Ruxandra Dima

Ruxandra I Dima

Professor

Crosley Tower

304

A&S Chemistry - 0172

Professional Summary

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. Since 2020 she is a Professor in Chemistry. 
The main areas of research in the Dima group are:
1) multiscale modeling of filamentous biomolecules
2) computational studies of the action of motors involved in cytoskeleton depolymerization
3) design and modeling of bio-inspired materials
4) development of machine learning methods for bio-design
5) GPU-based computing
We use a combination of molecular simulations, bioinformatics, data science, and theoretical modeling to address the various research problems.

Education

B.S.: University of Bucharest Bucharest, Romania, 1994 (Physics)

PhD: The Pennsylvania State University State College, PA, 1999 (Physics)

Research and Practice Interests

Modeling of mechanical response in large cellular protofilaments

Modeling the effects of confinement and crowding on the behavior of proteins

Modeling of protein-protein interactions with functional roles in cellular division and synaptic processes

Development of multiscale approaches to investigate the behavior of biomolecular assemblies on experimental timescales

Development of machine learning approaches for bio-inspired design of materials and sensors

Abbreviated Publications

Peer Reviewed Publications

Szatkowski, Lukasz, Varikoti, Rohith Anand, & Dima, Ruxandra I (2021). Modeling the Mechanical Response of Microtubule Lattices to Pressure. The journal of physical chemistry. B, 125(19), 5009-5021.

Varikoti, Rohith Anand, Fonseka, Hewafonsekage Yasan Y, Kelly, Maria S, Javidi, Alex, Damre, Mangesh, Mullen, Sarah, Nugent, Jimmie L, Gonzales, Christopher M, Stan, George, & Dima, Ruxandra I (2022). Exploring the Effect of Mechanical Anisotropy of Protein Structures in the Unfoldase Mechanism of AAA+ Molecular Machines. Nanomaterials (Basel, Switzerland), 12(11).

Damre, Mangesh, Dayananda, Ashan, Varikoti, Rohith Anand, Stan, George, & Dima, Ruxandra I (2021). Factors underlying asymmetric pore dynamics of disaggregase and microtubule-severing AAA+ machines. Biophysical journal, 120(16), 3437-3454.

Kliuchnikov, Evgenii, Klyshko, Eugene, Kelly, Maria S, Zhmurov, Artem, Dima, Ruxandra I, Marx, Kenneth A, & Barsegov, Valeri (2022). Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules' Growth, Catastrophe, Shortening, and Rescue. Computational and structural biotechnology journal, 20, 953-974.

Varikoti, Rohith A, Macke, Amanda C, Speck, Virginia, Ross, Jennifer L, & Dima, Ruxandra I (2020). Molecular investigations into the unfoldase action of severing enzymes on microtubules. Cytoskeleton (Hoboken, N.J.).

Szatkowski, Lukasz, Merz, Dale R, Jiang, Nan, Ejikeme, Ifunanya, Belonogov, Liudmila, Ross, Jennifer L, & Dima, Ruxandra I (2019). Mechanics of the Microtubule Seam Interface Probed by Molecular Simulations and in Vitro Severing Experiments. The journal of physical chemistry. B, 123(23), 4888-4900.

Barsegov, Valeri, Ross, Jennifer L, & Dima, Ruxandra I (2017). Dynamics of microtubules: highlights of recent computational and experimental investigations. Journal of physics. Condensed matter : an Institute of Physics journal, 29(43), 433003.

Mandal, Soumit Sankar, Merz, Dale R, Buchsteiner, Maximilian, Dima, Ruxandra I, Rief, Matthias, & Žoldák, Gabriel (2017). Nanomechanics of the substrate binding domain of Hsp70 determine its allosteric ATP-induced conformational change. Proceedings of the National Academy of Sciences of the United States of America, 114(23), 6040-6045.

Jiang, Nan, Bailey, Megan E, Burke, Jessica, Ross, Jennifer L, & Dima, Ruxandra I (2017). Modeling the effects of lattice defects on microtubule breaking and healing. Cytoskeleton (Hoboken, N.J.), 74(1), 3-17.

M. Bailey, N. Jiang, R. I. Dima, and J. L. Ross, "Microtubule Severing Enzymes Couple ATPase Activity with Tubulin GTPase Spring Loading", Biopolymers, 105, 547-556 (2016).

N. K. Bodmer,. K. E. Theisen, and R I. Dima, "Molecular investigations into the mechanics of a muscle anchoring complex", Biophysical Journal, 108, 2322-2332 (2015)

D. Bauer, D. R. Merz, B. Pelz, K. E. Theisen, G. Yacyshyn, D. Mokranjac, R. I. Dima, M. Rief, and G. Zoldak, "Nucleotides regulate a mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK", Proc. Natl. Acad. Sci. USA 112, 10389-10394 (2015).

