Proteins are far more than nutrients we track on a food label. Present in every cell of our bodies, they work like nature’s molecular machines. They walk, stretch, bend, and flex to do their jobs, pumping blood, fighting disease, building tissue, and many other jobs too small for the eye to see. Their power doesn’t come from shape alone, but from how they move. 

In recent years, artificial intelligence has allowed scientists to design entirely new protein structures not found in nature tailored for specific functions, such as binding to viruses, or mimicking the mechanical properties of silk for sustainable materials. But designing for structure alone is like building a car body without any control over how the engine performs. The subtle vibrations, shifts, and mechanical dynamics of a protein are just as critical to its functions as its form.

Now, MIT engineers have taken a major step toward closing the gap with the development of an AI model known as VibeGen. If vibe coding lets programmers describe what they want and then AI generates the software, VibeGen does the same for living molecules: specify the vibe — the pattern of motion you want — and the model writes the protein. 

The new model allows scientists to target how a protein flexes, vibrates, and shifts between shapes in response to its environment, opening a new frontier in the design of molecular mechanics. VibeGen builds on a series of advances from the Buehler lab in agentic AI for science — systems in which multiple AI models collaborate autonomously to solve problems too complex for any single model.

“The essence of life at fundamental molecular levels lies not just in structure, but in movement,” says Markus Buehler, the Jerry McAfee Professor of Engineering in the departments of Civil and Environmental Engineering and Mechanical Engineering. “Everything from protein folding to the deformation of materials under stress follows the fundamental laws of physics.”

Buehler and his former postdoc, Bo Ni, identified a critical need for what they call physics-aware AI: systems capable of reasoning about motion, not just snapshots of molecular structure. “AI must go beyond analyzing static forms to understanding how structure and motion are fundamentally intertwined,” Buehler adds.

The new approach, described in a paper March 24 in the journal Matter, uses generative AI to create proteins with tailor-made dynamics.