LAB MEMBERS

Dr. Ruxandra I. Dima

Principal Investigator  |  Professor in Chemistry

Ruxandra Dima has an interdisciplinary training in theoretical and computational physics and physical chemistry. She is working in the areas of computational biophysical chemistry and biocheminformatics. After receiving her undergraduate degree from the University of Bucharest, Romania in 1994, she studied at the Pennsylvania State University where she obtained her PhD in 1999. Her thesis was concerned with the determination of mean field free-energy potentials between amino acids in proteins. She then took a postdoctoral appointment with Prof. D. Thirumalai at the Institute for Physical Science and Technology, University of Maryland where she worked on problems related to protein aggregation, allostery, RNA folding and single-molecule biophysics. She joined the Department of Chemistry as an Assistant Professor in the Fall 2006. In 2020 she became a Professor in Chemistry. She has been the recipient of a number of awards throughout her career including the NSF-CAREER Award (NSF-'09),  A&S Rising Star Award College of Arts and Sciences (UC-'17), and most recently she was named the CINTACS Chemist of the Year in 2023 (ACS). She is an incredibly talented, curious and passionate scientist.

Shehani Kahawatte

Graduate Student  |  5th-year

Shehani holds a Bachelor’s degree in Statistics from the University of Colombo, Sri Lanka, and joined the Dima Lab in January 2022. Her primary research focuses on microtubule-severing enzymes, with particular emphasis on understanding how disease-associated point mutations perturb protein structure, dynamics, and allosteric communication pathways. Using large-scale molecular dynamics simulations, machine-learning models, and graph-based network analyses, she identifies key residues and alterations in communication networks that drive mutation-induced changes in protein behavior. In addition to her research, she has been actively involved in teaching, serving as a Teaching Assistant for General Chemistry I and II, Physical Chemistry, Biochemistry, and Big Data for Chemistry courses, where she conducted laboratory sessions and recitations.

Beyond her academic and research activities, she served as Secretary of the Chemistry Graduate Student Association in 2023 and as Vice President and President of the Sri Lankan Student Association in 2023 and 2024, reflecting her commitment to leadership, mentorship, and community engagement. In her free time, she enjoys painting, watching movies, and traveling.

Emily M. Stump

Graduate Student  |  4th-year

Emily joined the lab in August '21 when she was still an undergraduate at University of Cincinnati studying chemistry. She has since gone on to become a graduate student, and presently works on using simulations to better understand the role and mechanism of the neuronal protein tau. She is also involved in collaborations with other labs, including working with the lab of Dr. Pietro Strobbia at U.C. on the use of large language models like ChatGPT to aid in the design of nucleic acid-based biological sensors. She has also been able to work with a mentor at Proctor and Gamble through an internship program offered through U.C., where she studied the application of machine learning to small molecules.

Outside of the lab, Emily likes to watch horror movies, play video games, and play Dungeons & Dragons with friends.

Maryum Irshad

Graduate Student  |  4th-year

Maryum joined the lab in January '23 eager to apply her knowledge in the field of programming to computational biochemistry. She earned her bachelor's in Chemical Engineering from the University of Engineering and Technology Pakistan with a focus on industrial-scale manufacturing of bioethanol. Currently, her work focuses on understanding the allostery of kinesin 8 and 13, motor proteins that are essential for cellular functions. 

As a Teaching Assistant, she has contributed to General Chemistry I lab, General Chemistry II, and Organic Chemistry I recitations. Additionally, she assisted as the co-ordinator for NSF-funded summer REU program (2023) and currently holds the position of treasurer for the Chemistry Graduate Student Association. 

Madhavie Ranpati Dewage

Graduate Student  |  4th-year

Madhavie Ranpati Dewage, holding a B.Sc Honors degree in Chemistry from the University of Kelaniya, Sri Lanka joined the lab in January '23 with a keen interest in expanding her skills in programming and machine learning within the field of computational biophysical chemistry. With a background in Chemistry, Madhavie is eager to apply her newfound knowledge to the study of biological systems such as microtubules and severing enzymes.  In joining the lab, Madhavie aims to leverage her programming skills to contribute to the ongoing research, with a focus on understanding the effect of different Tubulin Isotypes on Katanin Severing Activity.

As a Teaching Assistant, she has also made significant contributions to the General Chemistry I lab during Fall '22, Spring '23, and Fall '23, as well as General Chemistry I recitations during Summer '23.