O. Kononova,Y. Kholodov, K. E. Theisen, K. A. Marx, R. I. Dima, F. I.  Ataullakhanov, E. L. Grishchuk, and V. Barsegov, "Tubulin bond energies and microtubule biomechanics determined from nano-indentation in silico", J. Am. Chem. Soc. 136, 17036−17045 (2014).

O. Kononova, J. Snijder, M. Brasch, J. Cornelissen, R. I. Dima, K. Marx, G. J. L. Wuite, W. H. Roos, and V. Barsegov, ”Structural characteristics and energy landscape for Cowpea Chlorotic Mottle Virus Capsid nanomechanics from dynamic force spectroscopy in vitro and in silico ”, Biophys. J. 105, 1893-1903 (2013)

Macke, Amanda C, Kelly, Maria S, Varikoti, Rohith Anand, Mullen, Sarah, Groves, Daniel, Forbes, Clare, & Dima, Ruxandra I (2022). Microtubule Severing Enzymes Oligomerization and Allostery: A Tale of Two Domains. The journal of physical chemistry. B, 126(50), 10569-10586.

J. Y. Lee, L. Duan, T. M. Iverson and R. I. Dima, (2012) "Molecular investigations into the role of topological frustration in actin refolding", J. Phys. Chem. B, 116, 1677-1686.

A. Zhmurov, O. Kononova, R. I. Litvinov, R. I. Dima, V. Barsegov, and J. W. Weisel, "Mechanical Transition from alpha-Helical Coiled-Coils to beta-Sheets in Fibrin(ogen)", J. Am. Chem. Soc., 134, 20396−20402 (2012) (on the cover of the December 19, 2012 issue)

Ji Y. Lee, Tyler M. Iverson, & Ruxandra I. Dima (2011). Molecular Investigations into the Mechanics of Actin in Different Nucleotide States. J. Phys. Chem. B, 115(1), 186.

Zhmurov, Artem, Brown, Andre E X, Litvinov, Rustem I, Dima, Ruxandra I, Weisel, John W, & Barsegov, Valeri (2011). Mechanism of fibrin(ogen) forced unfolding. Structure (London, England : 1993), 19(11), 1615-24.(highlighted by commentary: "Fibrinogen unfolding mechanisms are not too much of a stretch" by M. Guthold and S. S. Cho, Structure, 19, 1536-1538 (2011).)

Duan, Li, Zhmurov, Artem, Barsegov, Valeri, & Dima, Ruxandra I (2011). Exploring the mechanical stability of the C2 domains in human synaptotagmin 1. J. Phys. Chem. B, 115(33), 10133-46.

Zhmurov, A, Dima, R I, Kholodov, Y, & Barsegov, V (2010). Sop-GPU: accelerating biomolecular simulations in the centisecond timescale using graphics processors. Proteins, 78(14), 2984-99.

Zhmurov, A, Dima, R I, & Barsegov, V (2010). Order statistics theory of unfolding of multimeric proteins. Biophysical journal, 99(6), 1959-68.

Joshi, Harshad, Momin, Farhana, Haines, Kelly E, & Dima, Ruxandra I (2010). Exploring the contribution of collective motions to the dynamics of forced-unfolding in tubulin. Biophysical journal, 98(4), 657-66.

Dima, Ruxandra I, & Joshi, Harshad (2008). Probing the origin of tubulin rigidity with molecular simulations. Proceedings of the National Academy of Sciences of the United States of America, 105(41), 15743-8.

R. I. Dima and H. Joshi. "Probing the origin of tubulin rigidity with molecular simulations". Proc. Natl. Acad. Sci. USA (2008), 105, 15743-15748.

M. Mickler, R. I. Dima, H. Dietz, C. Hyeon, D. Thirumalai, and M. Rief. "Revealing the bifurcation in the unfolding pathways of GFP using single molecule experiments and simulations". Proc. Natl. Acad. Sci. USA (2007), 104, 20268.

J. Chen, R. I. Dima, D. Thirumalai. "Allosteric Communication in Dihydrofolate Reductase: Signaling Network and Pathways for Closed to Occluded Transition and Back". J. Mol. Biol. (2007), 374, 250-266.

E. O’Brien, R. I. Dima, B. Brooks, D. Thirumalai. "Interactions between hydrophobic and ionic solutes in Aqueous Guanidinium Chloride and Urea Solutions: Lessons for protein denaturation mechanism". JACS (2007), 129, 7346-7353.

C. Hyeon, R. I. Dima and D. Thirumalai. "Deciphering unfolding pathways and kinetic barriers in mechanical unfolding of RNA and proteins ". Structure (2006), 14, 1633-1645.

