The Graduate School has selected Sivanujan Suthaharan as its February 2025 GradBird Scholar recipient. GradBird Scholar is an initiative to recognize graduate students for their scholarly endeavors at Illinois State University.
Suthaharan developed a passion for complex scientific terms in high school, when he participated in the Stockholm Junior Water Prize competition. He and his colleagues developed a microbe-based system to remove nitrates from polluted water, which gave him his first real exposure to the investigative nature of science. This dedication to using science for the greater good led him to pursue a degree in chemistry at the University of Jaffna, Sri Lanka, and conduct atomistic simulations of battery electrode materials. His decision to pursue a graduate degree at Illinois State felt like the perfect step forward, allowing him to channel his passion for scientific inquiry into solving real-world challenges.
Believing science should extend beyond the lab, Suthaharan enjoys communicating science to general audiences so anyone can understand the progress being made. In his free time, he enjoys watching movies and playing tennis.
What is your favorite part of your program?
One of the best aspects of the chemistry program is the opportunity to work closely with outstanding faculty, whether through research projects or course work. The chemistry community at ISU is highly collaborative and inclusive, fostering an environment of support and innovation. Moreover, the graduate program encourages learning beyond disciplinary boundaries. I particularly enjoyed taking interdepartmental courses and engaging in thesis research that broadened my perspective.
Do you work with a specific faculty/staff member to help with your research? What has your experience been like working with them?
In spring 2023, I joined Professor Bhaskar Chilukuri’s Computational Research Lab (Chillab) at ISU, where I work at the intersection of experiment and theory with a joint effort of synthetic chemists, surface scientists, and characterization experts from United States and European Union regions. Since then, I’m continuing as a graduate research assistant under the NSF (National Science Foundation)-funded collaborative project on Cooperative Processes at Surfaces: Ligand Binding at the Single Molecule Level. The goal of this project is to understand the surface physical chemistry principles of self-assembly at ordered two-dimensional (2D) surfaces. I use scanning tunneling microscopy (STM), molecular and periodic quantum mechanical density functional theory (DFT) simulations, and molecular dynamics to develop a theoretical model based on experimental data and to understand the multitude of factors influencing cooperativity on the submolecular level.
Through atomistic quantum simulations I quantify the role of adsorbate—surface, inter-, and intramolecular interactions, stability of peripherally engineered macrocyclic adsorbates, spatial effects, symmetric and asymmetric substitutions, and establish a comparative investigation on the effect of interdigitation and isomeric equilibrium found in adsorbate systems. The imaging-aided simulations let us to draw interesting conclusions about interface stability and role of substrate and metalation in surface cooperativity, which I presented in the Royal Society of Chemistry Dalton Conference. At the conference I won the RSC Outstanding Presentation Award and the Catalysis Science & Technology journal’s Best Poster Prize. This was truly inspiring as a successful reflection of my first experiment-driven theoretical work. Though it was initially overwhelming to handle the collaborative nature, I overcome this through making weekly plans, developing resilience when things do not work, and discussing with my mentors and peers.
In among the macrocyclic systems, which we peripherally engineered with aromatic groups, I found through simulations that a higher degree of interdigitation between monolayer-forming molecules stabilized the interface system. With the aid of STM, I identified monolayer vacancies, which we later found to be the effect of phase aggregations in isomers. To shed light on monolayer stability, I modeled different conformations that could occupy within the observed vacancies. With the help of atomistic insights, I found answers to what type of intermolecular interactions become significant in monolayer stability and what is the extent of torsional degree of freedom of substituents when they transition between interface and gas/solution phase.
I presented these results at the American Chemical Society National Spring Meeting (ACS Spring 2024 in Louisiana) for which I was awarded the Illinois State Pinion travel award and Chemistry Club travel grant. Now this work has been accepted for an invited special issue from the Journal of Porphyrins and Phthalocyanines to commemorate eminent Professor Karl M. Kadish, for his legendary work on synthetic tetrapyrrole chemistry.
Working in the Chillab through collaborations with experimental groups of Professors K.W. Hipps and Ursula Mazur (both at Washington State) from chemistry and materials science gives me a firsthand experience on collaborative research where I exchange ideas across disciplines, learn multi-disciplinary technical skills, produce and present higher quality results, and of course have fun with group meetings.
As a supportive mentor, having recognized my efforts to learn and research, Dr. Chilukuri has nominated me for some prestigious graduate student fellowships. In the summers of 2023 and 2024, I received the NSF- Platform for the Accelerated Realization, Analysis, and Discovery of Interface Materials (PARADIM) Fellowships on DFT-aided experiments and modeling-aided materials chemistry respectively. In fall 2024, I was awarded the competitive D E Shaw Research Master’s Fellowship in computational chemistry.
