Staff Engineer – Automation/Controls

Molecular Assemblies is a San Diego-based company developing a revolutionary, enzymatic DNA synthesis technology capable of powering new products in industrial synthetic biology, personalized therapeutics, precision diagnostics, and eventually information storage, nanotechnology and more.

The staff level automation / controls engineer will be a key contributor in the design, build and programming of microfluidic systems for the automation of the company’s enzymatic synthesis technology. Responsibilities are wide and varied and encompasses hardware design for thermal and microfluidic systems, custom software programming for prototype systems, and automation for characterization and reliability testing of hardware components.


  • Work with team lead on the architecture, design, and integration of microfluidic systems
  • Program custom control software, translating requirements and feature requests through the various stages of development
  • Design a custom scripting environment for automated enzymatic synthesis workflows
  • Drive the design, fabrication and assembly to control thermal and fluidic subsystems, and associated diagnostic sensors (both analog and digital circuits)
  • Work cross-functionally with biochemistry, systems integration and fluidics engineering peers to meet target performance goals
  • Participate in the troubleshooting of complex fluidics systems, developing custom characterization tools for identifying root cause and corrective action implementation
  • Support the selection of critical fluidic and thermal components


  • B.S. in Computer Science, Electrical Engineering, Mechanical Engineering, Bioengineering, Systems Engineering or related field
  • 5+ years R&D experience, designing and implementing control solutions for integrated devices
  • Software programming experience in various languages (C#, C++, Python, etc…). Experience in MFCs in Visual Studios is preferred.
  • Demonstrated experience interfacing with components utilizing RS232, RS485, I2C and similar communication protocols
  • PCB layout, assembly, and troubleshooting for both digital and analog circuits is a plus
  • Knowledge of embedded system circuit design and microcontroller programming experience is a plus
  • Experience in applications integrating microfluidics, chemistry/assay and sensing components is a plus

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