Advanced Course

Essentials of Microbial Physiology and Fermentation Technology Online

Course description

This one-week online course is fully given in English and will have intensive and long days. To enable and ensure active participation by everyone attending, we offer a combination of theoretical (plenary and recorded lectures) and practical (exercises, and computer simulations) work. Online preparatory materials will be sent in advance to facilitate all participants to have the same basic knowledge at the start of the course.

15 – 19 March 2021

Delft University of Technology, the Netherlands

A limited number of fellowships is available for PhD students (reduced fee).


Advanced Course Essentials on Microbial Physiology and Fermentation Technology – Online

For a better understanding of the lectures and to enhance active participation, this intensive one-week online course consists of lectures, exercises and computer simulations.

Lectures and exercises

course_Microbial-PhysiologyThe online lectures are mainly scheduled in the mornings, and exercises in the afternoon. Attention will be paid to the following themes:

  • Energy transduction and growth thermodynamics
  • Black Box and stoichiometry of growth and product formation
  • Transport in fermentors, fed batch fermentation
  • Regulation of metabolism by environmental parameters
  • High-cell density fermentation
  • Metabolic networks: stoichiometry and fluxes
  • Regulation and control of metabolic fluxes
  • Metabolic engineering
  • Capita selecta

Study load

The course (including preparatory materials) is valued 49 hours of work.

Who should attend?

This Advanced Course is aimed at professionals (MSc, PhD or equivalent experience) in microbiology, biochemistry or biochemical engineering with a basic working knowledge of the two other disciplines. Also, molecular biologists with a microbial background may apply. The course is primarily aimed at those already employed in industry who wish to up-date their theoretical knowledge and practical insight in this field. In addition, this Advanced Course is an option in the two-year postgraduate programs of Delft University of Technology.

Course registration

Please register clicking the tab Register to attend the course. Applicants will be handled in order of the date of receipt.


Programme Online 2021:

Monday, 15 March 2021
Theme: Thermodynamics/Balances and rates/Black Box models
08.30 Outline of the course Han de Winde
09.00 Basic energetics of microbial metabolism Robbert Kleerebezem
10.15 Break
10.30 Balances and rates

q-rates, single nutrient limitation, Black Box model

Sef Heijnen
12.15 Lunch break
13.15 Participants work in two groups (switch at 14.30) Exercises Robbert Kleerebezem

Sef Heijnen

16.45 Break
17.00 Transport over biological membranes: mechanisms and thermodynamics Walter van Gulik
Tuesday, 16 March 2021

Theme: Stoichiometry in bioprocesses/Calculation of in-and outflows

09.00 Stoichiometry in bioprocesses using a thermodynamic based Black Box model Sef Heijnen
10.30 Break
10.45 Microbial growth with mixtures of carbon substrates Han de Winde
11.30 A game of balances: calculation of fermentor flows using stoichiometry Sef Heijnen
12.15 Lunch break
13.00 Exercises Sef Heijnen
15.30 Break
15.45 Exercises Sef Heijnen
Wednesday, 17 March 2021

Themes: Transport in fermentors/fed batch

09.00 Transport phenomena in industrial fermentors Henk Noorman
10.45 Break
11.00 Design of fed batch fermentation processes Sef Heijnen
12.00 Lunch break
13.00 Exercises Sef Heijnen
16.30 Break
16.45 Primary metabolism and its regulation Pascale Daran-Lapujade
Thursday, 18 March 2021

Theme: Physiology, metabolism, metabolic models

09.00 High cell density fermentation: Challenges and opportunities Han de Winde
10.00 Break
10.15 Metabolic network analysis Walter van Gulik
12.00 Lunch break
13.00 Exercises Walter van Gulik/Sef Heijnen
14.45 Metabolic flux balances Aljoscha Wahl
16.00 Computer exercises Aljoscha Wahl
Friday, 19 March 2021

