ML Research Scientist - Computational Biophysics

Merge Labs

$130K — $180K *
Pharmaceuticals & Biotech
Less than 5 years of experience
Job Overview by Ladders

Qualifications

  • 5-7 years of experience in deep-learning, protein structure modeling, and molecular dynamics.
  • Working knowledge of transfer-learning strategies.
  • Proficiency in Python/PyTorch/Jax and ability to produce clean, reproducible code.
  • Experience integrating machine learning with experimental science under resource constraints.
  • Collaborative mindset with systems-level thinking.

Responsibilities

  • Build frameworks for protein structure modeling and molecular dynamics.
  • Collaborate with scientists to define and encode optimization objectives.
  • Prototype and validate modeling frameworks using diverse datasets.
  • Democratize first-principles analytics for non-domain experts.
  • Develop ML frameworks incorporating first-principles knowledge.
  • Remain updated with advancements in molecular dynamics and deep learning.
  • Contribute to long-term research strategy and act as a thought leader.

Benefits

  • Collaboration across disciplines including engineering and data science.
  • Opportunity to lead the integration of machine learning and experimental campaigns.
  • Involvement in innovative biotechnology solutions with real-world applications.
  • Exposure to the latest research and advancements in the field.
Full Job Description


About the team:

Our Bio team designs, builds, and characterizes the biotechnologies that form the foundation of next-generation brain-computer interfaces. We combine molecular engineering, synthetic biology, neuroscience and advanced physical methods such as ultrasound to establish less invasive, high-bandwidth connections with neurons. The Bio team develops our core molecular technologies, validates their performance in vitro and in vivo, and demonstrates their advanced capabilities in animal models. We build custom experimental setups and pipelines and collaborate closely with engineers and data scientists. We work across disciplines to come up with creative ideas and solve some of the most challenging problems in biotechnology.

About the role:

We're hiring a Senior / Principal ML Biophysicist to lead the development of scalable molecular dynamics pipelines and integrate physics-based models with machine learning frameworks. Starting from first principles, you'll architect the company's molecular modeling foundations-establishing tools and workflows for simulating, analyzing, and interpreting biomolecular dynamics to function relationships. Over time, you'll help translate these into predictive frameworks that accelerate molecular engineering, inform experimental campaigns, and enable the discovery of highly functional molecules.

In this role, you will:
  • Build the scientific and engineering scaffolding for protein structure modeling, molecular dynamics, and integrations with downstream ML frameworks.
  • Collaborate with wet-lab scientists to define tractable optimization objectives and encode domain specific priors and constraints.
  • Prototype modeling frameworks using internal and public datasets; benchmark and validate performance.
  • Serve to non-domain experts for democratization of first-principles analysis
  • Drive the development of ML frameworks that explicitly incorporate first-principles priors.
  • Stay up-to-date with the latest research in deep-learning, molecular dynamics, and protein structure modeling and prototype novel algorithms that can be deployed to improve the company's discovery or development workflows.
  • Contribute to the long-term research roadmap and serve as a thought-leader for scientists.

You might thrive in this role if you have:
  • Strong grounding in deep-learning, protein-structure modeling, and molecular dynamics.
  • Working knowledge of transfer-learning strategies
  • Proficiency in Python / PyTorch / Jax and comfort writing clean, reproducible production grade code.
  • Experience bridging machine learning and experimental science-working with sparse, noisy, and or high-cost data.
  • A collaborative, systems-level mindset.


Nice to haves
  • Familiarity with neuroscience.
  • Familiarity with language / state-space models.

If you're excited about this role but don't meet every qualification, please apply. As we build, we're hiring for complementary strengths to form a high-impact team.

For more information about hiring at Merge, please visit our Hiring FAQ

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