Macke, Amanda C, Stump, Jacob E, Kelly, Maria S, Rowley Jamie, Herath, Vageesha, Mullen, Sarah, Dima, Ruxandra I (2024). Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms. J. Chem. Inf. Model.
Kelly, Maria S, Macke, Amanda C, Kahawatte, Shehani, Stump, Jacob E, Miller, Abby R, Dima, Ruxandra I (2023). The Quaternary Question: Determining Allostery in Spastin through Dynamics Classification Learning and Bioinformatics. J. Chem. Phys. 158, 125102.
Quarin, Steven M, Macke, Amanda C, Kissell, Lyndsay N, Kelly, Maria S, Dayananda, Ashan, Ungvary, Joseph, Stan, George, Dima, Ruxandra I, Strobbia, Pietro (2023). Design, Rationalization, and Automation of a Catalytic Sensing Mechanism for Homogeneous SERS Biosensors. ACS Sens. 8, 5, 2000-2010.
Lindsay, Alice K, Abdelhamid, Nedine, Kahawatte, Shehani, Dima, Ruxandra I, Sackett, Dan L, Finegan, Tara M, Ross, Jennifer L (2023). A Tale of 12 Tails: Katanin Severing Activity Affected by Carboxy-Terminal Tail Sequences. Biomolecules. 13, 620.
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.
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).
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.
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.
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 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).
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)
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)
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
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.
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.
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)