special attention is paid to transport of compounds over cell walls and biological membranes and linear elasticity in complex geometries.
The computer practical is used for illustration and ‘playing around’ with coupled processes to obtain insight in relevant parameters, rate-limiting factors, time and length scales. For example, transport processes (convective diffusion, effect of flow, planar versus radial diffusion) are coupled to reactions in bulk solution, adsorption, interfacial reactions, and uptake and excretion by cells and biofilm colonies. For this the computer package COMSOL is applied. COMSOL does not require extensive computer programming - all relevant differential equations are available as well as the means to couple different processes - students can focus on building 1D/2D/3D models and choosing the correct physics and boundary conditions. COMSOL uses computational fluid dynamics (CFD) to describe the effect of flow, but CFD will not be treated in detail in the course.
The course is an optional course aimed at master students Molecular Life Sciences. It fits in the line of other PCC courses on thermodynamics and soft matter.
After successful completion of this course students are expected to be able to:
- demonstrate clear understanding of thermodynamic concepts underlying the coupling of processes;
- relate and apply concepts from physical chemistry to processes in different kinds of soft matter systems;
- assess relevant parameters, rate-limiting factors, time and length scales;
- construct computer models in COMSOL, including selection of the correct boundary conditions and meshing issues to describe and predict the outcome of coupled processes;
- analyse and evaluate the results of the computer modelling in terms of impact of experimental, environmental and/or biological conditions.
- supervised tutorials;
- supervised computer modelling.
- Oral or written exam (50%, minimum mark to pass is 5.5);
- COMSOL modelling (50%, minimum mark to pass is 5.5);
- interim results are valid for three years.
Syllabus Coupled Processes in Soft Matter. Computer practical manual. Both will be handed out at the start of the course.