About Satomic

Satomic’s mission is to close the gap from idea to molecule with faster navigation of chemical space. We are building an automated chemistry platform that integrates laboratory robotics, software, and AI to transform small-molecule synthesis and drug discovery.

As an early-stage startup, we are not only building the technology but also the playbooks, partnerships, and culture that will shape a new paradigm for drug discovery and chemistry at scale.

This role is critical to Satomic’s mission of closing the gap from idea to molecule by building the core software systems that turn customer intent into reliable, executable chemical reality. In executing our mission, Satomic is building an API to Atoms and this role ensures the software behind that API gives a clear, frictionless experience for users who depend on it to solve some of the most important challenges in medicine and human health.

About the role

San Diego, CA

On-site is preferred, but fully remote is also acceptable, with travel to San Diego expected ~1–2 times per year

We are seeking a Senior Systems / Backend Engineer to own and build the execution backbone of Satomic’s automated synthesis platform. This role is responsible for designing, implementing, and owning the systems that translate molecule requests into existing instrument-executable reaction planning software, schedule real laboratory assets, orchestrate long-running workflows, and track progress and failures end-to-end.

You will be the technical owner of long-running, stateful systems that must operate under real-world constraints: limited inventory, procurement delays, instrument scheduling conflicts, partial failures, laboratory retries, and re-work. 

This is a hands-on execution-focused role for a senior engineer who has previously owned backend systems in production, understands how systems break as they scale, and is comfortable making architectural tradeoffs with incomplete information. You will partner closely with chemistry, automation, and data colleagues as a technical peer, with significant ownership over system design and outcomes.

This role prioritizes building correct, working systems first, with thoughtful evolution toward scale as real usage and constraints emerge. We value engineers who can distinguish between what must be robust from day one and what can be intentionally deferred.

This role does not own machine-learning model development or data science, but does own how those components are integrated into robust, production workflows.

Expected Outcomes:

By day 30, you will have:

• Produced a documented workflow diagram of Satomic’s synthesis execution lifecycle, from compound request through planning, laboratory execution, failure handling, and delivery, clearly identifying the inputs, outputs, system boundaries, and state transitions at each step.
• Completed a written review of the existing backend systems and infrastructure, outlining what to keep, what to evolve, and what to change, with the key risks, tradeoffs, and reasoning behind those recommendations.
• Shipped a tightly scoped, user-facing backend feature in the existing system that research operations currently use, without introducing major architectural changes.

By day 90, you will have:

• Produced a written execution architecture for workflow orchestration and state management, including a diagram and accompanying documentation that define system boundaries, core abstractions, ownership of state, explicit failure and retry behavior, and which design decisions are intentionally deferred.
• Delivered an MVP execution pipeline for Satomic’s production process, integrating synthesis planning, inventory, purchasing, and laboratory execution systems to support synthesis workflow from molecule request through delivery.
• Implemented a state-machine–driven, event-based execution model for the production MVP, with explicit states, transitions, and failure/retry behavior for a long-running, multi-step molecule delivery workflow.
• Established and documented backend engineering standards in active use for the production execution system, covering testing strategy, error handling, retries, and observability.
• Reduced manual intervention required to monitor and recover from production execution failures, demonstrated by clearer execution state, faster diagnosis, and more reliable recovery during molecule delivery.

By year 1, you will have:

• Built a stable, extensible execution platform that supports multiple concurrent customer synthesis programs.
• Clearly defined abstractions that allow new reaction types, assets, or constraints to be added through extension rather than core rewrites.
• Enabled the company to scale execution volume without proportional increases in operational overhead.
• Become the internal reference point for backend systems and execution architecture. 

By year 5, you will have:

• Helped evolve Satomic’s execution software into a core competitive advantage and industry reference.
• Enabled synthesis at scales and reliability levels that would not be feasible without automation-first software.
• Mentored future engineers working on orchestration, execution, and production systems.
• Left a durable architectural foundation that continues to power Satomic’s platform as the company scales.

What You Will Own 

• The architecture and implementation of backend execution systems
• Workflow modeling, state machines, and event-driven coordination
• System correctness, idempotency, and failure recovery
• Backend code quality, structure, and engineering standards
• Production readiness: observability, debugging, and operational clarity

What this Role Is (and Is Not)

This role is:

• A systems-heavy backend engineering role
• Focused on workflow orchestration, execution, and reliability
• Ownership-oriented and impact-driven
• Senior IC ownership with strong technical authority and a clear path to expanded scope

This role is not:

• A frontend only role
• An ML research or model-training position
• A DevOps-only or infrastructure-only role
• A role with narrowly defined designs or close day-to-day guidance

Qualifications

We are looking for an engineer who has owned backend systems end-to-end in production, including:

• Experience designing and operating long-running or asynchronous systems where failures are expected
• Prior ownership of backend services or workflows that scaled in complexity, load, or operational importance
• Strong intuition for correctness, idempotency, and state management
• Comfort making architectural tradeoffs and saying “not yet” when appropriate
• Ability to collaborate closely with non-software domain experts and translate real-world constraints into software systems
• Strong Python experience preferred; openness to other languages

Overview of Satomic’s Interview Process

• 10-minute phone screen: A brief introductory call to discuss the role and answer questions.
• 3 × 45-minute interviews: Conversations focused on systems you’ve owned end-to-end, the design decisions behind them, and how they behaved under failure and scale.
• 90-minute final round: A representative systems or workflow scenario discussed live with the interview panel.