Jobs openings

PhD positions

Starting:      September 2021
Duration:     4 years
Expires:        Applications are considered until the position is filled
Supervisor: Robert Vacha (robert.vacha@mail.muni.cz)
Employer:   CEITEC Masaryk University, Czech Rep.


Postdoc positions

Starting:      April 2021 or later
Duration:     2 years
Expires:        Applications are considered until the position is filled
Supervisor: Robert Vacha (robert.vacha@mail.muni.cz)
Employer:   CEITEC Masaryk University, Czech Rep.


Topics:

1) Selectivity of translocation across lipid membranes

We have shown that a specific class of transmembrane proteins, called scramblases, can facilitate not only spontaneous flip-flop of lipids but also a translocation of other amphiphilic molecules across cellular membranes. However, we miss information about the selectivity of this transport. The goal of this project is to determine the specificity of scramblase activity and obtain a molecular understanding of the selectivity. The main tool will be Molecular dynamics simulations with free energy calculations.

2) Synergistic translocation of multiple peptides 

Translocation of peptides across cell membranes is one of the mechanisms by which antimicrobial peptides can kill bacteria. Moreover, such peptides can act as cell-penetrating peptides delivering drug cargos to the cell. Despite the potential of such peptides, their development is hindered by the lack of knowledge about the peptide sequence-to-function relationship. In this project, we will take advantage of peptide synergism, in which peptide mixture is more effective than its components. In particular, the project is focused on the co-translocation of multiple peptides. The main tool will be Molecular dynamics simulations with free energy calculations. Part of the project could take advantage of Monte Carlo simulations with a highly coarse-grained model.

3) Association of proteins in phospholipid membranes

A large fraction of membrane proteins forms oligomers. These include receptors, ion channels, and fusion proteins, which association and dissociation control essential cellular processes. In the past, the membrane was viewed as a passive environment, in which the association takes place. Now we know that lipids can play an active role in determining the change of the oligomerization state. However, the interplay between the lipids and protein oligomerization state remains poorly understood. The goal of this project is to calculate the association of selected membrane proteins in the environments of various lipid compositions and determine the key features controlling the oligomerization state. We will do so by Molecular dynamics simulations with free energy calculations.

Eligibility: Outstanding candidates with experience in computer simulations and with an MSc/PhD degree in the fields of biophysics, soft matter physics, physical chemistry, computational chemistry, statistical mechanics, or related fields. Experience with molecular dynamics simulations (with GROMACS, CHARMM, NAMD, AMBER, LAMMPS, etc.) or other simulation techniques (Monte Carlo, DPD, etc.) at the atomistic or coarse-grained level would be an advantage.

Computing Resources: Successful candidates will have access to local computing clusters with 2500 cores and 100 GPUs. Access to Metacentrum NGI – National Grid Infrastructure for computing (with ~20,000 cores) will be also available. Additional resources include the possibility of applying for IT4Inovations, where the group is active.

Competitive salary: depending on the position - supported by grant projects including ERC consolidator grant.

Application procedure: Applications must include a CV, with list of publications and study results, short personal statement (description of research interests, past, and plans), and the name of a person willing to provide a letter of recommendation. Applications with all this material (preferably in a single pdf) should be sent to Robert Vacha (robert.vacha@mail.muni.cz).

Why join us?

Institute:

CEITEC is a scientific centre in the fields of life sciences, advanced materials and technologies whose aim is to establish itself as a recognized centre for basic as well as applied research. CEITEC offers a state-of-the-art infrastructure and great conditions to employ excellent researchers. Our institute values diversity and promotes an inclusive working environment with the aim to support the best scientists. CEITEC MU is a proud holder of the HR Excellence in Research Award by the European Commission.

Information about Brno, Czech Republic:

  • The capital of South Moravian Region and the second largest city in the Czech Republic with a population of almost 400,000 people
  • Modern, dynamic and fast growing centre of industry, trade, science, research and innovation with business incubators and centres of excellence in science
  • A city of universities with more than 86,000 students
  • More than 10,000 researchers; 2,200 IF publications/year; 600+ PhD graduates/year,
  • 500 mil. EUR of R&D investment per year, more than 350 companies with in-house R&D,
  • City of Gregor Mendel, the founder of genetics; the prestigious Mendel Lectures series takes place in Brno since 2003 (lectures of the world´s top scientists, including Nobel Prize winners),