Principal Embedded Software Engineer

Principal Embedded Software Engineer

Fluidic Controls & Instrumentation - BrainEx Platform

Bexorg, Inc.
On-site, New Haven, CT
About Bexorg

Bexorg is a precision neurology company working to improve how new medicines for central nervous system (CNS) diseases are discovered and developed.


Our team sits at the intersection of cutting-edge neuroscience, AI, engineering, and translational drug development. This work requires scientific rigor, responsible stewardship, and close collaboration across disciplines.

We are looking for people who are curious, accountable, and ready to tackle unique challenges. At Bexorg, you will work alongside colleagues who ask thoughtful questions, share ideas openly, and take ownership for moving complex work forward. Whether your background is in neuroscience, biology, engineering, data science, or operations, you can help build a stronger foundation for decisions that shape new CNS medicines.
The Role

We are seeking a Principal Embedded Software Engineer to own the electronics, firmware, and real-time control that make the BrainEx whole-brain perfusion platform work. BrainEx is a proprietary closed-loop physiological system that functions as an artificial cardiovascular, pulmonary, and renal system for an intact human brain - custom hardware and software regulating circulatory volume, cerebral blood flow, systolic pressure and pulsatility, pH, dissolved gases, temperature, metabolites, and drug dosing throughout each run.

This is deliberately not a pure-software job. We are looking for a genuine generalist - someone who writes production firmware in the morning, scopes a noisy pressure transducer signal after lunch, redesigns a fluidic manifold in CAD, and has a prototype printed or sent out for machining by the end of the week. You will be the person who takes a control problem from physiological requirement to schematic, to board, to firmware, to the Python supervisory layer above it, to a validated rig revision running on the production fleet.

You will report into the Technology team and work shoulder-to-shoulder with bioprocess engineers, surgeons, perfusion technicians, software engineers, and drug discovery scientists. Current priorities include tightening closed-loop control, extending run duration (today up to 24 hours, with active work toward multi-day and ultimately two-week runs), improving reproducibility across donors, and expanding the experimental envelope the rig can support.
What You'll Own

• Embedded Firmware & Real-Time Control
  
  • Own the embedded stack on BrainEx rigs - bare-metal and RTOS firmware (C/C++ on ARM Cortex-M; FreeRTOS or Zephyr) plus embedded Linux supervisory layers - from architecture through field deployment and versioned rollout across the fleet.
  • Implement the control loops that hold the brain in physiological range: PID, cascade, and feedforward control of pressure, flow, pulsatile waveform generation, temperature, pH, and gas exchange, with anti-windup, gain scheduling, bumpless transfer, and graceful degradation.
  • Build the state machines and interlocks governing rig setup and priming, calibration, run initiation, steady-state operation, perturbation and dosing protocols, fault detection, and safe shutdown - including watchdogs, sensor-plausibility checks, and defined safe states for every credible failure mode.
  • Guarantee determinism where it matters: loop-rate budgeting, interrupt and DMA design, jitter measurement, and instrumented timing so control behavior is provable rather than assumed.
  • Own the field buses and device integration - I²C, SPI, UART, RS-485/Modbus RTU, CAN/CANopen, EtherCAT or equivalent, USB, and Ethernet - across pumps, gas mixers, mass flow controllers, proportional valves, dialysis modules, and analyzers.

• Instrumentation, Electronics & Sensing
  • Design and bring up custom electronics: schematic capture and PCB layout (Altium, KiCad, or similar), analog front ends for bridge and ISE sensors, 16-24-bit ADC selection, isolation, EMI and grounding strategy, connectorization, and harnessing for a wet, salt-spray-adjacent lab environment.
  • Integrate and characterize the sensor suite: pressure transducers, ultrasonic and Coriolis flow meters, thermocouples/RTDs, pH and blood-gas analyzers, inline optical O₂ and metabolite sensors, bubble detectors, and load cells for gravimetric fluid balance - including calibration procedures, drift compensation, and uncertainty budgets.
  • Drive actuators precisely: stepper and BLDC motor control for peristaltic and centrifugal pumps, encoder feedback, solenoid and proportional valve drive, syringe and infusion pump control for compound dosing, and closed-loop verification of delivered volume rather than commanded volume.
  • Debug at every layer - oscilloscope, logic analyzer, SWD/JTAG, protocol sniffers, and bench fluidic loops - and close the loop with design fixes that prevent recurrence across the deployed fleet.