C. Hyeon, R. I. Dima and D. Thirumalai. "Size, shape and flexibility of RNA structures". J. Chem. Phys. (2006), 125, 194905-194914.

R. I. Dima and D. Thirumalai. "Determination of network of residues that regulate allostery in protein families using sequence analysis". Prot. Science (2006), 15, 258-268.

R. I. Dima, C. Hyeon and D. Thirumalai. "Extracting stacking interaction parameters for RNA from the data set of native structures". J. Mol. Biol. (2005), 347, 53-69.

Dima, Ruxandra I, Hyeon, Changbong, & Thirumalai, D (2005). Extracting stacking interaction parameters for RNA from the data set of native structures. Journal of molecular biology, 347(1), 53-69.

R. I. Dima and D. Thirumalai. "Probing the instabilities in the dynamics of helical fragments from mouse PrPC". Proc. Natl. Acad. Sci. USA (2004), 101, 15335.

R. I. Dima and D. Thirumalai. "Asymmetry in the shapes of folded and denatured states of proteins". J. Phys. Chem. B (2004), 108, 6564.

R. I. Dima and D. Thirumalai. "Proteins associated with diseases show enhanced sequence correlation between charged residues". Bioinformatics (2004), 20, 2345.

Dima, Ruxandra I, & Thirumalai, D (2004). Probing the instabilities in the dynamics of helical fragments from mouse PrPC. Proceedings of the National Academy of Sciences of the United States of America, 101(43), 15335-40.

Dima, Ruxandra I, & Thirumalai, D (2004). Proteins associated with diseases show enhanced sequence correlation between charged residues. Bioinformatics (Oxford, England), 20(15), 2345-54.

Thirumalai, D, Klimov, D K, & Dima, R I (2003). Emerging ideas on the molecular basis of protein and peptide aggregation. Current opinion in structural biology, 13(2), 146-59.

Dima, R I, & Thirumalai, D (2002). Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments. Biophysical journal, 83(3), 1268-80.

Dima, R I, & Thirumalai, D (2002). Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Protein science : a publication of the Protein Society, 11(5), 1036-49.

Chang, I, Cieplak, M, Dima, R I, Maritan, A, & Banavar, J R (2001). Protein threading by learning. Proceedings of the National Academy of Sciences of the United States of America, 98(25), 14350-5.

Dima, R I, Banavar, J R, & Maritan, A (2000). Scoring functions in protein folding and design. Protein science : a publication of the Protein Society, 9(4), 812-9.

Dima, R I, Banavar, J R, Cieplak, M, & Maritan, A (1999). Statistical mechanics of protein-like heteropolymers. Proceedings of the National Academy of Sciences of the United States of America, 96(9), 4904-7.

Evgenii Kliuchnikov, Eugene Klyshko, Maria S.Kelly, Artem Zhmurov, Ruxandra I. Dima, Kenneth A. Marx, Valeri Barsegov, "Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules’ Growth, Catastrophe, Shortening, and Rescue", Comp. Struct. Biotech. J., 20, 953-974 (2022)

Editorial

Cheung, Margaret S, Dima, Ruxandra I, & Hyeon, Changbong (2021). Tribute to Dave Thirumalai. The journal of physical chemistry. B, 125(51), 13831-13833.

Dima, Ruxandra I (2011). Stoichiometry and topology in protein folding. Journal of biomolecular structure & dynamics, 28(4), 617-8; discussion 66.

Peer Reviewed Conference/Workshop Proceedings

R. I. Dima and G. Stan, "Computational studies of mechanical remodeling of substrate proteins by AAA+ biological nanomachines", Modern Applications of Flory’s "Statistical Mechanics of Chain Molecules", ACS Symposium Series #1356 (2020)

Invited Publication

K. E. Theisen, N. J. Desai, A. M. Volski, and R. I. Dima, ”Mechanics of severing for large microtubule complexes revealed by coarse-grained simulations”, J. Chem. Phys. 139, 121926 (2013)

K. E. Theisen, A. Zhmurov, M. E. Newberry, V. Barsegov and R. I. Dima (2012). "Multiscale Modeling of the Nanomechanics of Microtubule Protofilaments", J. Phys. Chem. B, 116, 8545-8555.(peer-reviewed)

Book Chapter

R. I. Dima, B. Tarus, J. E. Straub and D. Thirumalai. "Scenarios for protein aggregation: Molecular Dynamics simulationsand Bioinformatic Analysis"; V. Munoz, Ed(s); the RoyalSociety, (2008).

R. I. Dima. "Protein-Protein interactions and aggregationprocesses". In Computational Structural Biology; Manuel C. Peitsch and Torsten Schwede, Ed(s); World Scientific Publishing Ltd., (2008).

