Senior Software Engineer, Platform

Location: Boston, MA

Silicon Therapeutics (“SITX”) is a privately held, physics-driven integrated drug discovery company. SITX’s discovery efforts as well as physics-based platform are all completely in-house, with a full wet lab as well as a team of experienced R&D professionals spanning biology, biochemistry, chemistry, biophysics (NMR + X-ray) & preclinical sciences. SITX’s engine leverages quantum mechanics and molecular dynamics, which are deployed on its own internal supercomputer composed of over 400 GPU’s and FPGA’s and allows SITX to accurately simulate the physical motion and properties of biological targets at an atomistic level resolution. We are the only company that owns the entire spectrum of physics-driven drug discovery from chip-to-clinic with a team of over 60 individuals in Boston. 

Our diversity and our cross-functional, multi-dimensional teams make us strong. We foster an open-minded culture where we come to work without preconceptions about how people think. With all channels open for communication, we can rapidly fuse information across disciplines and teams.

Job Summary

Silicon Therapeutics is seeking a highly motivated, collaborative, and talented Senior Software Engineer to work in a multi-disciplinary organization with a focus on overcoming challenging drug discovery bottlenecks using advanced molecular simulation methods to complement our integrated experimental capabilities. 


  • Work closely with Silicon Tx scientists to design, develop, and deploy computational methods and software for our drug discovery efforts
  • Conceptualize, implement, and maintain software engineering best practices
  • Ensure scalability, extensibility, and portability of platform code
  • Create, integrate, and maintain databases for storage and access of results
  • Investigate latest trends and scientific advancements in data analytics and high performance computing and propose adoption where appropriate
  • Coordinate joint software development efforts between our Boston and Suzhou offices and facilitate their communications and collaborations 

Required Qualifications

  • Fluent speaker in English and Chinese with strong communication skills
  • Outstanding development skills
  • Demonstrated track record of overcoming challenging problems
  • Experience leading projects with geographically distributed teams
  • Strong knowledge of Python
  • Familiarity with version control (such as Git) and test-and-release (such as Jenkins) frameworks.
  • Flexible work hours to accommodate colleagues in China

Additional Preferred Qualifications

  • Ability to mentor other software engineers and manage outsourced software development projects
  • Experience with parallel programming, especially data-parallel, using MPI, OpenMP, OpenACC or CUDA C/C++/Fortran
  • Experience working with containers
  • Ability to manage HPC clusters (CPU and GPU based)
  • Experience in using/deploying workflow frameworks such as Airflow, CWL, etc. 
  • Experience with scientific computing systems and schedulers
  • Passionate about developing software to advance drug discovery


Silicon Therapeutics provides equal employment opportunities to all employees and applicants for employment and prohibits discrimination and harassment of any type without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal, state or local laws.