个人简介

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.

研究领域

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.

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

近期论文

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Order statistics theory of unfolding of multimeric proteins. Zhmurov A, Dima RI, Barsegov V. Biophys J. 2010 Sep 22;99(6):1959-68. PMID: 20858442 [PubMed - in process] Sop-GPU: accelerating biomolecular simulations in the centisecond timescale using graphics processors. Zhmurov A, Dima RI, Kholodov Y, Barsegov V. Proteins. 2010 Nov 1;78(14):2984-99. PMID: 20715052 [PubMed - in process] Exploring the contribution of collective motions to the dynamics of forced-unfolding in tubulin. Joshi H, Momin F, Haines KE, Dima RI. Biophys J. 2010 Feb 17;98(4):657-66. PMID: 20159162 [PubMed - indexed for MEDLINE] Probing the origin of tubulin rigidity with molecular simulations. Dima RI, Joshi H. Proc Natl Acad Sci U S A. 2008 Oct 14;105(41):15743-8. Epub 2008 Oct 7. PMID: 18840679 [PubMed - indexed for MEDLINE] Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations. Mickler M, Dima RI, Dietz H, Hyeon C, Thirumalai D, Rief M. Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20268-73. Epub 2007 Dec 13. PMID: 18079292 [PubMed - indexed for MEDLINE] Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back. Chen J, Dima RI, Thirumalai D. J Mol Biol. 2007 Nov 16;374(1):250-66. Epub 2007 Aug 25. PMID: 17916364 [PubMed - indexed for MEDLINE] Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism. O'Brien EP, Dima RI, Brooks B, Thirumalai D. J Am Chem Soc. 2007 Jun 13;129(23):7346-53. Epub 2007 May 16. PMID: 17503819 [PubMed - indexed for MEDLINE] Size, shape, and flexibility of RNA structures. Hyeon C, Dima RI, Thirumalai D. J Chem Phys. 2006 Nov 21;125(19):194905. PMID: 17129165 [PubMed - indexed for MEDLINE] Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Hyeon C, Dima RI, Thirumalai D. Structure. 2006 Nov;14(11):1633-45. PMID: 17098189 [PubMed - indexed for MEDLINE] Determination of network of residues that regulate allostery in protein families using sequence analysis. Dima RI, Thirumalai D. Protein Sci. 2006 Feb;15(2):258-68. PMID: 16434743 [PubMed - indexed for MEDLINE] Extracting stacking interaction parameters for RNA from the data set of native structures. Dima RI, Hyeon C, Thirumalai D. J Mol Biol. 2005 Mar 18;347(1):53-69. Epub 2005 Jan 12. PMID: 15733917 [PubMed - indexed for MEDLINE] Probing the instabilities in the dynamics of helical fragments from mouse PrPC. Dima RI, Thirumalai D. Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15335-40. Epub 2004 Oct 19. PMID: 15494440 [PubMed - indexed for MEDLINE] Proteins associated with diseases show enhanced sequence correlation between charged residues. Dima RI, Thirumalai D. Bioinformatics. 2004 Oct 12;20(15):2345-54. Epub 2004 Apr 8. PMID: 15073020 [PubMed - indexed for MEDLINE]Free Article Emerging ideas on the molecular basis of protein and peptide aggregation. Thirumalai D, Klimov DK, Dima RI. Curr Opin Struct Biol. 2003 Apr;13(2):146-59. Review. PMID: 12727507 [PubMed - indexed for MEDLINE] Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments. Dima RI, Thirumalai D. Biophys J. 2002 Sep;83(3):1268-80. PMID: 12202354 [PubMed - indexed for MEDLINE] Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Dima RI, Thirumalai D. Protein Sci. 2002 May;11(5):1036-49. PMID: 11967361 [PubMed - indexed for MEDLINE] Protein threading by learning. Chang I, Cieplak M, Dima RI, Maritan A, Banavar JR. Proc Natl Acad Sci U S A. 2001 Dec 4;98(25):14350-5. Epub 2001 Nov 20. PMID: 11717394 [PubMed - indexed for MEDLINE] Scoring functions in protein folding and design. Dima RI, Banavar JR, Maritan A. Protein Sci. 2000 Apr;9(4):812-9. PMID: 10794424 [PubMed - indexed for MEDLINE] Statistical mechanics of protein-like heteropolymers. Dima RI, Banavar JR, Cieplak M, Maritan A. Proc Natl Acad Sci U S A. 1999 Apr 27;96(9):4904-7. PMID: 10220391 [PubMed - indexed for MEDLINE]