Dr. Thomas Millat

Bacteria not only ferment sugar to alcohol, but also chemicals that can replace fossil fuels. I work to analyze the process and to optimize it.

Postdocs (from 2004-01-01 until 2013-12-31)

is now a Research Fellow at the Faculty of Medicine & Health Sciences,  University of Nottingham.

Research interest

Finding the Future Energy Solution in Bacterial Fermentation

"Bacteria not only ferment sugar to alcohol, but also chemicals that can replace fossil fuels. I work to analyze the process and to optimize it."

Bacteria take up sugars and digest them during fermentation processes to generate energy and to derive resources for growth. The waste products during these conversion processes can be harnessed and used to substitute conventional petrochemical production lines. We need to alter the fermentation processes in order to increase the output of the bacterial "waste products".
The question we focus on is: How is the fermentative process regulated in C. acetobutylicum, how is controlled naturally, and how can we make changes to both aspects?
A fundamental property of life is the conversion of energy. A large fraction of these conversions take place as fermentations in bacteria. Studying these fermentation processes will help us to understand the global flux of carbon. Eventually this understanding will result in technical applications.
We are studying C. acetobutylicum, a bacterium that can choose between two different fermentation processes depending on the environment, e.g. the pH value. In an alkaline medium acidic "waste chemicals" are produced while in an acidic environment solvent "waste chemicals" are generated. These solvent chemicals are products of interest for the chemical industry. There exists a defined switch-network that decides among the two fermentation options. We constructed a model that allows predictions about the performance from the chemical industry point of view.
With a mathematical model at hand we are able to forecast optimal construction of the fermentation with respect to solvent production. This can be done on a computer, saving time and money in laboratory experiments. We found that not a single step but several of them control the overall productivity.

Academic background

2004 - 2013 Post Doc at Systems Biology & Bioinformatics
1999 - 2004 Doctoral thesis in theoretical physics
Quantum Theory & Many-Particle Systems Group
Absorption and Dynamical Collision Frequency in Non-ideal Plasmas
Dr. rer. nat. (Ph.D. in Physics)
University of Rostock, Rostock/Germany
1993 - 1999 Diploma study in physics, Diplom-Physiker (advanced degree in physics)
University of Rostock, Rostock/Germany
   

 

Selected publications

An explicit numerical scheme to efficiently simulate molecular diffusion in environments with dynamically changing barriers

Kossow C, Rybacki S, Millat T, Rateitschak K, Jaster R, Uhrmacher AM, Wolkenhauer O (2015)

Mathematical and Computer Modelling of Dynamical Systems.

Integrative modelling of pH-dependent enzyme activity and transcriptomic regulation of the acetone-butanol-ethanol fermentation of Clostridium acetobutylicum in continuous culture

Millat T, Janssen H, Bahl H, Fischer RJ, Wolkenhauer, O (2013)

Microbial Biotechnology 6 (5): 526 - 39

COSMIC - Systems biology of Clostridium acetobutylicim - A possible answer to dwindling crude oil reserves

Millat T, COSMIC consortium

9th International Conference on Systems Biology (ICSB), Gothenborg (Sweden), 23 August - 27 August 2008

A shift in the dominant phenotype governs the pH-induced metabolic switch of Clostridium acetobutylicum in phosphate-limited continuous cultures

Millat T, Janssen H, Thorn GJ, King JR, Bahl H, Fischer RJ, Wolkenhauer O (2013)

Applied Microbiology & Biotechnology 97: 6451-6466,

Simulations of Stressosome Activation Emphasize Allosteric Interactions Between RsbR and RsbT

Liebal UW, Millat T, Marles-Wright J, Lewis RJ, Wolkenhauer O (2013)

BMC Systems Biology 7:3

Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis

Liebal UW, Sappa PK, Millat T, Steil L, Homuth G, Völker U, Wolkenhauer O (2012)

Molecular Biosystems 8(4):1806-14

A Systems Biology Approach to Investigate the Effect of pH-induced Gene Regulation on Solvent Production by Clostridium acetobutylicum in Continuous Culture

Haus S, Jabbari S, Millat T, Janssen H, Fischer RJ, Bahl H, King JR, Wolkenhauer O (2011)

