Jobs openings

PhD positions

Starting :      January 2022
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:       January 2022 or later
Duration:     2+1 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)  Antimicrobial peptides and the role of membrane asymmetry

Cell penetrating peptides (CPPs) are peptides that can spontaneously translocate cell membranes. CPPs can thus carry drugs into the cell or act as drug themselves. However, it remains unclear what conditions enables peptides to translocate and how it is affected by membrane composition. The aim of this project is to investigate the translocation of selected peptides across phospholipid membranes under non-equilibrium conditions, which correspond to experiments. The main tool will be Molecular dynamics simulations with free energy calculations using Gromacs program package and coarse-grained force field. This project will be complemented by experiments providing verification and feedback of membrane disruption. The findings could be used in the design of new antimicrobial and cell-penetrating peptides.

2) Antimicrobial peptides and their key properties for membrane permeation

Antimicrobial peptides (AMPs) can disrupt the membrane barrier function and kill bacteria, including resistant bacteria recognized by the UN and WHO as one of the biggest threats to global health. AMPs are part of the host-defense system of many organisms and promising candidates to become a new class of therapeutics. The aim of this project is to design new peptides that disrupt the membranes of pathogens. To obtain such peptides, we will establish the relationship between peptide sequence motifs and their ability to disrupt bacterial membranes. This ERC funded project will be complemented by experiments providing verification and feedback of membrane disruption. The main tool will be Molecular dynamics simulations with free energy calculations using Gromacs program package.

3) Regulation of protein liquid droplets during transcription

Cells employ protein liquid droplets to form dynamic clusters, which function as nanoreactors or storages with the increased local concentration of specific protein components. These membrane-less organelles self-assemble based on weak protein-protein interactions of intrinsically disordered domains. However, the role of specific sequences remains elusive and the mixing between different protein droplets unexplored. This project is focused on the droplets involved in genome transcription, where posttranslational modifications control the droplet composition and regulate the transcription. Expected findings are not only important for the general knowledge but could also be useful in the design of new treatments because translocation malfunction is involved in numerous diseases including cancer. The research is strongly coupled to collaborations with excellent experimental teams and will be more closely discussed during the interview. The employed tools will contain multi-scale simulations using a wide range of advanced sampling techniques and development of protein parametrization.

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),