Research Scientist in Molecular Dynamics (M/F)

Qubit Pharmaceuticals is a French-American deeptech startup, focusing on discovering novel molecules for complex targets in healthcare and materials science. We leverage proprietary molecular simulation and quantum-physics based modeling technology to develop our own discovery programs that we either co-develop with or license out to pharmaceutical and industrial partners. This enables us to design more effective and safer drug candidates, aiming to significantly reduce the time and investment needed for discovery. In just 18 months, Qubit Pharmaceuticals grew its portfolio to 7 programs in oncology, immunology & antivirals.

Our cutting-edge technology is based on over 30 years of research by our academic founders, and relies on three main components: in-depth expertise in computational science and high-performance computing (HPC), quantum chemistry and artificial intelligence algorithms, and a powerful, automated cloud platform for molecular simulation with chemical accuracy. We recently announced the launch of the world's most powerful AI foundation model for molecular simulation.

As part of its development, Qubit Pharmaceuticals is looking for a Research Scientist to support Molecular Dynamics/FE-based approaches and their application in current and upcoming drug discovery projects.

The per fect fit for this job

We're looking for a Computational Scientist to join our team. The ideal candidate has deep, hands-on expertise in molecular dynamics and free energy calculation methods . You should be an innovative problem-solver, capable of both developing novel computational methodologies and applying the right approaches to advance our drug discovery projects.

Your role

As a member of CC team, you will be responsible for:

• Develop and execute innovative computational strategies, leveraging molecular dynamics, enhanced sampling, and free energy methods to solve complex challenges in drug discovery
• Partner closely with cross-functional teams including medicinal chemists, structural biologists, and AI/ML researchers to integrate computational insights and advance our drug discovery projects
• Analyze, interpret, and effectively present complex simulation data to both technical and non-technical audiences
• Contribute to GPCR Structure-Based Drug Discovery projects by applying computational chemistry and CADD approaches
• Stay up-to-date with the latest advancements in molecular modeling, enhanced sampling methods, and binding free energy approaches, integrating new methodologies to continuously improve our workflows

Your qualifications and skills

• PhD in biophysical chemistry, computational chemistry or related field
• A minimum of 4 years of hands-on experience in a research lab, pharmaceutical company, or biotech startup, with a focus on molecular dynamics and free energy calculations
• Deep understanding of thermodynamics, binding free energy, and enhanced sampling methods
• Proficiency in molecular dynamics simulation packages (e.g., Tinker, GROMACS, AMBER, OpenMM)
• Extensive experience with Free Energy (FE) methods, including Absolute, Relative, and Hydration FE calculations, and various enhanced sampling approaches
• Proven experience applying FE methods to a wide range of macromolecule-ligand systems
• Hands-on experience with High-Performance Computing (HPC) environments, including the use of job schedulers like Slurm
• Experience in developing, implementing, or optimizing new FE or enhanced sampling methods
• Experience with classical (AMBER, CHARMM, OPLS) and polarizable force fields (AMOEBA)
• Familiarity with advanced simulation package options, such as performance optimization and force field tuning
• Familiarity with ML-based potentials for molecular dynamics simulations, including an understanding of their development and application
• Skilled in using various computational tools to analyze and visualize interactions from MD simulations and docking poses
• Proven experience and deep understanding of GPCR structure, function, and signaling pathways

The proposal benefits & perks

• Duration: Full time – Permanent
• Starting from January 2026
• Salary according to profile
• Health insurance and provident fund 100% covered
• Lunch vouchers worth €9 covered at 50%.
• Location: Paris 14th arrondissement
• Possibility of remote work for 2 days per week.