Theme: From concepts to applications

09.00 Multi-level regulation of metabolic fluxes: transcripts vs. fluxes Pascale Daran-Lapujade
09.45 Evolutionary and reverse engineering of yeasts Robert Mans
10.30 Break
11.00 Metabolic engineering strategies for reducing cost Sef Heijnen
12.30 Lunch break
13.30 Multiscale modeling of industrial bioreactors Cees Haringa
14.30 Single cell studies of microorganisms/microfluidics Sander Tans
15.30 Closing Lecture: Gas fermentation:  a path to low carbon fuel and chemical production with impact Björn Heijstra
16.30 Closure Han de Winde/Sef Heijnen

Location of our course:

Faculty of Applied Sciences (building 58)
Department of Biotechnology
Delft University of Technology
Van der Maasweg 9
2629 HZ Delft
The Netherlands
P +31 (0)15 278 1922
F +31 (0)15 278 2355


Deadline for registration is 22 February 2021

The course fee is:

Early Bird €2400,-*
Regular Fee €2600,-
PhD Students €1250,-**

*To be eligible for the reduced early bird fee you need to register before 4 January 2021. If this date is exceeded, the regular fee applies.

**A limited number of fellowships is available for PhD students. To apply, please include a copy of your registration as a PhD student from your university.

The course fee is preferably paid by bank transfer. Payment by PayPal is possible. TU Delft employees can use their internal (project) code.

Preparatory texts will be sent one month before start of the course and after receipt of the course fee. The complete set of course books will be supplied at the start of the course.

In the event of your cancellation before 18 January 2021, a full refund will be granted. After this date, a 25% fee charge can be made.

Delay of payment past the final deadline as indicated on the invoice may result in cancellation of entry to the course. Re-entry is only possible in case of vacancies and the regular fee will be applied. Payment terms and deadlines will be indicated on the invoice and/or provided in an e-mail after registration, but the course fee should always be paid before the start of the course.

When the number of participants is too low to have a fruitful course, the Institute BioTech Delft will cancel the event no later than six weeks before the start of the course. The course fee will be reimbursed within three weeks after cancellation. In case a speaker will not be able to present his/her lecture, due to unforeseen circumstances, BioTech Delft will arrange an equivalent replacement.


Course board

Prof. Sef Heijnen

After his MSc studies in Chemical Engineering, Sef Heijnen worked at DSM (then: Gist Brocades) for 15 years and in this period he also completed his PhD thesis in bioprocess technology at Delft University of Technology. In 1988, he became full professor and group leader in Cell Systems Engineering within the Department of Biotechnology of Delft University of Technology. He has an impressive track record: he is (co-) author of over 400 scientific publications, has supervised 50 PhD students and is a member of the Royal Netherlands Academy of Arts and Sciences (KNAW). His research interests are (1) metabolic engineering and systems biology applied to industrial microbial processes using Saccharomyces cerevisiae, Penicillium chrysogenum and Escherichia coli, (2) metabolome measurement and 13C-tracer analysis in steady state and dynamic conditions, and (3) thermodynamic and kinetic modelling of metabolism and fermentation. Prof. Heijnen teaches a wide variety of courses, and was elected at TU Delft’s 2003 ‘Leermeester’ (best lecturer).

Prof. Han de Winde

Han de Winde holds an MSc in organic chemistry and biochemistry from the Vrije Universiteit of Amsterdam, and a PhD in molecular biology from the University of Amsterdam. He was NWO postdoctoral research fellow at the Amsterdam BioCenter and EU-HCM fellow and assistant professor at the Laboratory of Molecular Cell Biology, Catholic University of Leuven, Belgium. In 2000 he was appointed Senior Scientist Genetics & Physiology at DSM Bakery Ingredients. From 2002 he became full professor in Industrial Genomics, at TU Delft and from 2004 Principal Scientist Microbial Genetics and Physiology at DSM Food Specialties RD&T. From 2006 Han was Scientific Director at the Department of Biotechnology, TU Delft. He was business director of the Kluyver Center for Genomics of Industrial Fermentation (NWO-NGI Dutch National Centre of Excellence), and scientific director of the Delft Research Centre for Life Science and Technology (DRC-LST), and of the Graduate Research School ‘Biotechnological Sciences Delft-Leiden’ (BSDL (now: BioTech Delft)). Since April 2013 Han de Winde is vice dean, Faculty of Sciences, at Leiden University and chairholder of Industrial Biotechnology at the Leiden Institute of Biology.

