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Ruxandra I Dima

Title: Associate Professor
Office: 304 Crosley Tower
Tel: 513-556-3961
Email: ruxandra.dima@uc.edu
Web: https://sites.google.com/site/dimalabwebsite/home

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 2012 she is an Associate 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) GPU-based computing
We use a combination of molecular simulations, bioinformatics, 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 Information

Research Interests

Modeling of mechanical response in large cellular protofilaments

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

Modeling of protein-protein interactions with functional roles in the immune response and synaptic processes

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

Development of new computing approaches on novel architectures to enable probing of biomolecules on experimental timescales

Research Support

  • (PI), Ruxandra Dima, University Research Council. 07/01/2008 to 08/30/2008.
  • (Senior Personnel), Patrick Limbach (PI), NSF-ARI: Renovation of Chemistry Facilities at the University of Cincinnati , National Science Foundation. $1,257,000 . 09/01/2010 to 08/31/2013. Status: Active.
  • (PI), Ruxandra Dima, Career Branch Award, UC-LEAF. $3000. 01/15/2014 to 05/31/2014. Status: Active.
  • (PI), Ruxandra Dima, CAREER Multiscale Modeling of Micromechanics of Cytoskeletal Protofilaments, National Science Foundation. (MCB-0845002), 03/01/2009 to 02/28/2015. Status: Active.
  • (Senior Personnel), A. Gudmundsdottir (PI), B. Ault (PI), REU, National Science Foundation. 03-2013 to 02-2016. Status: Active.
  • (PI), Ruxandra Dima, CAREER Multiscale Modeling of Micromechanics of Cytoskeletal Protofilaments, National Science Foundation. (MCB-0845002), 03/01/2009 to 02/28/2015. Status: Active.
  • (Senior Personnel), A. Gudmundsdottir (PI), W. Connick (PI), REU, National Science Foundation. 03/01/2017 to 02/28/2020. Status: Active.
  • (co-PI), R. Dima; G. Stan, Conference: From Computational Biophysics to Systems Biology 2017, National Science Foundation. (MCB-1740908), 04/15/2017 to 03/31/2018. Status: Active.
  • (PI), Ruxandra Dima, Computational investigations of the biomechanics of protein-protein interactions involved in the control of microtubule disassembly, National Science Foundation. (MCB-1412183), 08/01/2014 to 07/31/2018. Status: Active.

Publications

Peer Reviewed Publications

  • 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).
  • 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.
  • N. Jiang, M. Bailey, J. L. Ross, and R. I. Dima "Modeling the effects of lattice defects on microtubule breaking and healing", Cytoskeleton, (2016).
  • 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.
  • 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)
  • 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.

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).

Editorial

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

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)

Presentations & Lectures

Invited Presentations

  • Ruxandra Dima (11/28/2016). Multi-scale Modeling of the Nanomechanics of Biomolecular Assemblies Department of Physics, University of Tennessee, Knoxville, TN.
  • Ruxandra Dima (10/22/2014). Large-scale Modeling of the Nanomechanics of Biomolecular Shells University of Cincinnati, Physics Dept., Cincinnati, OH.
  • Ruxandra Dima (10/10/2014). "Large-scale Modeling of the Nanomechanics of Biomolecular Shells University of North Carolina, Chapel Hill, NC.
  • Ruxandra Dima (05/09/2014). Large-scale simulations of mechanical proteins Technical University Munich, Munich, Germany.
  • Ruxandra Dima (03/31/2014). Exploring the nanomechanics of biomolecular filaments using multiscale simulations Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
  • Ruxandra Dima (04/17/2013). Multiscale modeling of dynamics in mechanical proteins Ohio State University, Columbus, OH.
  • Ruxandra Dima (07-2012). "Computational modeling of the force response in large protein complexes" Technical University Munich, Munich, Germany.
  • R. I. Dima (03/17/2011). Exploration of the role of protein-protein binding interactions in synaptic fusion Colloquium, Ball State 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.
  • R.I. Dima (10/09/2008). Exploring the micromechanics of microtubules by molecular simulations PChem seminar, Indiana University, Bloomington, IN.
  • R. I. Dima and H. Joshi (06-2008). Exploring the mechanics of microtubules bymolecular simulations 2008 CERMACS meeting, Columbus, OH.
  • 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.
  • 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.
  • (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.

Colloquia

  • R.I. Dima (11/06/2008). Exploring the micromechanics of microtubules by molecular simulations. Department of Physics, IUPUI, Indianapolis, IN.
  • R.I. Dima (06/05/2008). Modeling the micromechanics of the cell cytoskeleton: the case of tubulin. Department of Chemistry, Miami University, Oxford, OH.

