Marie Brut

My research explores biomolecular structure, dynamics, and reactivity through a close integration of theory and experiment. I develop and apply computational approaches to understand how biomolecules function, how enzymes catalyze reactions, and how molecular interactions shape biological activity.

Using advanced simulations - primarily at the atomic level - I investigate molecular systems in terms of structure, flexibility, reactivity, and interaction networks.

By combining molecular dynamics, quantum chemistry methods (DFT and semi-empirical approaches), QM/MM simulations, molecular docking, and related techniques, I perform in silico experiments that complement, interpret, and guide experimental studies.

Biological systems

My research focuses on enzymes as therapeutic targets and on understanding the mechanisms that govern their structure–function relationship. Using advanced multi-method simulations - primarily at the atomic scale - we characterize molecular targets in terms of structure, flexibility, reactivity, and interaction networks.

Our goal is to deepen the fundamental understanding of proteins of interest and to propose novel strategies for selectively targeting them therapeutically. We also investigate how mutations affect enzyme activity and contribute to drug resistance.

To address these questions, we employ computational approaches such as classical molecular dynamics and QM/MM simulations, and develop methodologies to predict the effects of perturbations—such as ligand binding or mutations—on molecular behavior.

These studies aim to elucidate enzyme catalytic mechanisms, characterize active sites for drug discovery, and understand how mutations contribute to disease or drug resistance. A key strength of this work lies in its close integration with experimental collaborations, which both to validate theoretical predictions at the molecular level and to provide mechanistic insight into observed biological processes.

Bio-hybrid systems

Recent advances in nanotechnology now enable the manipulation of matter at the atomic and molecular scales. Combined with progress in microfluidics, surface chemistry, nanotechnology, and electronic or optical detection, these developments make it possible to integrate biological components into bio-hybrid nanosystems.

Such systems open new opportunities for designing advanced materials and bio-inspired synthetic machines with unique and versatile functionalities, extending beyond traditional biological applications.

In this context, we use multiscale simulation approaches to investigate the behavior of biological molecules and bio-hybrid systems in non-biological environments, with the aim of integrating them as structural materials or functional elements.

This work addresses new fundamental questions arising from the convergence between biological and synthetic systems and contributes to the development of predictive models to support both fundamental research and technological innovation. It is conducted in close collaboration with experimental groups, particularly in the areas of surface functionalization and sensor design.