TU Delft

Two PhD researchers on the nwo VIDI project

“MODELLING  THE  ROLE  OF  SPECIFIC  BIOLOGY  IN  BIOFILM  FORMATION  AND  ACTIVITY”


TU Delft, Environmental Biotechnology Group


BACKGROUND


More than 90% of all microorganisms are associated with interfaces. These interfacial microbial communities are termed biofilm systems. Biofilms are of utmost significance in the medical field, where they cause serious infections persistent to antibiotic treatment. Biofilms are also present in nearly all technical systems where they cause biofouling, biodeterioration and biocorrosion. It is therefore extremely important to understand the structure and function of biofilm communities as well as the mechanisms regulating biofilm processes. Biofilm researchers face invariably the challenge of understanding complex relationships between physical, chemical and biological processes occurring at very different spatial and temporal scales. The best tool available for integrating the overwhelming amount of dispersed experimental observations in a rational environment is mathematical modelling.

In this context, the project proposes the development and validation of a completely new fourth generation of computational biofilm models. Specific biological mechanisms will be introduced in models for explaining biofilm spatial structure formation, its function and activity. Besides physicochemical processes traditionally existent in biofilm models, several biological processes of crucial importance for biofilm development will be incorporated: cell-cell communication, gene transfer, pili and flagellum formation. All of these affect biofilm life by regulating the biofilm polymeric matrix formation and lysis, by inducing microbial detachment, by controlling microbial motility, by inducing various microbial morphologies. 

A most important application of the new modelling approach is to rationally design strategies for removal of pathogenic biofilms, whose inherent resistance to antimicrobial agents are the cause of many persistent and chronic infections. Use of quorum-sensing inhibitory agents for biofilm suppression is highly attractive because such anti-pathogenic agents are less likely to pose a selective pressure for development of resistant mutants. In industrial applications, this approach will reduce reliance on toxic antimicrobial agents whose use is fundamentally at odds with the increasingly restrictive environmental regulations.

This project is financed by an NWO/VIDI award to Dr. C. Picioreanu.  Here are other individual grants from July 2006:  nwo

PROJECT GOALS


1. Develop and validate a computational tool to investigate the role of cell-cell communication in general and of quorum sensing in particular in biofilm formation 

2. Develop and validate a model to explain the role of microbial motility in biofilm morphology 

3. Integrate the tools in a comprehensive computational framework for biofilm development including physical, chemical and biological processes. 

4. Evaluate strategies for using quorum-sensing and quorum-sensing inhibitory agents in conjunction with antimicrobial-based therapy of resilient biofilms.


MODELLING EXAMPLES


Examples of preliminary simulations and experimental results from DTU (groups Tim Tolker-Nielsen and Soeren Molin) is shown below.

Please visit also the main pages presenting the biofilm modelling work at TU Delft:
Publications  and  Material

Simulations
(Picioreanu et al., Water Sci Technol, in press)
Experiments
(Klausen et al., 2003)
Case 1 - Biofilm development from a 1:1 mixture of yellow fluorescent pilA mutant (immotile) and blue fluorescent pilA mutant (immotile) Pseudomonas cells.
pilA_pilA_model.jpg


pilA_pilA_exp.jpg
Case 2 - Biofilm development from a 1:1 mixture of yellow fluorescent wild type (motile) and blue fluorescent pilA mutant (immotile) Pseudomonas cells.
wt_pilA_model.jpg
MOVIE

wt_pilA_exp.jpg
Case 3 - Biofilm development from a 1:1 mixture of yellow fluorescent and blue fluorescent wild type Pseudomonas cells.
wt_wt_model.jpg


wt_wt_exp.jpg


CANDIDATE REQUIREMENTS


To reach the project objectives, the 2 PhD students will work together in close cooperation. They are expected to 1. develop the computational models at TU Delft and 2. acquire the experimental data in other top laboratories from Europe, which have committed themselves to cooperation (Denmark, Germany, Switzerland).

Therefore, we are looking for enthusiastic and motivated researchers with a Master’s degree in chemical or biochemical engineering, computational biology or computational physics. Particularly, we are seeking candidates with affinity for theoretical and computational work, with a good numerical background and with knowledge of mathematical modelling of biological systems. Experience with computer software and programming skills (C/C++, Java and Matlab) is definitely required. We prefer candidates able to work accurately, independently, with initiative, who like to work in an internationally oriented environment. 

Knowledge of scientific English and the ability to express yourself clearly both in writing and orally is necessary.


CONDITIONS OF EMPLOYMENT


This position has a temporary employment basis of 4 years (48 months).

The extent of this position is a maximum of 38 hours per week (1 FTE).

The estimated monthly PhD starting salary is based on scale P with a maximum of € 2,472 per month gross based on a full-time appointment and depending on experience. Benefits and other employment conditions are in accordance with the Collective Labour Agreement for Dutch Universities.

The successful candidate will be employed by TU Delft for a fixed period of 4 years within which he/she is expected to write a dissertation leading to the title of Dr (PhD thesis).


ADDITIONAL INFORMATION 

Additional information about the vacancy can be obtained from Dr. Cristian Picioreanu:

Telephone number:        +31 15 2781166

Fax number:                  +31 15 2782355

E-mail address:              C.Picioreanu@tudelft.nl

For more information about the project, the research group and the university please visit

These vacancies have been published also in Academic Transfer.


APPLICATION


To apply for this job please send a detailed CV together with a letter of motivation to:

Dr. Cristian Picioreanu 

Delft University of Technology
Faculty of Applied Sciences
Department of Biotechnology
Julianalaan 67, 2628 BC, Delft
The Netherlands

E-mail address:   C.Picioreanu@tudelft.nl 


November 10, 2006 - updated by Cristian Picioreanu