Senior Application Research 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.

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.

About the Team

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.

Role Overview

As 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.

Preferred Mindset

Scientific 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.

Application Deadline

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.

Benefits

Expanding Drug Discovery Pipeline: Focused on critical therapeutic areas such as Oncology, CNS, and Immuno‑inflammation, with in‑vivo proof of concept and 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.

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: Offices 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.

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