M/F Thesis offer in Molecular Topology

Job Description

Thesis Subject

This thesis is within the field of molecular topology, an active and constantly evolving research area with significant challenges. We will focus in studying problems arising from biology using mathematical topology and combinatorics technics.

A knot is a closed simple curve with no self-intersection in 3-dimensional space. A link is an entanglement of several knots. An R-loop is a 3-stranded structure composed of an RNA-DNA complex and another single strand of DNA. The combination of mathematical modeling with the formalism of combinatorics and low-dimensional topology, especially knot theory, has led to advances that have influenced biology and biomedical research in general. The area of the topology of R-loop has attracted attention in recent years. The study of R-loop through topology/combinatorial analysis/tools has enabled significant scientific progress. Despite the progress made, many questions remain unanswered.

Experimental studies indicate that R-loops can play a destructive or regulatory role in cellular processes. It is therefore important to determine the factors influencing the formation and stability of R-loops. It is known that DNA sequence and geometry/topology affect R-loop formation. However, their geometric and topological entanglement properties are poorly understood.

The main goal of this thesis is to highlight the use of techniques related to knot theory and combinatorics to make progress on the knowledge of the structure and properties of R-loops. We are particularly interested in R-loop issues arising from a new method developed by a research group at the IGMM. We aim to gain a better understanding of these structures. One of the objectives is to determine/classify them in terms of knot type (or interlacing) by identifying an algebraic invariant, using braid theory, or applying combinatorial tools. In parallel, the topological properties of certain models will be analyzed.

We will also seek to combine topological/combinatorial techniques to study questions related to algorithmic aspects, such as the unknotting problem and its applications to the study of DNA for characterizing enzymes in terms of knot families produced when they act on trivial knots.

The applicant must have a solid background in mathematics (Master's level). Skills in knot theory and biology would be an asset, while computer skills and experience with programming languages would be appreciated. Above all, the candidate must be motivated by the prospect of conducting both theoretical and experimental research, has a strong sense of curiosity, and be eager to acquire new knowledge across different disciplines (mathematics and biology). Autonomy, initiative and willing to be open to explore new related subjects will be particularly valuable.

Your Work Environment

A 3 year full time contract. The successful candidate will be working at l'Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier. The IMAG is a joint research unit (CNRS, Université de Montpellier) which conducts research in pure and applied mathematics. This thesis is part of a 80PRIME project in molecular biology in collaboration with the Institute of Molecular Genetics of Montpellier (IGMM), CNRS, University of Montpellier. The doctoral student will interact with all participants of this project.

Constraints and risks

The PhD student will be required to discuss and to interact extensively with biologist colleagues from the IGMM, whose specific model needs will be one of the priorities of this thesis.
The doctarate will be encouraged to participate to national and international conferences.

Compensation and benefits

Compensation

2300 € gross monthly

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

The research professions