BMC Systems Biology 5: 10

A mathematical analysis of nuclear intensity dynamics for Mig1-GFP under consideration of bleaching effects and background noise in Saccharomyces cerevisiae

Frey S, Sott K, Smedh M, Millat T, Dahl P, Wolkenhauer O, Goksör M (2011)

Molecular BioSystems 7: 215-223

How mathematical modelling elucidates signalling in B. subtilis

Liebal UW, Millat T, de Jong I, Kuipers O, Völker U, Wolkenhauer O (2010)

Molecular Microbiology 77: 1083-1095

Dynamics of receptor and protein transducer homodimerisation

Vera J, Millat T, Kolch W, Wolkenhauer O (2008)

BMC Systems Biology 2: 92

The role of dynamic stimulation pattern in the analysis of bistable intracellular networks

Millat T, Sreenath SN, Soebiyanto RP, Avva J, Cho K H, Wolkenhauer O (2008)

BioSystems 92: 270-281

How quantitative measures unravel design principles in multi-stage phosphorylation cascades

Frey S, Millat T, Hohmann S, Wolkenhauer O (2008)

J Theor Biol 254: 27-36

Approximations and their Consequences in Dynamic Modelling of Signal Transduction Pathways

Millat T, Bullinger E, Rohwer J, Wolkenhauer O (2007)

Mathematical Biosciences 47: 40-57

Bioinformatics analysis of interactions of receptor homodimers with intracellular protein homodimers

Vera J, Kwon T, Schmitz U, Millat T, Wolkenhauer O

Rostocker Informatik-Berichte, 31, 2007

The pH-induced metabolic shift from acidogenesis to solventogenesis in Clostridium acetobutylicum - From experiments to models

Millat T, Janssen H, Bahl H, Fischer R-J, Wolkenhauer O

in: Proceedings of the 5th Internation ESCEC Symposium on "Experimental Standard Conditions of Enzyme Characterization", Kettner, C (ed.); Logos Verlag Berlin 2013.

ISBN 13 (print): 9783832533670

Mathematical modelling of the pH-induced metabolic shift in Clostridium acetobutylicum

Millat T, Haus S, Wolkenhauer O

in: Systems Biology of Clostridium acetobutylicum, Dürre P (ed.), Imperial College Press, 2014, 103-130.

ISBN 13 (print): 9781783264407

Modeling of Cellular Processes: Methods, Data, and Requirements

Millat T, Wolkenhauer O, Fischer, RJ, Bahl, H

in: Data Mining in Proteomics; Hamacher M, Eisenacher M, Stephan C (eds.); Springer 2011.

ISBN 13 (print): 9781607019864

DOI: http://dx.doi.org/10.1007/978-1-60761-987-1_27

Quantifying properties of cell signaling cascades

Frey S, Wolkenhauer O, Millat T

in: Control Theory and Systems Biology; Iglesias P A, Ingalls B (eds.); MIT press 2009.

ISBN 13 (print): 9780262013345

BIB: Download file

Modelling and simulation of dynamics in cells

Millat T, Wolkenhauer O

Systems Biology: From Molecules & Modeling to Cells, Gosau, Austria, 12 March - 18 March 2005

Venue: Gosau, Austria

Butyrate re-assimilation in C. acetobutylicum re-evaluated using modelling

Millat T

7th Annual SysMo-Conference, Berlin, Germany, 6 February - 8 February 2013

Venue: Berlin, Germany

Continuous states on a grid enable an efficient simulation of diffusion in environments with excluded volumes

Kossow C, Rybacki S, Millat T, Rateitschak K, Uhrmacher AM, Wolkenhauer O

Biotec Forum ''Bioinformatics and Computational Biology'', Dresden, Germany, 06 December - 07 December 2012

Venue: Dresden, Germany

Mathematical Modelling of the pH-induced Metabolic Shift in C. acetobutylicum Unravels a Heterogeneous Phase Transition

Millat T

Clostridium XII, Nothingham, UK, 9 September - 12 September 2012

Venue: Nothingham, UK

The pH-induced metabolic shift from acidogenesis to solventogenesis in Clostridium acetobutylicum

Millat T

5th International Beilstein Symposium on Experimental Standard Conditions of Enzyme Characterizations, Rüdesheim, Germany, 12 September - 16 September 2011

