Master thesis on Modeling and Simulation of Anomalous Protein Diffusion in Membranes through Generalized Langevin Equation-based Approaches
Forschungszentrum Jülich

Master thesis on Modeling and Simulation of Anomalous Protein Diffusion in Membranes through Generalized Langevin Equation-based Approaches

  • PhD / Postdoc / Thesis (From 25 to 36 months)
  • Jülich (Germany)
  • Published on September 4 2021
Master thesis on Modeling and Simulation of Anomalous Protein Diffusion in Membranes through Generalized Langevin Equation-based Approaches

One of the research activities of IAS-5/INM-9 at Forschungszentrum Jülich focuses on the mesoscale modeling of the complex network of molecular interactions responsible for the transmission of information through neuronal cells. This network of interactions regulates very complex tasks such as memory, learning, motivation or motion, and involves many different partner molecules (e.g. proteins and neurotransmitters), located in different cellular compartments, which have to diffuse, meet and interact at the correct time in the correct place. In our institute we develop stochastic models borrowed from statistical physics as well as computational tools to describe diffusion, encounter, and partners recognition processes occurring at subcellular level on time and special scales of the order of millisecond and micrometer. The phenomenological parameters used as input to such mesoscopic models are derived in a mean field-type approach by higher resolution atomistic simulations. The aim is to understand how physico-chemical features such as cellular membrane composition, electric fields, long-range electrodynamic interactions, shape signaling transduction and induce specific cellular responses to external stimuli.

Scope of the Master Thesis:
Within this context the master student will tackle the problem of the anomalous lateral diffusion of proteins embedded in cellular membranes. Indeed, the signaling typically initiate at the cellular membrane, consisting of a phospholipid bilayer, acting as a selectively permeable barrier between the extracellular environment and the interior of the cell (the cytosol), which embeds or links membrane proteins. Upon an external stimulus some membrane proteins are activated and initiate a cascade of interactions (involving other proteins), which then propagate from the membrane to the inner cell volume. For many of such interactions, diffusion is the rate-limiting step, thus determining the kinetics of the processes. Cell membrane fluidity shapes lipids and proteins lateral diffusion in the membrane plane. Both proteins and lipids diffusion deviate from a simple Brownian motion as predicted by the standard Langevin-equation, showing the characteristic features of a viscoelastic system (i.e. systems that both dissipate and store mechanical energy in response to an applied shear strain). Using Generalized Langevin equation-based approaches, the student will model such "anomalous" behavior to study how membrane composition, concentration of proteins in membrane, and compartmentalization affect the diffusion of proteins and lipids in membrane.

Your Profile:

  • Bachelor degree in Physics
  • A good knowledge in statistical physics and numerical methods is recommended
  • Interest in bio/soft matter and simulation
  • Experience in programming languages and Linux-based clusters usage is a plus
  • Fluent in English (spoken and written)
Our Profile:

  • Highly motivated scientists of different subject areas working together
  • Interdisciplinary work applying statistical physics and computational methods to biological problems
  • Intensive supervision by one or more experienced and helpful colleague(s)
  • Friendly and welcoming work environment
Due to the SARS-CoV-2 regulations, work is done in home office if possible. Safety is of paramount importance for us. All necessary equipment (computers etc.) is provided. We are committed to equality and diversity and welcome applications from everyone! If you are interested, you are more than welcome to contact us by email including a motivation letter, a CV, and the exams transcripts.

Contact:

Forschungszentrum Jülich GmbH,
Institute of Advanced Simulations & Institute of Neuroscience and Medicine (IAS-5/INM-9)
52425 Jülich

More information: https://www.fz-juelich.de/ias/ias-5/EN/Research/2-Methods/Mesoscale%20Modeling/_node.html