Julie Schlanz

Graduate Student  |  3rd-year

Julie Schlanz joined the lab in January '24 excited to learn how to use computational tools to analyze biological systems. She received her B.S. in Biochemistry at Marietta College, where she completed her research honors thesis under the advisement of Dr. Suzanne Parsons. Her research honors thesis involved conducting cholesterol and ceramide assays on melanoma cells treated with mononitroparaben to determine the involvement of lipids in cell death. In the Dima lab, Julie looks forward to combining her biochemistry background with her new skills in computational biochemistry.

Outside of the research lab, Julie has been a teaching assistant for the Biochemistry lab and recitation. She also enjoys being around animals, such as by volunteering to walk dogs at the local animal shelter, as well as crocheting, sewing, and reading. In her free time, you will find her with her cat, Al Catpone.

Carter St.Clair

Graduate Student | 2nd-year

Carter joined us for the Summer of 2023 for the NSF-REU program. He dedicated his summer to learning programming & modelling and their applications to allostery through machine learning and graph networks.

He is now a second year chemistry graduate student in our lab. He works with a microtubule associated protein, doublecortin (DCX), and its impacts on the dynamics of the microtubule lattice. He does this by running and analyzing molecular dynamics simulations and elastic network models through statistical and machine learning models. Carter also spent time as a teaching assistant for General Chemistry and Biochemistry labs.

Outside of the lab, Carter loves to play D&D and video games, sing and perform in musicals, and lift weights.

Korina Beran

Graduate Student | 1st-year

Korina joined the lab in January '25 with an interest in computational chemistry. She received her B.S. in Chemistry and Applied Mathematics from the University of Pittsburgh at Johnstown, where she conducted undergraduate research in a synthetic chemistry lab. 

She is currently working on the STS-1 protein, where she models and evaluates mutations using active learning-directed evolution (ALDE) frameworks combined with molecular simulations. Korina has also served as a teaching assistant for General Chemistry and Biochemistry labs.

Outside of the lab, Korina enjoys spending time with her cats, hiking, and watching the Pittsburgh Penguins. 

Maria S. Gillen

Scientific Writer II  |  Forge Biologics

Formerly a Graduate Student ('21-'25 ). Maria Gillen joined the lab in the Spring of '21. She aims to learn everything she can about machine/deep learning and how it can be applied to real-world problems. She earned a B.S. in Chemistry from Franciscan University of Steubenville. As an undergraduate, she was selected for UC's very own Research Experience for Undergraduates (NSF-REU) program in the summer of '19 where she worked with Dr. Hairong Guan. Through those experiences she was introduced to computational chemistry and the rest is history. Since arriving, she has worked on a wide variety of projects and many collaborations inside and outside of the department. Notably, she collaborated with UC Zimmer Scholar Dr. Paolo Carloni (Forschungszentrum Jülich) on using metadynamics to identify new intermediate states for severing enzymes that have not been identified from cryo-EM. She also contributed to the development of several methods such as a classification algorithm used for MADDY (available on Gihub - Barsegov), a method for explaining allosteric perturbations, and a method for diagnosing cancers from the Raman spectra of exosomes. Since joining the department, she has co-coordinated the NSF-REU program ('21-'23), served as the treasurer of the Chemistry Graduate Student Association ('21), and was a University Research Council (URC) Graduate Student Stipend and Research Cost Program for Faculty-Student Collaboration awardee ('24). 

Amanda C. Macke

Bioinformatics Scientist  |  Nationwide Children's Hospital

Formerly a Graduate Student ('19-'23) in the Dima Group.  Amanda Macke joined the lab in the Spring of '19 with an interest in proteins and biological systems. She earned a B.S. in ACS Chemistry from Eastern Kentucky University. In fulfillment of the requirements of the EKU Honors Program, she joined the lab of Dr. Martin Brock to study the structure and behavior of thermophilic systems using malate dehydrogenase as the model system. After joining, she quickly learned how to program (with sweat and many tears) and fell in love with machine learning, microtubules, severing enzymes and allostery. She has contributed to developing several methods used across groups in the department including the StELa double clustering algorithm, the StrobeProbe algorithm, and Allosteric Mapping (available on GitHub). Since joining the group she has acted as coordinator for the NSF-funded summer REU program ('19), the service co-chairman for CGSA, developed a Data Science Workshop for the REU, taught General Chemistry (Summer '21), started an inter-group (w/ the Stan Group) Journal Club, and interned at the P&G Digital Accelerator @ The University of Cincinnati where she has been using conformational analysis to study biodegredation. She was a Post-Doctoral Research Fellow at the University of Delaware in the Perilla Lab (May '24 - Aug '25). 