• Mechanical Design & Fabrication
  • Design fluidic and mechanical hardware in CAD (SolidWorks, Onshape, or similar): manifolds, sensor housings, reservoirs, bubble traps, sealed enclosures, and rig-integration hardware, with attention to O-ring and gasket sealing, dead-volume minimization, tolerance stack-ups, and biocompatible, cleanable material selection.
  • Prototype fast and manufacture well: SLA and FDM 3D printing in-house for rapid fluidic iteration, and machined parts for production-grade hardware - you should design for the process, speak fluently with machinists, and be able to run the equipment yourself as we expand in-house precision machining capability.
  • Select and qualify wetted components: tubing, connectors, quick-disconnects, and polymers evaluated for chemical compatibility with our synthetic-blood perfusate, sterilization or sanitization method, hemocompatibility, and long-duration performance.

• Software Integration, Telemetry & Operator Experience
  • Build the Python supervisory layer above the firmware: control services, device abstraction, protocol definitions, configuration management, and reproducible run scripting so that a protocol change is a versioned artifact rather than a knob turned by hand.
  • Write the tooling that makes the hardware tractable: Python calibration routines, bench automation, sensor-characterization harnesses, log parsers, and analysis notebooks - the instrumentation around the instrument.
  • Deliver real-time monitoring, alarming, and operator interfaces that let a perfusion technician supervise a multi-day run safely with minimal technical intervention, with a rational alarm hierarchy and clear operator guidance on every fault.
  • Stream and structure the data: telemetry pipelines into our AWS data lake, integration with LIMS/ELN tooling and higher-level orchestration, and time-based alignment so physiological signals, dosing events, and sampling are analyzable downstream.
  • Establish engineering hygiene appropriate to a mission-critical instrument: version control, code review, CI, hardware-in-the-loop and simulated-rig testing, firmware release process, traceability, and rollback.

• Reliability, Iteration & Collaboration
  • Move fast without breaking runs: rapidly prototype mechanical, fluidic, electrical, firmware, and control changes, then bring them to production-grade rig revisions on a fast cadence.
  • Define acceptance tests and performance metrics for each revision - control-loop performance envelopes, sensor accuracy, perfusion confirmation metrics, BBB integrity, run-success rate - and drive mean time between failures, run yield, reproducibility across donors, and the platform's duration ceiling.
  • Serve as a senior technical authority on embedded and control architecture within Bexorg, setting standards and mentoring junior engineers, technicians, and perfusionists on the rig's design, operation, and troubleshooting.
  • Translate experimental need into hardware: work directly with neuroscientists, surgeons, perfusion specialists, and drug discovery teams, and communicate clearly with non-technical stakeholders including collaborators at major biopharma companies, foundation partners, and government grantors.

What We're Looking For
Required Qualifications

• Extensive hands-on experience shipping embedded systems in production or mission-critical environments - instruments, medical devices, lab automation, industrial control, or comparable - where a firmware defect has physical consequences.
• Deep fluency in C/C++ on microcontrollers, with real working knowledge of RTOS concurrency, interrupt design, memory constraints, and low-level peripheral programming.
• Strong Python skills - not just scripting. You will build supervisory control services, device abstraction layers, calibration and test harnesses, data pipelines, and analysis tooling in Python, with the engineering discipline (typing, testing, packaging, async I/O, version control) that production instrument software requires.
• Demonstrated track record of owning projects end-to-end: requirements, schematic and board design, firmware, bring-up, commissioning, validation, and long-term support.
• Strong practical control-systems ability - you can tune a real loop on real hardware, reason about stability and sensor noise, and implement PID/cascade and state-machine logic that behaves correctly at the edges.
• Experience with fluidic or process control systems: pumps, valves, manifolds, flow and pressure measurement, gas handling, dosing, or gas exchange. This is a strong preference - the physics of the fluid path is the core of this platform.
• Hardware fluency across domains: schematic capture and PCB layout, analog signal conditioning, sensor and actuator integration, and confident bench debugging with scope and logic analyzer.
• CAD proficiency in SolidWorks, Onshape, or equivalent, with real design-for-manufacture judgment.
• Hands-on fabrication experience with 3D printing and CNC machining - experience programming and operating advanced CNC platforms (Kern, DMG MORI, Haas, Tormach, or similar) is a significant plus, along with the judgment to design parts that are genuinely machinable.
• Comfortable working in a wet-lab environment with biological tissue, plumbing, fluidics, and active hardware bring-up.
• Proven ability to operate as an aggressive self-starter with strong ownership, moving quickly and driving projects forward with minimal supervision, and excellent communication and mentoring skills.
• Bachelor's degree in Electrical Engineering, Computer Engineering, Mechatronics, Biomedical Engineering, Mechanical Engineering, Controls, Computer Science, or a related field - or equivalent industry experience with a strong track record of impact.