Venue: Rüdesheim, Germany

Protein diversity of the stressosome - Stress sensitivity and Response magnitude

Liebal U, Millat T, Marles-Wright J, Lewis R, Wolkenhauer O

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011

Venue: Heidelberg/Mannheim, Germany

Automated analysis of flow cytometry data from heterogeneous bacterial populations

Millat T, Rubenis O, Liebal U, Wolkenhauer O, de Jong I, Kuipers O

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011

Venue: Heidelberg/Mannheim, Germany

Protein Diversity of the Stressosome - Stress Sensitivity and Response Magnitude

Liebal UW, Millat T, Marles-Wright J, Lewis R, Wolkenhauer O

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011

Venue: Heidelberg/Mannheim, Germany

The dynamics of the phosphorelay and the initiation of sporulation in Bacillus subtilis - a systematic study

Millat, Liebal U, Wolkenhauer O, de Jong I, Kuipers O

11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10 October - 15 October 2010

Venue: Edinburgh, UK

Systems Biology of Clostridium acetobutylicum and the Optimization of Butanol Production

Jabbari S, Haus S, Millat T, Wolkenhauer O, King JR

11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10 October - 15 October 2010

Venue: Edinburgh, UK

Modelling the pH-dependent metabolic shift in Clostridum acetobutylicum

Thomas Millat, Sylvia Haus, Olaf Wolkenhauer, Ralf-Jörg Fischer, Holger Janssen, Hubert Bahl, Sara Jabari, John King

11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10-15 October 2010

Venue: Edinburgh, UK

How integrals over dynamic signals can unravel characteristic properties of signal transduction pathways

Thomas Millat, Simone Frey, Olaf Wolkenhauer

11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10-15 October 2010

Venue: Edinburgh, UK

Modelling the pH-dependent metabolic shift in Clostridum acetobutylicum

Millat T, Haus S, Wolkenhauer O, Fischer RJ, Janssen H, Bahl H, Jabari S, King J

11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10 October - 15 October 2010

Venue: Edinburgh, UK

A mathematical analysis of nuclear intensity dynamics for Mig1-GFP under consideration of bleaching effects and background noise in S. cerevisiae

Simone Frey, Kristin Sott, Maria Smedh, Thomas Millat, Peter Dahl, Olaf Wolkenhauer, Mattias Goksör

11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10-15 October 2010

Venue: Edinburgh, UK

Using a modelling approach to elucidate unexpected reporter gene signals for sigmaB activity in B. Subtilis

Liebal U, Sappa PK, Millat T, Steil L, Völker U, Wolkenhauer O

Conference on Systems Biology of Microorganisms, Paris, France, 22 March - 24 March 2010

Venue: Paris, France

Downloads & more:

Systems Biology - How Modelling and Simulation improve our understanding of complex biological systems

Millat T

Systems Biology of Neurodegenerative Diseases, Kuopio, Finland, 16 June - 18 June 2009

Venue: Kuopio, Finland

Dynamic Motifs in Pathway Modelling

Millat T

Rijksuniversiteit Groningen, Groningen Biomolecular Sciences and Biotechnology
Institute (GBB), Department of Genetics, Molecular Genetics, Haren, The Netherlands, 3 April 2009

Venue: Haren, The Netherlands

Mathematical Modelling and Simulation of Cellular Processes

Wolkenhauer O, Millat T

Vorlesungsreihe Biosystem-Material-Interaktion an der Interdisziplinären
Fakultät der Universität Rostock, Rostock, Germany, 27 October 2008

Venue: Rostock, Germany

Analysis of a Model of sigB Activation Following Glucose Starvation

Liebal U, Millat T, Wolkenhauer O, Sappa PK, Steil L, Völker U

10th International Conference on Systems Biology (ICSB), Stanford, USA, 30 August -4 September 2009

Venue: Stanford, USA

Downloads & more:

The Metabolic Shift of Clostridium acetobutylicum - The Role of pH-Dependent Enzyme Activities

Millat T, Haus S, Wolkenhauer O, Fischer RJ, Janssen H, Bahl H

10th International Conference on Systems Biology (ICSB), Stanford, USA, 30 August - 4 September 2009

Venue: Stanford, USA

The Effect of pH on the Metabolic Shift in AB Fermentation in Clostridium acetobutylicum

