Congratulations to our 2021 PhD Graduates!
Jesus Aguilar Diaz De Leon, PhD Biochemistry
Mentor: Chad Borges
Characterization of Glycan Features in Whole Biospecimens using Glycan Node Analysis and the Role of Low-Density Lipoprotein Sialylation in Cancer Immunity
“Jesús is an independent thinker and hard-working experimentalist. He developed multiple new approaches and applications for the analysis of glycans in complex biological fluids. During his time as a graduate student at ASU Jesús won multiple travel awards as well as the John Kacoyannakis (Koko) Award, presented to an outstanding graduate student in analytical chemistry. His can-do attitude will be missed. We wish him well at his new postdoctoral position in the Barb lab at the Complex Carbohydrate Research Center at the University of Georgia.” -Chad Borges
Zina Al-Sahouri, PhD Biochemistry
Mentor: Wei Liu
Biophysical Methods Advancing Lipidic Cubic Phase Membrane Proteins Studies
“Zina is extremely talented and she worked diligently for many years on an incredibly challenging project, of GPCR structural determination. Instead of quitting, she put in even more effort and finally devised a proof. While brilliance is valuable, brilliance + effort is even more so. She’s a real trooper. Graduation is not an end, but rather to be a beginning of her fantastic career.” -Wei Liu
Alex Buchberger, PhD Chemistry
Mentor: Nicholas Stephanopoulos
Hierarchical Assembly of Nucleic Acid/Coiled-Coil Peptide Nanostructures
“Alex designed, synthesized, and analyzed an exciting new class of peptide-DNA nanomaterials relying on the self-assembling coiled-coil motif. He was the first to report a hybrid nanofiber assembly of DNA nanostructures driven by multivalent peptide interactions, and extended this work to peptide-DNA cages and fibers assembled by expressed proteins bearing coil peptide fusions. He also contributed to the reversible, dynamic control of biomaterial hydrogels using DNA linkers. Alex always thought deeply about these new molecular materials, and his incisive ability to forge new areas will be missed.” -Nick Stephanopoulos
Swarup Dey, PhD Chemistry
Mentor: Hao Yan/Rizal Hariadi
Membrane Protein Mimetic Dynamic DNA Nanostructures for Biosensing Applications
“Swarup is a creative thinker and an innovator. The principle of innovation that matters is captured in his project of a DNA-based transmembrane sensor that has the potential to allow less painful cancer biopsies and new methods for cell isolation. His Ph.D. thesis provides the foundational science for a newly-formed lab spin-off (Exodigm Biosciences, Inc). Within the lab, he is known for his expertise in exosomes, lipid biochemistry, and DNA origami design. We will remember Swarup for his hard work and his desire for excellence.” -Rizal Hariadi
“Swarup is a creative and independent thinker. He is dedicated and hardworking and has developed his own vision for bionanotechnology. He carried out his research projects with a systematic approach. He has successfully designed and implemented a transmembrane sensor and gated nanopore based on DNA nanotechnology. The transmembrane nanosensor technology has recently led to a new ASU spin-off company. Swarup will go to Harvard for a postdoc position.” -Hao Yan
Nicholas Halloran, PhD Biochemistry
Mentor: Giovanna Ghirlanda
Engineering Metalloproteins for Solar Driven Hydrogen Production
“Nick is a very talented scientist with a knack for coming up with creative solutions. He set up a high-throughput assay for hydrogen detection, and endless methods to carry out his projects; he is curious, knowledgeable, and always ready to help out other students. He has been very productive, in particular his work demonstrated light driven hydrogen production by artificial metalloenzymes, and established methods to generate libraries of mutants. Nick’s experience and leadership will be missed!” -Giovanna Ghirlanda
Nikita Kumari, PhD Chemistry
Mentor: Marcia Levitus
Photophysical Studies to Advance Fluorescence Applications in Biophysics
“Nikita has made significant contributions to the field of fluorescent probes in biophysical research. Her attention to detail and high standards of rigor have earned her respect from our collaborators and contributed to advancing the field of fluorescent probes for single molecule spectroscopy. Nikita also exceled as a teacher assistant and participated in numerous outreach activities. She will be greatly missed, and we wish her the best for her future endeavors.” -Marcia Levitus
Symon Levenberg, PhD Biochemistry
Mentor: Neal Woodbury
Biophysical characterization of Aptamer-protein Molecular Interactions Through Machine Learning and DNA Microarrays as an Alternative to NGS for Simultaneous Monitoring of Informative Species in an Enriched Library of Oligonucleotides
“Symon Levenberg developed and analyzed nucleic acid structures with functional properties. He was involved in the development of photonic DNA nanostructures and he worked on the enrichment of DNA aptamers and their analysis. The later involved high throughput molecular recognition measurements of various kinds coupled to machine learning approaches designed to result in functional prediction.” – Neal Woodbury
