Ruxandra Dima - Publications

Affiliations: 
Chemistry University of Cincinnati, Cincinnati, OH 
Area:
Physical Chemistry, General Biophysics

31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Macke AC, Kelly MS, Varikoti RA, Mullen S, Groves D, Forbes C, Dima RI. Microtubule Severing Enzymes Oligomerization and Allostery: A Tale of Two Domains. The Journal of Physical Chemistry. B. PMID 36475672 DOI: 10.1021/acs.jpcb.2c05288  0.362
2022 Varikoti RA, Fonseka HYY, Kelly MS, Javidi A, Damre M, Mullen S, Nugent JL, Gonzales CM, Stan G, Dima RI. Exploring the Effect of Mechanical Anisotropy of Protein Structures in the Unfoldase Mechanism of AAA+ Molecular Machines. Nanomaterials (Basel, Switzerland). 12. PMID 35683705 DOI: 10.3390/nano12111849  0.389
2022 Kliuchnikov E, Klyshko E, Kelly MS, Zhmurov A, Dima RI, Marx KA, Barsegov V. 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. PMID 35242287 DOI: 10.1016/j.csbj.2022.01.028  0.443
2021 Damre M, Dayananda A, Varikoti RA, Stan G, Dima RI. Factors Underlying Asymmetric Pore Dynamics of Disaggregase and Microtubule Severing AAA+ Machines. Biophysical Journal. PMID 34181904 DOI: 10.1016/j.bpj.2021.05.027  0.349
2021 Szatkowski L, Varikoti RA, Dima RI. Modeling the Mechanical Response of Microtubule Lattices to Pressure. The Journal of Physical Chemistry. B. 125: 5009-5021. PMID 33970630 DOI: 10.1021/acs.jpcb.1c01770  0.331
2020 Varikoti RA, Macke AC, Speck V, Ross JL, Dima RI. Molecular Investigations into the Unfoldase Action of Severing Enzymes on Microtubules. Cytoskeleton (Hoboken, N.J.). PMID 32170815 DOI: 10.1002/Cm.21606  0.325
2019 Szatkowski L, Merz DR, Jiang N, Ejikeme I, Belonogov L, Ross JL, Dima RI. The Mechanics of the Microtubule Seam Interface Probed by Molecular Simulations and In Vitro Severing Experiments. The Journal of Physical Chemistry. B. PMID 31117616 DOI: 10.1021/Acs.Jpcb.9B03059  0.344
2019 Szatkowski L, Dale MR, Ross JL, Dima RI. Mechanical Stability of Microtubule Lattices - Molecular Dynamic Indentation Studies Biophysical Journal. 116: 257a. DOI: 10.1016/J.Bpj.2018.11.1401  0.354
2017 Barsegov V, Ross J, Dima R. Dynamics of microtubules: highlights of recent computational and experimental investigations. Journal of Physics. Condensed Matter : An Institute of Physics Journal. PMID 28812545 DOI: 10.1088/1361-648X/Aa8670  0.41
2017 Jiang N, Dima R. Exploring Microtubule Breaking and Recovering Mechanisms using Large Scale Molecular Simulations Biophysical Journal. 112: 566a. DOI: 10.1016/J.Bpj.2016.11.3048  0.416
2017 Jiang N, Ross J, Dima R. Multi-Scale Modeling of the Nanomechanics of Microtubule Filaments Biophysical Journal. 112: 564a-565a. DOI: 10.1016/J.Bpj.2016.11.3041  0.496
2016 Jiang N, Bailey ME, Burke J, Ross JL, Dima RI. Modeling the effects of lattice defects on microtubule breaking and healing. Cytoskeleton (Hoboken, N.J.). PMID 27935245 DOI: 10.1002/Cm.21346  0.41
2015 Bauer D, Merz DR, Pelz B, Theisen KE, Yacyshyn G, Mokranjac D, Dima RI, Rief M, Žoldák G. Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK. Proceedings of the National Academy of Sciences of the United States of America. 112: 10389-94. PMID 26240360 DOI: 10.1073/Pnas.1504625112  0.705
2015 Kononova O, Kholodov Y, Theisen KE, Marx KA, Dima RI, Ataullakhanov FI, Grishchuk EL, Barsegov V. 52 Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico. Journal of Biomolecular Structure & Dynamics. 33: 35-6. PMID 26103263 DOI: 10.1080/07391102.2015.1032601  0.755
2015 Bodmer NK, Theisen KE, Dima RI. Molecular investigations into the mechanics of a muscle anchoring complex. Biophysical Journal. 108: 2322-32. PMID 25954889 DOI: 10.1016/J.Bpj.2015.03.036  0.719