Symposium

  • Ruxandra Dima (07/25/2016). Effects of lattice defects on microtubule breaking and healing from coarse-grained simulations. Telluride workshop on Coarse-grained simulations of biomolecules, Telluride, CO. Professional Meeting. Level: National.
  • Ruxandra Dima (05/16/2016). Large-scale modeling of the mechanics of biomolecular assemblies. 5th Bluegrass Molecular Biophysics Symposium, Lexigton, KY. Professional Meeting. Level: Regional.
  • Ruxandra Dima (12/16/2015). Exploring the role of nucleotides in regulating the mechanical stability of biomolecules. The 3rd International Conference on Protein and RNA Structure Prediction, 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. ACLS Summer School in Computational Chemistry, Purdue University. Workshop. Level: Regional.
  • Ruxandra Dima (08/07/2014). Coarse-grained modeling of the nanomechanics of cytoskeletal filaments. Telluride workshop on "Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules", Telluride, CO. Professional Meeting. Level: National.
  • Ruxandra Dima (07/08/2014). Large-scale simulations of the mechanics of microtubules interactions with motor proteins. The 7th World Congress of Biomechanics, 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 workshop on "Protein and Peptide Interactions in Cellular Environments", Telluride, CO. Professional Meeting. Level: National.
  • Ruxandra Dima (03/13/2014). Modeling mechanical transitions in large biomolecular systems. Technical University Munich Winter Workshop, Antholz, Italy. Workshop. Level: International.
  • Ruxandra Dima (02/03/2014). Multiscale Modeling of the Nanomechanics of Biomolecular Filaments. The XVI Annual Linz Winter Workshop on Single Molecule Biophysics, Linz, Austria. Conference. Level: International.
  • Ruxandra Dima (12/04/2013). "Exploring structural diversity in proteins using single-molecule approaches". Zing Protein & RNA Structure Prediction, Xcaret, Mexico. Conference. Level: International.
  • Ruxandra Dima (08/05/2013). "Exploring the mechanical action of molecular motors during the depolymerization of cytoskeletal filaments". workshop on "Rise of the Machines", Telluride, CO. Professional Meeting. Level: National.
  • Ruxandra Dima (05/15/2013). Multiscale simulations of the mechanics of filamentous proteins. Biomolecules and Nanostructures -BioNano4 workshop, 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",. Zing Conference "Mathematical and Computational Medicine Conference 2012", Xcaret, Mexico. Conference. Level: International.
  • Ruxandra Dima (10-2012). "Modulation of the mechanical response of biomolecular complexes by the dynamics of applied tension". International Conference and Expo on Material Science & Engineering" (Material Science-2012), Chicago, IL. Conference. Level: National.
  • Ruxandra Dima (08-2012). "Multiscale Modeling of the Nanomechanics of Biomolecular Filaments". 244th ACS National Meeting, Philadelphia, PA. Conference. Level: National.
  • Ruxandra Dima (07-2012). "Coarse-grained models for studying the dynamics of filamentous proteins". Telluride workshop on "Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules", Telluride, CO. Workshop. Level: National.
  • Ruxandra Dima (06-2012). "Development of multi-scale models for biomechanics of large cellular complexes". Telluride workshop on "Protein and Peptide Interactions in Cellular Environments", Telluride, CO. Workshop. Level: National.
  • R. I. Dima (12/05/2011). Design of coarse-grained molecular simulations for dynamics in mechanical proteins. Zing Conference on Protein and RNA structure prediction, Xcaret, Mexico. Conference. Level: International.
  • R. I. Dima (08/30/2011). Large-scale molecular simulations of dynamics in mechanical proteins. ACS National Meeting: Marie Curie Symposium, Denver, CO. Professional Meeting. Level: National.
  • R. I. Dima (06/15/2011). GPU-based modeling of the mechanical behavior of large biomolecules. Albany 2011:The 17th Conversation, Albany, NY. Conference. Level: National.
  • R. I. Dima (09/29/2010). Molecular investigations into the mechanics of actin in different nucleotide states. The 10th KIAS Conference on Protein Structure and Function, 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. Gordon Research Conference in Protein Folding, 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. The 4th International Conference on Protein and RNA Structure Prediction, Montego Bay. Conference. Level: International.

Honors & Awards

  • Summer Faculty Research Fellowship, University Research Council, University of Cincinnati, 07-2008 to 08-2008.
  • NSF-CAREER Award, National Science Foundation, 03/01/2009.
  • UC-LEAF Career Branch Award, University of Cincinnati LEAF, 01/01/2014 to 05/01/2014.
  • Diana Lowenstein award, 05-2015 to 04-2017.
  • A&S Rising Star Award, College of Arts and Sciences, University of Cincinnati, 01/13/2017.

Experience & Service

Post Graduate training and Education

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

Events Organized

  • Computational Chemistry session at CERMACS (05/23/2007.
  • Prof. Meeting. Computational Chemistry Session (05/20/2016, CERMACS - Covington, KY.
  • Workshop. From Computational Biophysics to Systems Biology (CBSB2017) (05/18/2017 to 05/20/2017) , University of Cincinnati.