CENTRALE LYON - PhD Effects of the Hofmeister ions series on the adsorption of sepsis metabolit[...]

CENTRALE LYON - PhD Effects of the Hofmeister ions series on the adsorption of sepsis metabolites on a gold layer. Molecular dynamics simulations study enhanced with a validation by surface plasmon resonance analysis. Application to sepsis diagnosis

• On-site

Background:

Sepsis is a blood infection, often of bacterial origin. It is the leading cause of preventable death in developed countries. Currently, it takes several days to diagnose the disease because bacteria can be present in very low concentrations in the blood. However, patients' chances of survival can decrease by the hour. Thus, there is an urgent need for a diagnostic tool that can provide results in just a few minutes. A range of blood metabolites have been identified as biomarkers of sepsis. However, metabolites are low molecular weight molecules embedded in the blood among an abundance of nonspecific molecules. Their detection is still a challenge.

The INL laboratory has been working since 2021 on the modeling of the impact of chemical modification of surfaces on the adsorption of metabolites, from fluid samples, and their subsequent detection by mass spectrometry, by combining molecular dynamics simulations and experiments. The present PhD thesis will investigate the effects of additional specific ions in fluid samples (Hofmeister ions series) on the organization of interfacial water molecules and metabolites adsorption on gold surfaces.

The principal objective of the thesis is to model the intermolecular interactions between metabolites and a chemically modified gold surface in the presence of different ions. Molecular modeling will be performed with Ecole Centrale de Lyon cluster “Newton”, with the classical OPLS force field. The first step will be the identification, by all‑atom molecular dynamics simulations, of ions able to improve the specific adsorption of a panel of sepsis metabolites on chemically modified gold surfaces. The effects of ions on the organization of interfacial water molecules will be investigated, as well as the impact of the organization of water molecules on the selective adsorption of metabolites depending on their physicochemical properties. Simulation results will be assessed by experimental surface plasmon resonance (SPR) analysis on gold surfaces. The student will develop a data analysis method (e.g. statistical methods) to identify the main parameters driving metabolite‑surface interactions in the presence of different concentrations and ratios of ions. If time permits, mass spectrometry analysis will be carried out through collaborations to assess the method within a clinical framework.

Scientific environment:

The PhD student will be supervised by Dr Christelle Yeromonahos (specialist of molecular dynamics simulations) and Prof. Jean‑Pierre Cloarec (specialist of surface plasmon resonance) at the INL lab. The Chemistry and Nanobiotechnology group, at INL, is conducting interdisciplinary research activities on coupling numerical methods, nanotechnology and molecular biology for health and environmental applications.

Job requirements

The PhD candidate should ideally have a background in engineering sciences, material sciences or physical chemistry. A culture in computer science, numerical simulations and data analysis via Python or Matlab is required. Knowledge about computational chemistry, and High‑Performance Computing on datacenter would be a plus. Also, the candidate must be able to work at the interface between chemistry, mathematics, and physics. An interest for experimental chemistry and surface plasmon resonance is required.

Funding:

In the framework of the “Ecole Doctorale Matériaux”, the candidate will apply in April 2026 to a PhD grant beginning in October 2026 for 3 years. In complement to this grant, the candidate can also participate to the teaching of ECL’s students if desired.