Han de Winde has obtained thorough expertise in research, development and education at BSc, MSc, PhD and advanced level. His scientific expertise is in microbial molecular genetics and metabolic engineering, specifically in the area of nutrient- and environment-induced signal transduction and control of physiology, growth and development of bacteria, yeast and fungi. He is expert in implementation and development of applied functional genomics and systems biology in microbial strain and process improvement. He is (co)author of over 85 peer reviewed scientific publications and of 10 filed patents families.

Faculty staff

Dr. Pascale Daran-Lapujade

Pascale Daran-Lapujade is assistant professor at the TU Delft Department of Biotechnology in the Industrial Microbiology section. Her research investigates the physiology of the yeast Saccharomyces cerevisiae, to unravel the molecular mechanisms that drive its response to diverse environmental stimuli and to identify the evolutionary circumstances that have shaped their genomes. Although many of her research questions are inspired by industrial applications of yeasts, she also seeks to contribute to a deeper understanding of fundamental aspects of cellular physiology and metabolism, using S. cerevisiae as a model. In addition she is editor of the journal FEMS Yeast Research and member of the board of the Microbial Biotechnology section of the Dutch Society for Microbiology (KNVM).

Dr. Walter van Gulik

Delft University of Technology, Cell Systems Engineering, Delft, the Netherlands

Ir. Robert Mans

Robert Mans has completed his degree as a master of science in 2012 in the study of Life, Science & Technology. In his thesis research he has focused on yeast physiology and both metabolic and evolutionary engineering. He is currently working as a PhD student in the Industrial Microbiology group under the supervision of Ton van Maris, Jean Marc Daran and Jack Pronk, where he focusses on free energy (ATP) conservation in S. cerevisiae. Of specific interests to him are evolutionary engineering, cloning techniques and yeast physiology.

Dr. Robbert Kleerebezem

Delft University of Technology, Environmental Biotechnology, Delft, the Netherlands

Dr. Aljoscha Wahl

Aljoscha Wahl is assistant professor at TU Delft with a focus on fluxomics and metabolomics in eukaryotic microorganisms. He studies the interactions of metabolism and its regulation under dynamic environmental conditions. Dr. Wahl contributes to experimental and computational approaches for (1) 13C flux analysis under metabolic dynamic conditions, (2) compartmentalized fluxomics and metabolomics using intracellular sensor reactions, (3) transport system studies.  He teaches several master courses at TUD and was active in the iGEM competition (supervisor of the TUD team and organization of the European Jamboree). In addition, he is member of the editorial board of Applied and Environmental Microbiology (AEM)

Guest lecturers

Prof. Henk Noorman

Henk Noorman was trained as Chemical Engineer from Groningen University (NL). He obtained a PhD in Bioprocess Technology from Delft University of Technology (NL, 1991), on microbal systems modeling. He became a post-doc fellow in a Nordic research consortium, and co-ordinated a fermentation scale-up project among academic groups in Sweden, Denmark and Norway. He then joined Gist-brocades and DSM in Delft (NL) and worked on fermentation development and implementation projects, mainly in the area of antibiotics and bio-based products. He also has been project manager for innovation projects, and received the DSM R&D Award 2010. Henk Noorman is currently working as Corporate Scientist Bioprocess Technology in the DSM Biotechnology Center and involved in numerous projects in Industrial Biotechnology, Food Specialties, Anti-Infectives, and the Corporate Research Program. In addition he is honorary professor at Technical University Delft working on Bioprocess Design and Integration. Teaching activities include courses in Delft, Wageningen (NL), Brac (Croatia) and Shanghai (China).

Sander Tans

Kalvi Institute of NanoScience, Delft University of Technology

and AMOLF institute, Amsterdam, the Netherlands

Cees Haringa

DSM Biotechnology Center

Delft, the Netherlands

Björn Heijstra

Director Process Validation

Lanzatech, USA


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