Preferred Qualifications

• Direct experience with extracorporeal life support or organ perfusion systems: ECMO, cardiopulmonary bypass, normothermic machine perfusion (liver, kidney, heart, lung), or hemodialysis platforms.
• Systems that must run unattended and reliably for long durations - multi-day to multi-week - with graceful handling of consumable depletion, sensor drift, and partial hardware failure.
• Embedded Linux at the platform level: Yocto or Buildroot, device drivers, device tree, PREEMPT_RT, systemd, and secure OTA update.
• Industrial control or ROS 2 ecosystems; SCADA/PLC or LabVIEW experience; digital-twin or simulation-based control development.
• Medical-device or regulated-environment background: IEC 62304, IEC 60601, ISO 13485, ISO 14971, ISO 10993, GMP/GxP, or FDA submissions.
• Background working with synthetic blood, hemoglobin-based oxygen carriers, perfluorocarbons, or other engineered perfusates.
• Familiarity with biostatistics, DOE, and process capability analysis applied to instrument and bioprocess validation.
• Machine vision, thermal or CFD modeling, or model-based/model-predictive control applied to fluidic systems.
• Advanced degree (MS or PhD) in a relevant field.

Who Thrives at Bexorg

We tend to be most successful with individuals who:

• Operate with a high level of ownership and accountability
• Are energized by fast-paced, evolving environments
• Balance strategic thinking with strong execution
• Communicate directly, thoughtfully, and collaboratively
• Are willing to roll up their sleeves and contribute wherever needed
• Bring curiosity, adaptability, and a solutions-oriented mindset
• Value scientific rigor, operational excellence, and teamwork

Why This Role Matters

• Work on a truly unique, first-of-its-kind platform at the intersection of physiology, embedded engineering, and CNS drug discovery - there is nothing else like BrainEx in the world.
• Unusual breadth of ownership: firmware, electronics, controls, CAD, and fabrication in one role, on hardware you can put your hands on the same day you design it.
• Your engineering improvements directly translate into better human-brain pharmacology data and, ultimately, into therapeutics for Alzheimer's, Parkinson's, ALS, and other devastating neurodegenerative diseases.
• Collaborate with world-class scientists, engineers, surgeons, and clinicians in a fast-moving, well-funded TechBio company with active partnerships across major biopharma, leading academic institutions, and the Michael J. Fox Foundation.
• On-site, hardware-focused work in New Haven, CT, with in-house 3D printing, a growing fabrication capability you will help shape and spec, and daily hands-on access to the systems you design and improve.
• If you're excited to own the embedded and control engineering of a platform that could fundamentally change how the world develops CNS therapeutics, we'd love to hear from you.

Compensation & Benefits

Salary Range: $180,000 - 220,000

Bexorg offers a competitive compensation package that may include:

• Competitive base salary
• Bonus opportunity
• Equity participation
• Medical, dental, and vision coverage
• Paid time off
• 401(k)
• Professional development opportunities

Work Environment & Expectations

Bexorg is a collaborative, high-accountability environment where employees are expected to operate with professionalism, urgency, adaptability, and strong follow-through. Team members should be comfortable navigating ambiguity, prioritizing effectively, and contributing beyond narrowly defined responsibilities when needed.
Equal Opportunity Statement

Bexorg is an equal opportunity employer and does not discriminate on the basis of race, religion, color, national origin, gender, sexual orientation, age, marital status, veteran status, disability status, or any other protected status under applicable law.