Senior Application Research Scientist H/F Aqemia

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 currentlyin 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.
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About our Team
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.
About the TeamThe 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.

Role OverviewAs a Senior Application Research 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.

Key Responsibilities

• Design and lead large-scale simulation studies (e.g., relative and absolute binding free energy predictions).
• Evaluate and improve modelling 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.

Qualifications & Experience

• PhD in Computational Chemistry, Biophysics, Statistical Mechanics, or related discipline.
• 5+ years of experience in molecular simulations, ideally within an industrial drug discovery context.
• Deep knowledge of free energy methods, molecular dynamics, and simulation software.
• Experience running and analysing binding free energy calculations.
• Strong programming/scripting ability (Python) and experience with code sharing platforms (GitHub).
• Demonstrated ability to lead scientific projects and communicate effectively across disciplines.

Nice-to-Have

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

PreferredMindsetScientific Rigour: Champion high scientific standards and promote best practices across the team.Humble and Willing to Learn: Lead by example with curiosity and openness to new ideas.Excited by Challenging Scientific Problems: Passionate about solving complex, cutting-edge problems and guiding others through them.Pragmatic and Impact-Driven: Combine strategic thinking with practical execution to deliver real-world impact in a fast-paced environment.Leadership through Influence: Inspire and mentor colleagues while fostering a collaborative, high-performance culture.We will be accepting applications until 14th April. Once the role closes, our team will review all submissions and reach out to candidates selected for interview.
Why Join Us ?
At AQEMIA, we work for a mission: joining us means having your own impact on changing the way drugs are discovered, and helping to shape thedirectionof our fast-growing company and team.
Expanding Drug Discovery Pipeline : Focused on critical therapeutic areas like Oncology, CNS, Immuno-inflammation... with in vivo proof of concept/patent stage programs. Collaborations with top Pharma, including a $140M Sanofi deal.World-Class Interdisciplinary Team: work alongside exceptional talent at the intersection of technology and life sciences. Our teams combine deep expertise in AI, physics-based modeling, biology, and medicinal chemistry to push the boundaries of innovation.DeepTech Recognition: AQEMIA is proud to be part of the French Tech 120 and France 2030, highlighting our role as a key player in Europe's DeepTech ecosystem.Prime Location with Flexibility : Our offices are located in the heart of Paris and London (King's Cross), with flexible work arrangements including up to two remote days per week.Strong Financial Backing : $100M raised from leading European and International investorsWe may use artificial intelligence (AI) tools to support parts of the hiring process, such as reviewing applications, analyzing resumes, or assessing responses. These tools assist our recruitment team but do not replace human judgment. Final hiring decisions are ultimately made by humans. If you would like more information about how your data is processed, please contact us.