Code last year: (PCC-51303)
|Teaching method||Contact hours|
|Course coordinator(s)||dr. JA Dijksman|
|dr. B Bera|
|Lecturer(s)||dr. B Bera|
|dr. JA Dijksman|
|Examiner(s)||dr. JA Dijksman|
|dr. B Bera|
Language of instruction:
Assumed knowledge on:
PCC-21802 Introductory Thermodynamics or PCC-22306 Driving Forces in Chemistry, Physics and Biology; PCC-20806 Soft Matter.
Physical Modeling BCT 30806, thesis PCC.
Many processes in Nature are influenced by multiple mechanisms. Diffusion depends on changing temperatures, reaction rates depend on an evolving local concentration, et cetera. Such coupling of different mechanisms makes the corresponding dynamics complex, but is necessary to understand for accurate quantitative modelling of these processes. Perhaps more importantly, the coupling of dynamical processes can itself introduce new physical, chemical and biological dynamics originally absent in the basic mechanisms that are being coupled. This course discusses the relevant concepts from physical chemistry, thermodynamics and fluid dynamics needed to understand how processes can be coupled. Focus is on transport and rate processes such as diffusion and convection, migration in electric fields, adsorption, (bio)chemical reactions, and mechanical deformation. An introduction to fluid dynamics is also provided, and we discuss briefly how linear non-equilibrium thermodynamics creates a distinct class of coupled processes. Special attention is paid to transport of compounds over cell walls, reaction-diffusion systems and even linear elasticity in complex geometries.
Coupled processes are often mathematically complex, so we will work with easy-to-use computer modelling approaches to explore the relevant mathematics. 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 numerical work 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. This course is an optional course aimed at master students Molecular Life Sciences. It is in line with other PCC courses on thermodynamics and soft matter. BCT 30806 Physical Modelling is a related course that discusses the procedures behind numerical modelling itself in more detail. This BCT course is therefore an excellent complementary course to take.
After successful completion of this course students are expected to be able to:
- relate and apply concepts from physical chemistry to coupled processes in different kinds of soft matter systems;
- assess relevant modelling parameters, rate-limiting factors, time and length scales;
- demonstrate a clear understanding of (thermodynamic) concepts underlying the coupling of processes;
- 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 the context of the underlying theory.
- supervised tutorials;
- supervised computer modelling.
Written open book exam with open questions on the lecture subjects (3 hours).
Rreport/presentation of the COMSOL modelling project.
The final mark is a weighted average of the written exam (50%) and the report/presentation (50%). For both elements a minimum grade of 5.5 is required to pass.
Interim results are valid for three years.
Syllabus Coupled Processes in Soft Matter and lecture slides and computer practical manual. All will be handed out during the course.
|Restricted Optional for:||MML||Molecular Life Sciences||MSc||D: Spec. D Physical Chemistry||4AF|