Senior Research Programmer, Platform

Posted: Aug. 03, 2020


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 over 25 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 40 individuals in Boston. The Company’s lead program is ramping up for IND enabling studies entry to the clinic in 2020. 

Job Summary 

Silicon Therapeutics is seeking a highly motivated Senior Research Programmer to work in a multi-disciplinary organization with a focus on overcoming challenging drug discovery bottlenecks using physics-based simulation methods.


Job Responsibilities

  • Write scripts and workflows to streamline drug discovery efforts 
  • Build software infrastructure to support platform development 
  • Implement and maintain software engineering best practices 
  • Ensure scalability, extensibility, and portability of platform code 
  • Implement novel computational methods to address critical drug discovery needs 
  • Work closely with our drug discovery team to understand project needs 
  • Investigate the latest trends in scientific methods and software engineering practices 


  • Experience in molecular modeling techniques 
  • Experience with Molecular Dynamics codes, such as AMBER, NAMD, or OpenMM 
  • Extensive programming experience (Python and C/C++ preferred) 
  • Advanced knowledge of scientific algorithm development 

Additional Qualifications 

  • Highly motivated to develop physics-based methods for discovering better medicines 
  • Ability to 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 

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.