Search

link to homepage

Navigation and service


Master Project: Brownian Dynamics Simulation of Reaction-Diffusion Systems in Crowded Environments

Advertising institute: IBG-1 - Biotechnology
Reference number: D122/2013, Physics, theoretical chemistry

Background
Biochemistry of live, on the cellular level, is mainly driven by two elementary physical phenomena: diffusion of enzymes and metabolites, and enzyme-catalyzed conversion of metabolites (reactions). The cytoplasm, the cellular interior where diffusion and reactions take place, is overcrowded with molecules. Hence, physicochemical conditions inside the cells differ significantly from what is typically observed in in vitro experiments and simulations. In particular, self-diffusion coefficients of both enzymes and metabolites decreases significantly, and the diffusion process can anomalously slow down under certain conditions (subdiffusion). In contrast to the slow-down of molecular motion, most enzyme-catalyzed reactions occur at faster rates inside the cells, rather than in vitro. This effect could be caused by enzymatic channeling, i.e. when intermediate metabolites are not released into the cytoplasm but passed directly from one enzyme to another.

Project description
DThe objective of this project is to study diffusion and reactions in crowded environments, and to reveal physical mechanisms responsible for anomalous diffusion and channeling. The successful candidate will study systematically the dependence of diffusivity on molecular crowding by means of Brownian Dynamics (BD) simulations. He or she will further apply this knowledge to investigate potential channeling and reaction acceleration effects in cytoplasm-like conditions.

Requirements
We are looking for enthusiastic and motivated students with a background in physics, theoretical chemistry, or similar, in their final year. The project requires programming experience in C/C++, bash, python, as well as good communication skills and strong interest in multidisciplinary research. The project can start immediately.

For further information and application please contact

Dr. Eric von Lieres
Head of Modeling and Simulation
Institute of Bio and Geosciences
IBG-1: Biotechnology
Forschungszentrum Jülich
52425 Jülich
Germany

+49 (2461) 61-2168
e.von.lieres@fz-juelich.de

Dr. Svyatoslav Kondrat
Postdoctoral Researcher
Institute of Bio and Geosciences
IBG-1: Biotechnology
Forschungszentrum Jülich
52425 Jülich
Germany

+49 (2461) 61-1959
s.kondrat@fz-juelich.de


IBG-1: Biotechnology: www.fz-juelich.de/ibg/ibg-1/EN


Servicemeu

Homepage