Senior Application Scientist

About AQEMIA

AQEMIA is a drug invention company dedicated to creating entirely new medicines to address major unmet medical needs. At the core of our mission is QEMI
, our proprietary molecule-invention platform, which uniquely combines cutting‑edge science with advanced technology. Powered by physics‑based modeling, statistical mechanics, and generative AI, QEMI allows our teams to design novel drug candidates from first principles.

What makes AQEMIA different is our commitment to true innovation: our research is dedicated to the invention of new molecular entities, not the refinement of existing ones. We focus on inventing never‑before‑seen molecules
, without relying on experimental data, and advancing them into a growing pipeline of proprietary programs and strategic partnerships with leading pharmaceutical companies.

Our most advanced preclinical programs are currently in vivo optimization
, targeting diseases still waiting for effective treatments, offering our teams the opportunity to work on science that can make a real difference in people’s lives.

For more information, visit  and Linked In.

AQEMIA brings together a diverse, multidisciplinary team of 65+ professionals based in Paris and London. Our scientists and engineers, including chemists, physicists, machine learning experts, and software engineers, work side by side to push the boundaries of early‑stage drug discovery.

This close collaboration across disciplines is central to our approach, enabling us to tackle complex scientific challenges from first principles and translate cutting‑edge ideas into novel therapeutic candidates. At AQEMIA, team members are encouraged to contribute their expertise, learn from one another, and play an active role in shaping the future of drug invention.

The mission of the Molecular Simulations Team is threefold:

• Support drug discovery programs by maximizing the impact of binding free energy calculations in decision‑making.
• Build, benchmark and continuously improve reproducible and scalable pipelines for binding free energy calculations, enabling support for multiple programs in parallel.
• Collaborate closely with our Physics Research Team to integrate innovations from Aqemia’s proprietary binding free energy methods.

As a Senior Application Scientist in the Molecular Simulations Team, you will be a scientific leader and technical expert, contributing to the strategy and delivery of Aqemia's Binding Free Energy Technology. You will help define and evolve how physics‑based simulations inform and accelerate drug discovery decisions at Aqemia.

• Design and lead large‑scale simulation studies (e.g., relative and absolute binding free energy predictions).
• Evaluate and improve modeling protocols for reproducibility, accuracy, and efficiency.
• Serve as a mentor to junior scientists, promoting best practices in simulation and analysis.
• Contribute to cross‑functional planning and the integration of simulations with experimental and AI‑based insights.
• Stay at the forefront of developments in molecular simulations and suggest innovations to the team.
• Support the development and scaling of workflows that can serve multiple drug discovery projects.
• Work closely with the Research Team to implement improvements and updates to Aqemia’s proprietary binding free energy methods.

• MSc or PhD in Computational Chemistry, Biophysics, Statistical Mechanics, or related discipline.
• 5+ years of experience in molecular simulations, ideally within a drug discovery context.
• Deep knowledge of free energy methods, molecular dynamics, and simulation software.
• Strong programming/scripting ability and experience with workflow automation.
• Demonstrated ability to lead scientific projects and communicate effectively across disciplines.

• Experience in machine learning applications for physics‑based modeling.
• Track record of scientific publications and contributions to the computational drug discovery community.

Scientific Rigour:
Champion high scientific standards and promote best practices across the team.

Humble and Willing to Learn:
Lead by…