The Application Research Scientist will conduct molecular simulations, analyze results, collaborate with interdisciplinary teams, and optimize internal processes to guide drug discovery.
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 AQEMIA.com and our LinkedIn.
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 Team
The mission of the Molecular Simulations Team is threefold:
- Support drug discovery programs by maximising 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 Overview
As an Application Scientist in the Molecular Simulations Team, you will work at the interface of molecular modelling, statistical physics, and drug discovery. Your focus will be on applying, implementing and improving Aqemia’s physics-based simulation methods to guide medicinal and computational chemistry and help identify high-potential drug candidates.
What you’ll do
- Execute molecular simulations (e.g., free energy calculations, Molecular Dynamics) to support drug discovery programs.
- Analyse simulation results to generate insights for project teams.
- Collaborate with computational chemists, biologists, AI researchers and medicinal chemists to design simulation strategies.
- Contribute to the optimisation of internal protocols and workflows.
- Document and present findings to multidisciplinary teams.
Qualifications & Experience
- Master’s degree plus at least 3 years of industry experience, or a PhD with at least 2 years of relevant experience in Computational Chemistry, Biophysics, Statistical Mechanics, or a related discipline.
- Hands-on experience with Molecular Dynamics, free energy methods, or protein-ligand modelling.
- Proficiency in Python and simulation tools (e.g., GROMACS, AMBER, OpenMM for instance).
- Strong communication skills and a collaborative mindset.
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.
Preferred Mindset
Scientific Rigour: Committed to high standards of accuracy, reproducibility, and method validation.
Humble and Willing to Learn: Open to feedback and continuously seeking to grow scientifically and professionally.
Excited by Challenging Scientific Problems: Motivated by tackling complex, unsolved questions at the frontier of molecular simulation.
Pragmatic and Impact-Driven: Focused on delivering practical outcomes that drive real-world impact in drug discovery.
We will be accepting applications until 7th April. Once the role closes, our team will review all submissions and reach out to candidates selected for interview.
Polite note: UK visa sponsorship not currently available for this role at this time
Aqemia’s Recruitment team leads all recruitment activities for the company. We will not recognise any notional ownership recruitment companies claim over candidates presented directly to hiring managers without our Recruitment team's consent. Unsolicited resumes sent to us from recruiters do not constitute any type of relationship between the recruiter and Aqemia, and we will not be obligated to pay fees should we hire from those resumes.
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 the direction of 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 investors
Top Skills
Amber
Gromacs
Openmm
Python
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