In fall 2023, Chillab collaborated with Dr. Alfonso Martinez-Felipe’s Chemical and Materials Engineering research group at the University of Aberdeen in the United Kingdom and his colleagues from EU regions to study the surface-binding phenomena of novel bent-core liquid crystals (BCLCs). Dr. Alfonso is currently a visiting scientist in our group with whom I perform STM imaging experiments of BCLCs on 2D surfaces along with simulations. At the initial phase, we wanted to understand structure-property relationships of different E and Z isomers of binary mixtures containing two BCLCs. From DFT simulations, coupled with optical polarization and impedance spectroscopy experiments, we discovered the effect of isomerization-driven local dipole moments on packing arrangements and aggregation.
Our collaboration received the prestigious Royal Society of Edinburgh-International Joint Project Grant and the initial phase study was published in Journal of Molecular Liquids in spring 2024. Continuing from this, I investigated the competition between interface stability and intermolecular interaction of BCLCs on substrate via STM-driven periodic simulations. We employed annealing STM experiments and identified the stability of multiple domains of self-assembly. I presented the key findings at the renowned Dresden Computational Materials Summer School (DCMS August 2024 in Germany) for which I was awarded the Technische Universität Dresden-Open International Summer Scholarship.
Can you explain your research and the importance of it within your field?
We are a group of computational chemists aiming to solve problems at the atomistic level with the use of supercomputers. Our research spans a wide spectrum of topics, from the two-dimensional self-assembly of organic systems to the self-assembly of fundamental genetic building blocks like RNA. By employing advanced computational techniques, we explore how molecular interactions drive the formation of complex structures, shedding light on fundamental processes in chemistry.
In the microscopic world of our cells, intricate molecular interactions drive essential biological processes, often without a predefined blueprint. One such phenomenon involves the self-assembly of RNA structures, a process that remains largely unexplored. Among RNA’s fundamental components is uracil, a key nucleotide that, under certain conditions, can form unexpected molecular arrangements. Recent research has revealed that four uracil molecules from different RNA chains can spontaneously organize into a unique, stable structure known as a “tetramer.” However, the precise factors that drive the formation of these structures—and whether they contribute to cellular function or dysfunction—remain an open question.
To address this mystery, my research investigates the atomic-level interactions that govern RNA self-assembly. Using advanced imaging techniques and computational simulations, I explore how these molecular structures emerge and stabilize. A useful analogy lies in the construction of Lego models: individual bricks may seem unremarkable on their own, but under the right conditions, they can spontaneously form complex structures.
In this molecular assembly process, metal ions play a crucial role. Imagine a positively charged metal ion as a central organizing element, analogous to a red Lego brick, attracting negatively charged uracil molecules, our blue bricks. Rather than assembling randomly, these molecular components arrange themselves in a precise, flat pattern, suggesting a fundamental organizing principle. My findings indicate that strong electrostatic forces drive this self-assembly: The metal ion acts as a scaffold, drawing uracil molecules together, while additional molecular interactions stabilize the overall structure.
Why do you enjoy researching this topic and what more do you hope to learn about it?
This phenomenon, termed metal-induced self-assembly, provides new insights into RNA’s structural dynamics. Understanding these mechanisms could have profound implications, potentially revealing novel pathways in molecular biology and inspiring biomedical applications. As we continue to refine our findings, we are in the process of publishing this study, aiming to contribute to the broader understanding of RNA behavior and its potential role in cellular function.
What do you hope further research about this topic will do to benefit the greater of society?
The structural study of biomolecules such as RNA, DNA, and proteins has long been instrumental in understanding therapeutic effects, guiding drug design, and even predicting diseases. These investigations demand an atomistic-level focus to uncover fundamental molecular interactions. My research, which explores the interplay between metal ions and RNA bases at the atomic scale, holds significant implications for the broader scientific community in several key areas including fundamental insights into molecular interactions. By analyzing the energetics of metal ion–RNA nucleobase interactions, our study provides a theoretical foundation that can serve as a reference for future molecular-level investigations.
Would you like to highlight anything else about your research or promote anything specific you are involved in?
Most of our project findings have been published in reputed journals (listed below), while several others are currently in progress and on the path to publication.
- Matthew Beckman, Suthaharan, S., Kashi C., Hipps K W, Bhaskar Chilukuri, Mazur U. Substituent, and Isomeric Effects on Self-Assembled Phthalocyanine Monolayers on HOPG as Studied by Scanning Tunneling Microscopy and DFT Calculations. Journal of Porphyrins and Phthalocyanines 2025. [In Press] [Invited special issue honoring legendary scientist Prof. Karl Kadish]
- Liebsch, J.; Strachan, R.; Suthaharan, S.; Dominguez-Candela, I.; Auria-Soro, C.; San-Millan, A.; Walker, R.; Chilukuri, B.; Blanca Ros, M.; Martinez-Felipe, A. Tailoring the Dielectric and Ferroelectric Response of Mixtures Containing Bent-Core Liquid Crystals through Light-Irradiation and Composition. Journal of Molecular Liquids 2024, 399, 124371. DOI: https://doi.org/10.1016/j.molliq.2024.124371