Under Review

Maria S. Kelly, Amanda C. Macke, Maria S. Kelly, Shehani Kahawatte, Jacob E. Stump, Abigail R. Miller, and Ruxandra I. Dima, "The Quaternary Question: Determining Allostery in Spastin through Dynamics Classification Learning and Bioinformatics", submitted to J. Chem. Phys.

K. Alice Lindsay, Nedine Abdelhamid, Shehani Kahawatte, Ruxandra I. Dima, Dan L. Sackett, Tara M. Finegan, and Jennifer L. Ross, "A Tale of 12 Tails: Katanin Severing Activity Affected by Carboxy-Terminal Tail Sequences", submitted to Biomolecules

Presentations

Invited Presentations

Ruxandra Dima (10-08-2021. ) Computational modeling and machine learning of the dynamics of large biomolecules .Purdue Univ. Ft. Wayne, Other Institution. . Level:University

Ruxandra Dima (03-25-2022. ) Using simulations and Machine Learning to understand the dynamics of biomolecules .Eastern Kentucky University. Other Institution. . Level:Department

Poster Presentations

Bkaht Hayate, M. Kelly, A. Macke, and R. I. Dima (08-2022. ) Allosteric Studies of Katanin with Machine Learning .REU poster session, UC. . UC. . Level:Department

Maria Kelly, A. Macke, S. Kahawate, and R. I. Dima (10-2022. ) Identifying Allosteric Networks of Severing Enzymes Using Markov State Models and Classification Models .Oesper Symposium and ACS Local section, University of Cincinnati. . UC. . Level:Local

Shehani Kahawatte, M. Kelly, A. Macke, and R. I. Dima (10-2022. ) Exploring the Effects of Tubulin Isotypes on the Action of Microtubule Severing Proteins Using Simulations and Machine Learning .Oesper Symposium and ACS Local section, University of Cincinnati. . UC. . Level:Local

Emma Meilinger, M. Kelly, A. Macke, S. Kahawatte, and R. I. Dima (10-2022. ) "Effects of Tubulin Tail Charge Density on Severing Enzyme Dynamics .Oesper Symposium and ACS Local section, University of Cincinnati. . UC. . Level:Local

Amanda Macke, M. Kelly, and R. I. Dima (02-2022. ) Breaking down microtubule severing motors with Machine Learning .Biophysical Society Annual Meeting, San Francisco, CA. . Professional Meeting. . Level:National

Paper Presentations

Maria Kelly, R. A. Varikoti, V. Barsegov, and R. I. Dima (03-2022. ) Microtubule Studies on Lattice Dynamics and Severing Machine Guided Regulation .Chicago, IL. Professional Meeting. Level:National

Symposium

Ruxandra Dima (06-2021. ) Modeling the severing of microtubules .Telluride Science Research Center. Conference. Level:International

Ruxandra Dima (03-2021. ) Clustering and dimensionality reduction methods applied to biomolecular ensembles .American Physical Society March Meeting. Professional Meeting. Level:International

Ruxandra Dima (02-2022. ) To cut or not to cut: the inner workings of microtubule severing machines .San Francisco. Professional Meeting. Level:International

Ruxandra Dima (06-2022. ) Microtubule severing enzymes oligomerization and allostery: a tale of two domains .Telluride, CO. Conference. Level:International

Event Organized

Molecular Machines --sessions at the APS National March Meeting

Molecular Machines --sessions at the APS National March Meeting Prof. Meeting 03-2022 03-2022 Chicago, IL Level:National

Honors and Awards

07-2008 -08-2008 Summer Faculty Research Fellowship University Research Council, University of Cincinnati Status:Recipient Level: University Type:Fellowship

03-01-2009 NSF-CAREER Award National Science Foundation Status:Recipient Level:National Type:Grant

01-01-2014 -05-01-2014 UC-LEAF Career Branch Award University of Cincinnati LEAF Status:Recipient Level:University Type:Fellowship

05-2015 -04-2017 Diana Lowenstein award Status:Recipient Level:Department Type:Recognition

01-13-2017 A&S Rising Star Award College of Arts and Sciences, University of Cincinnati Status:Recipient Level:College Type:Recognition

04-2021 Fellow of the Graduate School University of Cincinnati Status:Recipient Level:University Type:Recognition

04-2022 Excellence in Undergraduate Research Mentorship Award University of Cincinnati Status:Recipient Level:University Type:Recognition

Service

(Chemistry Head Search Committee ) Committee Member Type:Departmental Service Level:Department 05-2022 -06-2022

Post Graduate Training and Education

01-2000-07-2005 Research Associate, University of Maryland, , College Park, MD

Keywords

biophysics, bioinformatics, theory, data science