Ph.D. Student Maps Brain Geography with Math at Oden Institute

When A. Derya Bakiler arrived at the Oden Institute for Computational Engineering and Sciences at The University of Texas at Austin to conduct research as a Ph.D. student, she knew exactly what had led her here.  

She had watched a short introductory video about the institute years earlier, while completing her master's degree at Bilkent University in Ankara, Türkiye. In it, Professor Omar Ghattas described the Institute's mission in a way that stopped her in her tracks.  

"I realized the Oden Institute would be the place I would want to be if I wanted to go further with this line of research,” she recalled. 

Finding Her Field 

Earlier, in her third year at Bilkent while pursuing her undergraduate degree in mechanical engineering, Bakiler became convinced she had chosen the wrong field. But then a course on the molecular simulation of materials introduced her to computational mechanics, a field she had never known existed.  

"I realized it was perfect for me, because I always enjoyed coding and understanding the underlying physics of systems and materials," she said. 

She liked the topic and the professor’s mentorship so much that she stayed to pursue a three-year master's degree, continuing to work on modeling instabilities in soft materials. 

What are soft material instabilities? Consider the human brain. Its characteristic folds and creases, known as sulci, form because the brain's white and gray matter have different stiffnesses and grow at different rates. The skull constrains that growth, so the brain "buckles" to fit inside the skull.  

Because brain tissue is extraordinarily soft, modeling these large deformations requires specialized mathematical tools. That problem drew Bakiler in, and the resulting computational techniques she developed eventually drew her to Austin. 

Groundbreaking Potential 

As a doctoral student in Oden’s Computational Mechanics Group, Bakiler is now working on modeling the glymphatic system, the brain's waste disposal network, which enables cerebrospinal fluid to flow through pathways in the skull and along pipes surrounding arteries and veins, mixing with the fluid inside the brain tissue, gathering metabolic waste and then carrying it back out. When the system malfunctions, proteins accumulate into plaques — the biomarkers for Alzheimer's disease. 

"We don’t know yet if the plaques are the cause or effect of Alzheimer's," Bakiler explained. "That is the critical knowledge gap we are trying to address.”  

Her goal is to build a computational model of the glymphatic system calibrated to real-patient data that can simulate how plaque formation progresses in a specific individual's brain. Without computation, this work would require repeated invasive procedures directly on a patient's brain.  

Collaborating Across Disciplines 

The environment at the Oden Institute has reshaped how Bakiler approaches problems. Before arriving, she had little experience working across disciplines. Now she collaborates with imaging specialists, biologists and clinicians, aggregating the knowledge across fields. 

Bakiler’s long-term vision for her research is ambitious. Within five years, she hopes to have a pipeline that takes a patient's brain MRI as input and produces long-term plaque formation predictions as output, eventually without relying on invasive experimental procedures. In the 10-year view, she sees patient-specific computational models like hers becoming a genuine part of clinical practice, shifting medicine toward prevention rather than treatment.  

"I truly believe that digital twins will be the next big revolution in healthcare," she said, "and will change how we approach many diseases that we currently do not have a cure for, like Alzheimer's disease." 

Read much more in the original feature, “The Brain's Hidden Plumbing and the Math Behind It,” written by Tariq Wrensford for the Oden Institute website.