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.

Amanda C. Macke

Graduate Student  |  6th-year

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. 

In her free time, she likes to play with her cat Linus Pawling, watch true crime documentaries and read! 

She will be graduating soon and is currently looking for employment! 

Can be contacted at:

mackeac@mail.uc.edu

amacke718@gmail.com 

Maria S. Kelly

Graduate Student  |  4th-year

Maria Kelly 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 is currently collaborating 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 has 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).

In her spare time, you can find her making honey lattes with her cat Oliver and running in the Flying Pig Marathon!

Shehani Kahawatte

Graduate Student  |  3rd-year

Shehani Kahawatte possessing a Bachelor's degree in Statistics from the University of Colombo, Sri Lanka, joined Dima Lab with great enthusiasm in January '22. Her strong interest lies in applying her statistical expertise to the field of computational biochemistry. Currently, she is actively engaged in various projects related to microtubule severing enzymes. Since joining the lab, she has gained experience in running Molecular Dynamics (MD) simulations, implementing machine learning approaches, and working with graph-based networks. Also, as a third-year graduate student, she recently successfully completed her candidacy exam. 

In her role as a Teaching Assistant, she has made valuable contributions to the department, conducting lab sessions for General Chemistry I, Chemistry II, Physical Chemistry, and recitations for General Chemistry I and Introduction to Biochemistry.

Beyond her academic contributions, she served as the Secretary of the Chemistry Graduate Student Association (CGSA) in the year '23 and currently holds the position of President at the Sri Lankan Student Association (SLSA).

Jacob E. Stump

Graduate Student  |  2nd-year

Jacob, who also goes by Coby, joined the lab in August '21 when they were still an undergraduate at University of Cincinnati studying chemistry. They have 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. They are 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. They've also been able to work with a mentor at Proctor and Gamble through an internship program offered through U.C., where they studied the application of machine learning to small molecules.

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

Maryum Irshad

Graduate Student  |  2nd-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  |  2nd-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  |  1st-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.

Stephanie Kramer

Undergraduate Student  |  Junior

Stephanie Kramer joined the lab in October of 2023. She is a current undergraduate student working on a B.S. in Biochemistry, with an expected graduation for Spring of 2025.  Her current project utilizes computational tools to predict binding affinity of microtubule associated proteins towards microtubules, to learn how associated proteins affect microtubule structure and dynamics, and to learn how microtubules probe for certain protein interactions.  She has interned and worked in labs at Nationwide Children’s Hospital Abigail Wexner Research Institute Center for Gene Therapy in Dr. Allison Bradbury’s lab in Columbus, Ohio, as well as in the Experimental Hematology and Cancer Biology department in Dr. Nicolas Nassar’s lab at Cincinnati Children’s Hospital Cancer and Blood Diseases Institute in Cincinnati, Ohio.  Outside of academics, she is an executive/leadership member for UC’s Women’s Club Ultimate Frisbee team. She enjoys crocheting, camping, hiking, and fishing. Stephanie has one cat named Bonnie. She is interested in a career in biomedical sciences. Stephanie is planning to apply for graduate school programs in Fall 2024, aiming for admission in the year 2025.

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 Missouri - St. Louis

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 is currently teaching Physical Chemistry and General Chemistry and pursing computational research at the University of Missouri - St. Louis ( https://www.umsl.edu/chemistry/Faculty/szatkowski.html ).

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

Assistant 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 modellling, 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.