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

Research Support

Grant: #MCB-1817948 Investigators:Dima, Ruxandra 08-01-2018 -07-31-2022 National Science Foundation Computational modeling of the mechanisms of microtubule disassembly by biological nanomachines Role:PI $787,940.00 Active Type:Grant Level:National

Grant: #CHE-1950244 Investigators:Dima, Ruxandra; Gudmundsdottir, Anna 05-01-2020 -04-30-2023 National Science Foundation REU Site: Research Experiences for Undergraduates in Chemistry at the University of Cincinnati Role:Collaborator $364,000.00 Awarded Level:Federal

Abbreviated Publications

Peer Reviewed Publications

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).

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).

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)

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)

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)

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.

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, 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).)

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

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.

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.

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.

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.

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.

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

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.

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. "Proteins associated with diseases show enhanced sequence correlation between charged residues". Bioinformatics (2004), 20, 2345.

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

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

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.

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 protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Protein science : a publication of the Protein Society, 11(5), 1036-49.

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.

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.

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)

Editorial

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

Book Chapter

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).

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).

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)

Under Review

M. Damre, A. Dayananda, R. A. Varikoti, G. Stan and R. I. Dima, "Factors Underlying Asymmetric Dynamics of Disaggregase and Microtubule Severing AAA+ Machines"

"Modeling the Mechanical Response of Microtubule Lattices to Pressure” Lukasz Szatkowski, Rohith Anand Varikoti, and Ruxandra I. Dima

Presentations

Invited Presentations

Ruxandra Dima (11-28-2016. ) Multi-scale Modeling of the Nanomechanics of Biomolecular Assemblies .Department of Physics, University of Tennessee, Knoxville, TN. Other Institution. .

Ruxandra Dima (10-22-2014. ) Large-scale Modeling of the Nanomechanics of Biomolecular Shells .University of Cincinnati, Physics Dept., Cincinnati, OH. UC. . Level:Department

Ruxandra Dima (10-10-2014. ) "Large-scale Modeling of the Nanomechanics of Biomolecular Shells .University of North Carolina, Chapel Hill, NC. Other Institution. . Level:Department

Ruxandra Dima (05-09-2014. ) Large-scale simulations of mechanical proteins .Technical University Munich, Munich, Germany. Other Institution. . Level:International

Ruxandra Dima (03-31-2014. ) Exploring the nanomechanics of biomolecular filaments using multiscale simulations .Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. Other Institution. . Level:International

Ruxandra Dima (04-17-2013. ) Multiscale modeling of dynamics in mechanical proteins .Ohio State University, Columbus, OH. Other Institution. . Level:State

Ruxandra Dima (07-2012. ) "Computational modeling of the force response in large protein complexes" .Technical University Munich, Munich, Germany. Other Institution. . Level:University

R. I. Dima (03-17-2011. ) Exploration of the role of protein-protein binding interactions in synaptic fusion .Colloquium, Ball State University. Other Institution. . Level:University

J. Y. Lee, T. M. Iverson and R. I. Dima (06-16-2010. ) Molecular simulations of actin flexibility .The the 42nd Central Regional Meeting of the ACS, Dayton, OH. Professional Meeting. . Level:Regional

R.I. Dima (10-09-2008. ) Exploring the micromechanics of microtubules by molecular simulations .PChem seminar, Indiana University, Bloomington, IN. Other Institution. . Level:Department

R. I. Dima and H. Joshi (06-2008. ) Exploring the mechanics of microtubules bymolecular simulations .2008 CERMACS meeting, Columbus, OH. Professional Meeting. . Level:Regional

R. I. Dima and H. Joshi (04-2008. ) Forced unfolding of proteins: the role ofchain dynamics .2008 March Meeting of the American Chemical Society, New Orleans. Conference. . Level:National

R. I. Dima, C. Hyeon and D. Thirumalai (06-2007. ) Probing pathways and kinetic barriers in the mechanical unfolding and refolding of proteins .SUNY at Albany. Conference. . Level:International

(2006. ) Probing the low-resolution dynamics of biopolymers under force .American Physical Society, Baltimore, MD.

