From bottleneck to breakthrough: Student engineers unlock fully autonomous electroporation at UCLA

Inside the California NanoSystems Institute at UCLA, where some of the most advanced and technical automated infrastructure on campus resides, two students saw an opportunity hiding in plain sight.

The Living Biofoundry, a core resource of the BioPACIFIC Materials Innovation Platform, had just installed the powerful Fisher Scientific BTX Gemini X2 Electroporation System. The instrument enables researchers to efficiently insert DNA or RNA into organisms ranging from bacteria and yeast to mammalian cells.

But there was a catch.

Despite its speed and flexibility, the electroporator still required human hands: pressing the lid-release button, lifting the lid, placing plates, launching protocols. In a facility built for fully automated, end-to-end synthetic biology pipelines, these manual steps created a bottleneck.

Students Beatrice Mihalache (Biophysics ’25) and Benjamin Flom (2nd year, Electrical Engineering) decided to remove it.

Completing the Automation Chain

At the Living Biofoundry, automation is not an add-on – it is the operating principle. The Laboratory Automation System (LAS) orchestrates workflows in which robotic movers shuttle 96- or 384-well plates between instruments. Robotic arms can transfer plates to liquid handlers, incubators, and thermal cyclers without human intervention.

The electroporator, however, was not yet part of that digital choreography.

“Automated high-throughput biology is the future,” Mihalache said. “We wanted the electroporator to function as a seamless station within those synthetic biology pipelines.”

Existing automated electroporation systems on the market did not offer twin wave functionality i.e. the ability to switch between exponential decay pulses, ideal for microbes with thicker cell walls, and square waves which are preferred for mammalian cells. Preserving that versatility while delivering full automation was essential.

Their solution would require both software innovation and mechanical know-how.

Software Meets Steel

Mihalache focused on digital integration. She pioneered a new application: linking a physical device to the automation environment via a custom communication framework.

Because the electroporator lacked a public API, she developed a software bridge that translated commands between systems. The interface allows users to specify inputs such as names and the number of plate columns to run, while feeding real-time status updates back into the automation scheduler.

“It was challenging to pioneer this integration,” she said. “We had to think creatively about autonomously operating the BTX protocol program.”

Meanwhile, Flom was building the physical bridge.

The HT-200 plate handler still required someone to press the lid-release button, lift and close the lid and initiate runs. To eliminate those manual steps without permanently modifying the instrument Flom collaborated with his younger brother, Alex, to design a custom enclosure fitted with actuators. The back of the enclosure remains accessible so the robotic arm can insert and remove plates.

“By trusting Alex to take ownership of meaningful parts of the build, from designing key mounts to assisting with wiring, calibration, and enclosure troubleshooting, I could focus on other aspects,” said Flom. “Together we made more progress than I could have alone, and the system was stronger because we each leaned into our strengths.”

Ultimately, their design preserves full manual operation, a crucial feature in a shared-use facility.

Engineering for the Real World

Automation, they quickly discovered, is less about dramatic breakthroughs and more about invisible details.

“A person compensates for misalignment, timing and small inconsistencies almost instinctively,” Flom said. “Once it’s autonomous, the system has to operate consistently and safely every single time without supervision.”

He engineered safety interlocks and enclosure protections to create safe unattended performance. Mihalache worked to ensure that software status signals aligned with mechanical states – lid open, plate seated, pulse complete – so that no error compounded. 

The collaboration extended beyond the two students. They worked with engineers from BTX and ThermoFisher, and with Living Biofoundry technical director Mike Lake and associate project scientist Ikechukwu “Ike” Okorafor to ground engineering decisions in biological reality.

For Mihalache, the experience reshaped how she thinks about research design as she begins graduate studies at UCSF in Biophysics. For Flom, who started the project while finishing high school, it revealed how much room remains for innovation in synthetic biology workflows.

“I assumed something so central to transformation workflows would already be automated,” he said. “Realizing it wasn’t, showed me how many essential research steps are still manual.”

Expanding Access, Expanding Possibility

In a shared facility like the Living Biofoundry, autonomy carries implications beyond efficiency.

Because the lab’s automation infrastructure can be accessed remotely, researchers do not need to be physically present on campus to run experiments. Integrating the electroporator into that ecosystem expands access to advanced gene delivery capabilities for academic and industry collaborators alike.

The Gemini X2 itself offers scalability, and built-in safety features. Now, with Mihalache and Flom’s automation framework, it also operates in a fully autonomous synthetic biology pipeline.

For both students, the most meaningful outcome is not the actuators or the code. It is what the system enables.

“As someone with many ideas of my own to test, being part of a project that completes the automated end-to-end workflow for microbe engineering is really exciting,” Mihalache said.

Flom agrees. “If our system makes researchers’ work more efficient and expands what they’re able to do, the impact extends far beyond our own lab. The real value is in what it allows other scientists to achieve.”

The Gemini X2 is available to researchers based at UCLA, from other academic institutions, and working in industry. For information, training or assistance, contact Ike Okorafor at iokorafor@cnsi.ucla.edu, or Mike Lake, technical director of the Living Biofoundry, at mlake@cnsi.ucla.edu. 

The BioPACIFIC MIP is funded by an NSF cooperative agreement (DMR-2445868)