Haus S, Jabbari S, Millat T, Wolkenhauer O, King JR

10th International Conference on Systems Biology (ICSB), Stanford, USA, 30 August - 4 September 2009

Venue: Stanford, USA

COSMIC - Systems biology of Clostridium acetobutylicim - A possible answer to dwindling crude oil reserves

Millat T, COSMIC consortium

9th International Conference on Systems Biology (ICSB), Gothenborg, Sweden, 23 August - 27 August 2008

Venue: Gothenburg, Sweden

Modeling of ABE Fermentation in Clostridium acetobutylicum

Haus S, Millat T, Wolkenhauer O

9th International Conference on Systems Biology (ICSB), Göteborg (Gothenburg), Sweden, 23 August - 28 August 2008

Venue: Gothenburg, Sweden

How Quantitative Measures unravel Design Principles in multi-stage Phosphorylation Cascades

Frey S, Millat T, Hohmann S, Wolkenhauer O

9th International Conference on Systems Biology (ICSB), Göteborg (Gothenburg), Sweden, 23 August - 28 August 2008

Venue: Gothenburg, Sweden

The Role of Dynamic Stimulation Pattern in the Analysis of Bistable Intracellular Systems

Millat T, Sreenath SN, Soebiyanto RP, Avva J, Cho KH, Wolkenhauer O

9th International Conference on Systems Biology (ICSB), Göteborg (Gothenburg), Sweden, 23 August - 28 August 2008

Venue: Gothenburg, Sweden

pH-Dependent Modelling of ABE Fermentation in Clostridium acetobutylicum

Haus S, Millat T, Wolkenhauer O

SysMo Evaluation Conference, Bad Honnef, Germany, 1 July - 2 July 2008

Venue: Bad Honnef, Germany

Modelling Aspects of Stress Response mediated by sigB

Liebal UW, Hildisch H, Millat T, Völker U, Wolkenhauer O

SysMo Evaluation Conference, Bad Honnef, Germany, 1 July - 2 July 2008

Venue: Bad Honnef, Germany

Exploring cell signalling homodimer receptor-homodimer protein interactions and their dynamical consequences

Vera J, Millat T, Kwon T, Schmitz U, Wolkenhauer O

German Conference on Bioinformatics, Potsdam, Germany, 26 September - 28 September 2007

Venue: Potsdam, Germany

Von der Notwendigkeit der mathematischen Modellierung in den Biowissenschaften

Wolkenhauer O, Millat T, Assmuss, H

Interdisziplinäre Ringvorlesung - Modellierung und Simulation - Techniken und gesellschaftliche Implikationen, Rostock, Germany, 19 April 2007

Venue: Rostock, Germany

Bistable Systems - a dynamic view

Millat T

Winter School on Systems Biology for Medical Applications, Puerto de la Cruz, Tenerife, Spain, 26 February - 2 March 2007

Venue: Tenerife, Spain

Quantitative measures to characterize properties of signal transduction pathways

Frey S, Millat T, Rateitschak K, Wolkenhauer O

Winter Simulation Conference (WSC '06), December 2006

From Experiments to Models: Assumptions, Approximations and their Consequences

Millat T

SYMBIONIC 2005, Course on Methods, Data Handling and Standards in Neuronal Systems Biology, Trieste, Italy, 31 August - 3 September 2005

Venue: Trieste, Italy

Dynamics Motifs in Pathway Modelling

Millat T

SYMBIONIC 2005, Course on Methods, Data Handling and Standards in Neuronal Systems Biology, Trieste, Italy, 31 August - 3 September 2005

Venue: Trieste, Italy

Assumptions in Dynamic Modelling of Biochemical Networks and their Consequences

Millat T, Wolkenhauer O

FEBS Systems Biology Workshop, Gosau, Austria, March 2005

Venue: Gosau, Austria,

Modelling of Cellular Processes - Methods, Data, and Requirements

Millat T

Biosystem-Material-Interaktion (Vorlesungsreihe der Interdisziplinären
Fakultät der Universität Rostock), Rostock (Germany),
17 January 2011

Von der Notwendigkeit der mathematischen Modellierung in den Biowissenschaften

Assmus H, Millat T, Wolkenhauer O

Modellierung und Simulation, 125-136, Universität Rostock, December 2008
ISBN: 978-3-86009-047-3