(03-31-2005. ) University of Texas at Austin .Sources of instability in prion proteins: Glancing at early,

(03-2005. ) Glancing at the early-steps of conformational transition in prion proteins through MD simulations .March Meeting of the American Chemical Society, San Diego.

(02-09-2005. ) Potentials of mean force for structure prediction in RNA; Glancing at early steps in the conformational transition in prions .University of Massachusetts Lowell,

(01-20-2005. ) Sources of instability in prion proteins: Glancing at early steps in the conformational transition .North Carolina State University,

(12-09-2004. ) Boston University .Sources of instability in prion proteins: Glancing at early steps in the conformational transition,

(10-18-2004. ) Conformational conversion in prions: A Molecular dynamics perspective .IPST, University of Maryland.

(02-19-2004. ) Surprising instabilities in prion proteins: Evidence from computational methods applied to sequences and NMR structures .University of North Carolina, Chapel Hill,

(02-13-2004. ) Surprising instabilities in prion proteins: Evidence from computational methods applied to sequences and NMR structures .University of Pittsburgh, Center for Computational Biology and Bioinformatics.

(03-10-2003. ) Surprising instabilities in proteins related to Mad Cow disease: Evidence from NMR structures and sequence alignments .Albert Einstein College of Medicine,

(09-2002. ) Surprising instabilities in prions: Evidence from NMR structures and sequence alignments .Computational Biophysics: Integrating Theoretical Physics and Biology, San Feliu de Gixols, Spain.

(04-25-2002. ) Surprising conformational instabilities in prions .Computational Biophysics Section, Laboratory of Biophysical Chemistry, NHLBI, NIH.

(04-23-2002. ) Surprising instabilities in proteins related to Mad Cow disease .Statistical Physics Seminar, IPST.

R. I. Dima, D. Thirumalai (04-2002. ) Exploring Protein Aggregation using simple models: Phase diagram and Kinetics .American Chemical Society, Orlando, FL.

Colloquium

R.I. Dima (11-06-2008). Exploring the micromechanics of microtubules by molecular simulations . Department of Physics, IUPUI, Indianapolis, IN. Other Institution. Level:Department

R.I. Dima (06-05-2008). Modeling the micromechanics of the cell cytoskeleton: the case of tubulin . Department of Chemistry, Miami University, Oxford, OH. Other Institution. Level:Department

Symposium

Ruxandra Dima (07-25-2016. ) Effects of lattice defects on microtubule breaking and healing from coarse-grained simulations .Telluride, CO. Professional Meeting. Level:National

Ruxandra Dima (05-16-2016. ) Large-scale modeling of the mechanics of biomolecular assemblies .Lexigton, KY. Professional Meeting. Level:Regional

Ruxandra Dima (12-16-2015. ) Exploring the role of nucleotides in regulating the mechanical stability of biomolecules .Punta Cana, Dominican Republic. Professional Meeting. Level:International

Ruxandra Dima (08-15-2014. ) Development of multi-scale simulations for investigations of the mechanics of protein assemblies .Purdue University. Workshop. Level:Regional

Ruxandra Dima (08-07-2014. ) Coarse-grained modeling of the nanomechanics of cytoskeletal filaments .Telluride, CO. Professional Meeting. Level:National

Ruxandra Dima (07-08-2014. ) Large-scale simulations of the mechanics of microtubules interactions with motor proteins .Boston, MA. Conference. Level:International

Ruxandra Dima (06-24-2014. ) Investigations into the mechanical basis of interactions between cytoskeletal filaments and associated proteins during mitosis .Telluride, CO. Professional Meeting. Level:National

Ruxandra Dima (03-13-2014. ) Modeling mechanical transitions in large biomolecular systems .Antholz, Italy. Workshop. Level:International