Tara MacCulloch, PhD Chemistry
Mentor: Nicholas Stephanopoulos
Rational Design of Self-Assembling Crystal Scaffolds and DNA-Peptide Hybrid Materials
“Tara pioneered a number of exciting new directions in peptide-DNA conjugates and self-assembling DNA crystals. She developed methods for creating synthetic peptide-DNA antibodies, triblock DNA-peptide-DNA molecules, and for coating DNA nanostructures with bioactive peptides. In collaboration with Prof. Hao Yan's lab, Tara contributed to the rational design of self-assembled DNA crystals, and methods for using them to scaffold peptides and proteins. Her diverse projects and ability to cross interdisciplinary boundaries is a testament to her work ethic, intelligence, and ability to manage complex collaborations.” -Nick Stephanopoulos
Narges Masoumi, PhD Chemistry
Mentor: Andrew Chizmeshya/George Wolf
First-Principles DFT Study of Imide and Fluoride Analogs of Silicon Oxide, Silicon Oxynitride, and Their Alloys
“Narges’ passion for quantum-based computational science has driven her to develop an expertise in both molecular and solid-state simulations. This uncommon skill set led her to develop an approach to consistently treat heterogeneous reaction systems at finite temperatures. This methodology then enabled comparative ab initio thermochemistry studies of the properties of novel nitride-oxynitride analogs of silica, as well the detailed P-T phase diagram the halide analog BeF2, revealing new polymorphic behavior. We offer our heart-felt congratulations for the completion of her doctoral studies and wish her success in her future scientific pursuits.” -Andrew Chizmeshya
Raghu Narayanan Pradeep, PhD Chemistry
Mentor: Hao Yan/Nicholas Stephanopoulos
Design and Study of Hybrid DNA Nanostructures and Complex 3D DNA Materials
“Raghu is interested in pivotal scientific questions and challenging research tasks and has strong motivation in testing his hypotheses and research ideas. His persistence makes him successful in carrying out challenging research projects involving DNA-peptide hybrid nanomaterials. Raghu is never afraid of talking about new ideas, he has a creative mind and has the courage to test his ideas. He works diligently toward his goal and possesses great technical and analytical skills.” -Hao Yan
“Raghu forged a number of exciting projects at the intersection of the Yan and Stephanopoulos labs. He spearheaded diverse projects, like incorporating host-guest complexes into DNA nanotechnology, using cryo-EM to solve hybrid protein-DNA nanostructures or characterize new 3D designs, and probing the crystal assembly of DNA origami cages. He was fearless in probing diverse directions, and working with a wide range of collaborators. His hard work and true enthusiasm for science made him a joy to work with.” -Nick Stephanopoulos
Akanksha Singh, PhD Chemistry
Mentor: Neal Woodbury
Functional Studies of Interactions in Proteins
“Akanksha Singh worked on the development of quantitative relationships between the amino acid sequence of potential epitopes and the binding to specific monoclonal antibodies. She did a systematic study, combining high throughput measurements of binding on peptide arrays with machine learning approaches. She also explored ways of interfacing functional biological molecules with porous electrodes.” – Neal Woodbury
Darren Thifault, PhD Biochemistry
Mentor: Petra Fromme
Structure Elucidation of Medically Important Proteins by X-ray Crystallography
“Darren was an outstanding student and excellent experimentalist. He has spearheaded a new project in my lab where we collaborate with the cancer center at U of Arizona on structure-based design of stapled peptides that inhibit the formation of the focal adhesion complex, which plays a key role in cancer progression. The target was FAK, the key protein in the assembly process. Darren has solved the first structure of the protein in complex with the therapeutic peptide at high resolution forming the basis for structure-based drug design. Darren thesis also includes his important XFEL related work on time resolved XFEL studies of the protein KDO8 which is a novel target for multi-drug resistant gram negative bacterial pathogens. Darren is an outstanding scientist and I want to thank him for years of hard work and congratulate him to his Ph.D. in Biochemistry.” -Petra Fromme
Xu Zhou, PhD Chemistry
Mentor: Hao Yan
Engineered Excitonic Complex Directed by Programmable DNA Architectures
“Xu has made pivotal contributions to a DOE funded project to develop DNA directed excitonic networks to mimic nature’s light harvesting systems. And in the process, has demonstrated a breadth of knowledge and skills one typically associates with the very best researchers. He develops his own ideas and carries out the research with great diligence and attention to details.” -Hao Yan