Dr. Rohith Anand Varikoti

Postdoctoral Research Associate  |  Pacific Northwest National Laboratory

Formerly a Graduate Student ('16-'21) in the Dima Group. He earned an M.S. in Pharmacoinformatics from National Institute of Pharmaceutical Education Research in '13 and a B.S. from the Care College of Pharmacy in '11. While in the group he worked on microtubule severing mechanism with gSOP, microtubule severing enzyme mechanism and conformational dynamics resulting in a number of publications. He is currently a Postdoctoral Research Associate at PNNL where he is working on machine learning-driven molecular design for drugs and SARS-CoV-2 therapeutics. 

Dr. Lukasz Szatkowski

Assistant Teaching Professor of Chemistry |  University of Cincinnati

Formerly a Post-Doctoral Research Assistant in the Dima Group and a Visiting Professor for the Department of Chemistry ('18-'20). He earned a M.S. in Computational Chemistry ('07) and a PhD in Physical & Computational Chemistry ('12) from Lodz University of Technology. He then had a post-doc appointment at Texas A&M then Arizona before coming to Ohio. During his time in the group he used his extensive experience in multi-scaled modelling to study microtubule dynamics, the effects of crowding, and the Wedge model of severing microtubules. He taught Physical Chemistry and General Chemistry and pursed computational research at the University of Missouri - St. Louis from August '22 to August '24. He began as an educator at the University of Cincinnati August '24.

Dr. Mangesh Damre

Clinical Trial Manager |  Medpace

Formerly a Post-Doctoral Research Assistant ('19-'21) in the Dima Group. He earned his M.S. from the National Institute of Pharmaceutical Education and Research ('13) and his PhD from SISSA ('18). During his time in the group he modelled and studied the conformational dynamics of quaternary ensembles of katanin and spastin (severing enzymes). He is currently a Clinical Trial Manager at Medpace.

Dr. Dale Merz Jr.

Senior AI Engineer | Proctor & Gamble

Formerly a Graduate Student ('13-'18) in the Dima Group. He earned an M.S. in Theoretical Biophysics from Georgia Institute of Technology in '13 and a B.S. from the University of Pittsburgh in '08. During his time in the group he worked on projects related to Hsp70, microtubule dynamics, and molecular motors. He is currently a Data Engineer at Proctor & Gamble.

Dr. Nan Jiang

Researcher | XX

Formerly a Graduate Student ('14-'17) in the Dima Group. While he was in the group he was studying microtubule dynamics.  He is currently a Researcher and Development Manager at Sinochem group.

*the Jiangsu Industrial Technology Research Institute (JITRI) in China.

Dr. Nicholas K. Bodmer

Post Doctoral Researcher | Washington University School of Medicine

Formerly a Graduate Student ('10-'15) in the Dima Group. While he was in the group he was studying protein-protein interactions with emphasis on Z-disc associated proteins (the Titin-telethonin complex).  Prior to UC, he earned his Bachelor's Degree from Xavier University ('02) in Philosophy and Classics. He came to UC to pursue his M.S. in Biochemistry before pursuing his PhD. He is currently a Post Doctoral Research Scholar at the Washington University School of Medicine in St. Louis where he studies proteins in the extracellular matrix.

Dr. Kelly Theisen

Associate Professor of Biochemistry | SUNY Plattsburgh

Formerly a Graduate Student ('09-'13) in the Dima Group. Prior to joining, she completed her B.A. in ACS Biochemistry at Ohio Wesleyan University. During her time in the group, she worked on protein folding/unfolding with the self-organized polymer (SOP) model and comparing results with AFM experiments. She is currently an Assistant Professor of Biochemistry at SUNY Plattsburgh ( https://www.plattsburgh.edu/academics/schools/arts-sciences/chemistry-biochemistry/faculty/theisen-kelly.html ). Currently her research focuses on determining the mechanical stability of proteins through modelling, and how drug compounds can alter stability. 

Dr. Ji Young Li

Staff | University of Pittsburgh

Formerly a Graduate Student ('08-'10) in the Dima Group. During his time in the group, he worked on Actin filaments. He is currently staff at University of Pittsburgh.

Dr. Li Duan

Formerly a Graduate Student ('09-'10) in the Dima Group. During his time in the group, he worked on Synaptotagmin 1, and actin filaments.