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Thesis topic proposal
 
Synergetic Combination of Experiment and Simulation in the Study of the Interaction between Phospholipid Membranes and Guest Molecules

THESIS TOPIC PROPOSAL

Institute: Eötvös Loránd University, Budapest
chemistry
György Hevesy Doctoral School of Chemistry

Thesis supervisor: András Wacha
Location of studies (in Hungarian): Research Group for Biological Nanochemistry, Institute for Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences
Abbreviation of location of studies: H-REN


Description of the research topic:

"Phospholipid membranes act not just as structural elements of living organisms, but also perform different functions in the course of the biochemical processes of cells, some of which are not even fully known yet. Artificial lipid membranes also have versatile uses, including drug delivery and nano-confined chemical synthesis. In-depth understanding of these self-assembled systems is therefore of utmost importance, but a nearly impossible task in their full complexity. Synthetically prepared membranes are frequently used in physico-chemical studies by isolating the relevant features of the system. These so-called model membranes have been successfully used to elucidate membrane behaviour, actiion mechanisms of various drugs and antimicrobial agents, membrane fusion and disruption processed, etc, manifesting themselves on the atomic or superatomic scale.

Two frequently used structural characterization methods are small-angle X-ray scattering (SAXS) and molecular dynamics (MD). Being a pair of experimental and in silico methods, they are often employed to understand static and dynamic structural properties of biomacromolecules in aqueous state from atomic up to supramolecular level. Using the two in concert is advantageous, whereby simulations help the interpretation of the inherently indirect experimental results, which in turn can be fed back to validate and/or steer the model system. While this approach has often been successfully used in the isotropic case (protein solutions etc.), anisotropic systems, such as phospholipid bilayers pose a challenge, due to them requiring completely different treatment with both methods.

The main task of the doctoral student will be to aid the development of such a combination technique on a wide scale of research activities, starting from preparing a scientifically relevant bilayer/guest molecule benchmark systems and extending to the interpretation of the results. During his/her PhD research, the applicant will get a good grasp on SAXS and MD, including steered MD and metadynamics. The work will be hosted by the Research Group for Biological Nanochemistry of the HUN-REN Research Centre for Natural Sciences, where both aforementioned methods are available, in the form of an in-house developed small-angle X-ray scattering instrument (https://credo.ttk.hun-ren.hu) and a computing cluster where the most common molecular dynamics programs (GROMACS, PLUMED etc.) are already available. As one of the main areas of expertise of the research group since its inception is phospholipid self-assembled systems, a wide range of other physico-chemical characterization methods are also available.
"

Required language skills: English
Further requirements: 
MSc or equivalent degree in physics or chemistry, dependable knowledge in statistical mechanics or thermodynamics, as well as basic analysis (complex numbers, multi-dimensional integrals). For a successful work in this PhD topic, programming knowledg

Number of students who can be accepted: 1

Deadline for application: 2024-05-31


2024. IV. 17.
ODT ülés
Az ODT következő ülésére 2024. június 14-én, pénteken 10.00 órakor kerül sor a Semmelweis Egyetem Szenátusi termében (Bp. Üllői út 26. I. emelet).

 
All rights reserved © 2007, Hungarian Doctoral Council. Doctoral Council registration number at commissioner for data protection: 02003/0001. Program version: 2.2358 ( 2017. X. 31. )