2014 Kononova O, Kholodov Y, Theisen KE, Marx KA, Dima RI, Ataullakhanov FI, Grishchuk EL, Barsegov V. Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico. Journal of the American Chemical Society. 136: 17036-45. PMID 25389565 DOI: 10.1021/Ja506385P  0.761
2014 Kononova O, Kholodov Y, Theisen KE, Marx KA, Dima RI, Ataullakhanov FI, Grishchuk EL, Barsegov V. Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico Journal of the American Chemical Society. 136: 17036-17045. DOI: 10.1021/ja506385p  0.725
2013 Kononova O, Snijder J, Brasch M, Cornelissen J, Dima RI, Marx KA, Wuite GJL, Roos WH, Barsegov V. Structural transitions and energy landscape for cowpea chlorotic mottle virus capsid mechanics from nanomanipulation in vitro and in silico Biophysical Journal. 105: 1893-1903. PMID 24138865 DOI: 10.1016/J.Bpj.2013.08.032  0.306
2013 Theisen KE, Desai NJ, Volski AM, Dima RI. Mechanics of severing for large microtubule complexes revealed by coarse-grained simulations. The Journal of Chemical Physics. 139: 121926. PMID 24089738 DOI: 10.1063/1.4819817  0.747
2012 Zhmurov A, Kononova O, Litvinov RI, Dima RI, Barsegov V, Weisel JW. Mechanical transition from α-helical coiled coils to β-sheets in fibrin(ogen). Journal of the American Chemical Society. 134: 20396-402. PMID 22953986 DOI: 10.1021/Ja3076428  0.309
2012 Theisen KE, Zhmurov A, Newberry ME, Barsegov V, Dima RI. Multiscale modeling of the nanomechanics of microtubule protofilaments. The Journal of Physical Chemistry. B. 116: 8545-55. PMID 22509945 DOI: 10.1021/jp212608f  0.735
2012 Lee JY, Duan L, Iverson TM, Dima RI. Exploring the role of topological frustration in actin refolding with molecular simulations. The Journal of Physical Chemistry. B. 116: 1677-86. PMID 22243338 DOI: 10.1021/jp209340y  0.385
2011 Zhmurov A, Brown AE, Litvinov RI, Dima RI, Weisel JW, Barsegov V. Mechanism of fibrin(ogen) forced unfolding. Structure (London, England : 1993). 19: 1615-24. PMID 22078561 DOI: 10.1016/J.Str.2011.08.013  0.366
2011 Duan L, Zhmurov A, Barsegov V, Dima RI. Exploring the mechanical stability of the C2 domains in human synaptotagmin 1. The Journal of Physical Chemistry. B. 115: 10133-46. PMID 21776988 DOI: 10.1021/Jp2025945  0.334
2011 Lee JY, Iverson TM, Dima RI. Molecular investigations into the mechanics of actin in different nucleotide states. The Journal of Physical Chemistry. B. 115: 186-95. PMID 21141951 DOI: 10.1021/jp108249g  0.312
2011 Zhmurov A, Brown AE, Litvinov RI, Dima RI, Weisel JW, Barsegov V. Molecular Structural Origins of Clot and Thrombus Mechanical Properties Blood. 118: 2257-2257. DOI: 10.1182/Blood.V118.21.2257.2257  0.39
2010 Zhmurov A, Dima RI, Kholodov Y, Barsegov V. SOP-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors Proteins: Structure, Function and Bioinformatics. 78: 2984-2999. PMID 20715052 DOI: 10.1002/Prot.22824  0.343
2010 Joshi H, Momin F, Haines KE, Dima RI. Exploring the contribution of collective motions to the dynamics of forced-unfolding in tubulin. Biophysical Journal. 98: 657-66. PMID 20159162 DOI: 10.1016/j.bpj.2009.10.043  0.348
2008 Dima RI, Joshi H. Probing the origin of tubulin rigidity with molecular simulations. Proceedings of the National Academy of Sciences of the United States of America. 105: 15743-8. PMID 18840679 DOI: 10.1073/pnas.0806113105  0.417
2007 Mickler M, Dima RI, Dietz H, Hyeon C, Thirumalai D, Rief M. Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations. Proceedings of the National Academy of Sciences of the United States of America. 104: 20268-73. PMID 18079292 DOI: 10.1073/Pnas.0705458104  0.366
2003 Thirumalai D, Klimov DK, Dima RI. Emerging ideas on the molecular basis of protein and peptide aggregation Current Opinion in Structural Biology. 13: 146-159. PMID 12727507 DOI: 10.1016/S0959-440X(03)00032-0  0.321
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