Ruxandra Dima (02-03-2014. ) Multiscale Modeling of the Nanomechanics of Biomolecular Filaments .Linz, Austria. Conference. Level:International

Ruxandra Dima (12-04-2013. ) "Exploring structural diversity in proteins using single-molecule approaches" .Xcaret, Mexico. Conference. Level:International

Ruxandra Dima (08-05-2013. ) "Exploring the mechanical action of molecular motors during the depolymerization of cytoskeletal filaments" .Telluride, CO. Professional Meeting. Level:National

Ruxandra Dima (05-15-2013. ) Multiscale simulations of the mechanics of filamentous proteins .Pultusk, Poland. Workshop. Level:International

Ruxandra Dima (12-2012. ) "Computational Modeling of the Nanomechanics of Large Biomolecular Filaments with roles in heart disease and cancer", .Xcaret, Mexico. Conference. Level:International

Ruxandra Dima (10-2012. ) "Modulation of the mechanical response of biomolecular complexes by the dynamics of applied tension" .Chicago, IL. Conference. Level:National

Ruxandra Dima (08-2012. ) "Multiscale Modeling of the Nanomechanics of Biomolecular Filaments" .Philadelphia, PA. Conference. Level:National

Ruxandra Dima (07-2012. ) "Coarse-grained models for studying the dynamics of filamentous proteins" .Telluride, CO. Workshop. Level:National

Ruxandra Dima (06-2012. ) "Development of multi-scale models for biomechanics of large cellular complexes" .Telluride, CO. Workshop. Level:National

R. I. Dima (12-05-2011. ) Design of coarse-grained molecular simulations for dynamics in mechanical proteins .Xcaret, Mexico. Conference. Level:International

R. I. Dima (08-30-2011. ) Large-scale molecular simulations of dynamics in mechanical proteins .Denver, CO. Professional Meeting. Level:National

R. I. Dima (06-15-2011. ) GPU-based modeling of the mechanical behavior of large biomolecules .Albany, NY. Conference. Level:National

R. I. Dima (09-29-2010. ) Molecular investigations into the mechanics of actin in different nucleotide states .Seoul, South Korea. Conference. Level:International

R. I. Dima (01-12-2010. ) Exploring factors that determine the mechanical response of proteins: from globular proteins to protofilaments .Ventura, CA. Conference. Level:National

Ruxandra Dima (12-05-2017. ) Exploring the breaking and healing of microtubules: role of lattice defects and enzyme binding sites .Montego Bay. Conference. Level:International

Ruxandra Dima (07-24-2018. ) Modeling the breaking and healing of cytoskeletal lattices .Telluride, CO. Professional Meeting. Level:National

R. I. Dima (08-2019. ) Multi-scale Modeling of the Nanomechanics of Microtubule Filaments .San Diego, CA. Professional Meeting. Level:National

Event Organized

Computational Chemistry session at CERMACS

Computational Chemistry session at CERMACS 05-23-2007

Computational Chemistry Session

Computational Chemistry Session Prof. Meeting 05-20-2016 CERMACS - Covington, KY Level:Regional

From Computational Biophysics to Systems Biology (CBSB2017)

From Computational Biophysics to Systems Biology (CBSB2017) Workshop 05-18-2017 05-20-2017 University of Cincinnati Level:International

Oesper symposium

Oesper symposium Symposium 11-09-2018 11-09-2018 University of Cincinnati Level:Local

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

Post Graduate Training and Education

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

Keywords

biophysics, bioinformatics, theory, data science

Faculty Development Activities

10-22-2013 Conflict Management and Negotiation Workshop workshop designed for junior/mid-level STEM faculty to develop negotiation and conflict management skills specific to the academic environment, UC-Leaf University of Cincinnati Type:Workshop

03-06-2016 -05-2016 Master Mentors College of Arts and Sciences University of Cincinnati Type:Workshop