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Assistant Professor
Chemistry - Tenure-Track Faculty
1302 Crosley Tower
513-556-3961
ruxandra.dima@uc.edu

Research Support

(PI) Ruxandra Dima, University Research Council. Funded 07/01/2008 to 08/30/2008.

Peer Reviewed Publications

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 AqueousGuanidinium 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.

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.

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

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

Book Chapters

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. Peitschand Torsten Schwede, Ed(s); World Scientific Publishing Ltd., (2008).

Invited Presentations

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

(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.

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

(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.

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.

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 (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.

Poster Presentations

(06-2007). Probing pathways and kinetic barriers in the mechanical unfolding and refolding of proteins. Albany 2007: the 15th Conversation, .

Colloquia

R.I. Dima (06/05/2008). Modeling the micromechanics of the cell cytoskeleton: the case of tubulin. Oxford, OH.

R.I. Dima (11/06/2008). Exploring the micromechanics of microtubules by molecular simulations. Indianapolis, IN.

Events Organized

Computational Chemistry session at CERMACS (05/23/2007), .

Honors & Awards

Summer Faculty Research Fellowship, University Research Council, University of Cincinnati.