Devarajan Thirumalai, Ph.D. - Publications

Affiliations: 
Chemistry and Biochemistry University of Maryland, College Park, College Park, MD 
Area:
biophysics and theoretical biochemistry
Website:
http://www.chem.umd.edu/devarajan-thirumalai/

245 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
2020 Mugnai ML, Caporizzo MA, Goldman YE, Thirumalai D. Processivity and Velocity for Motors Stepping on Periodic Tracks. Biophysical Journal. 118: 1537-1551. PMID 32367805 DOI: 10.1016/J.Bpj.2020.01.047  0.32
2020 Hathcock D, Tehver R, Hinczewski M, Thirumalai D. Myosin V executes steps of variable length via structurally constrained diffusion. Elife. 9. PMID 31939739 DOI: 10.7554/eLife.51569  1
2019 Chakrabarti S, Jarzynski C, Thirumalai D. Processivity, Velocity, and Universal Characteristics of Nucleic Acid Unwinding by Helicases. Biophysical Journal. PMID 31400912 DOI: 10.1016/J.Bpj.2019.07.021  0.6
2019 Thirumalai D, Samanta HS, Maity H, Reddy G. Universal Nature of Collapsibility in the Context of Protein Folding and Evolution. Trends in Biochemical Sciences. PMID 31153683 DOI: 10.1016/J.Tibs.2019.04.003  0.68
2019 Samanta HS, Mugnai ML, Kirkpatrick TR, Thirumalai D. Giant Casimir Non-Equilibrium Forces Drive Coil to Globule Transition in Polymers. The Journal of Physical Chemistry Letters. PMID 31066561 DOI: 10.1021/acs.jpclett.9b00695  0.68
2019 Thirumalai D, Hyeon C, Zhuravlev PI, Lorimer GH. Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines. Chemical Reviews. PMID 31017391 DOI: 10.1021/Acs.Chemrev.8B00760  1
2019 Samanta HS, Thirumalai D. Origin of superdiffusive behavior in a class of nonequilibrium systems. Physical Review. E. 99: 032401. PMID 30999548 DOI: 10.1103/PhysRevE.99.032401  0.68
2019 Li X, Thirumalai D. Share, but unequally: a plausible mechanism for emergence and maintenance of intratumour heterogeneity. Journal of the Royal Society, Interface. 16: 20180820. PMID 30958159 DOI: 10.1098/rsif.2018.0820  0.96
2019 Baul U, Chakraborty D, Mugnai ML, Straub JE, Thirumalai D. Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins. The Journal of Physical Chemistry. B. PMID 30913885 DOI: 10.1021/Acs.Jpcb.9B02575  1
2018 Liu L, Shi G, Thirumalai D, Hyeon C. Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci. Plos Computational Biology. 14: e1006617. PMID 30507936 DOI: 10.1371/journal.pcbi.1006617  1
2018 Denesyuk NA, Hori N, Thirumalai D. Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding. The Journal of Physical Chemistry. B. PMID 30468380 DOI: 10.1021/acs.jpcb.8b08142  0.52
2018 Samanta HS, Chakraborty D, Thirumalai D. Charge fluctuation effects on the shape of flexible polyampholytes with applications to intrinsically disordered proteins. The Journal of Chemical Physics. 149: 163323. PMID 30384718 DOI: 10.1063/1.5035428  0.68
2018 Zeno WF, Baul U, Snead WT, DeGroot ACM, Wang L, Lafer EM, Thirumalai D, Stachowiak JC. Synergy between intrinsically disordered domains and structured proteins amplifies membrane curvature sensing. Nature Communications. 9: 4152. PMID 30297718 DOI: 10.1038/S41467-018-06532-3  0.32
2018 Chen J, Thirumalai D. Interface Residues That Drive Allosteric Transitions Also Control the Assembly of L-Lactate Dehydrogenase. The Journal of Physical Chemistry. B. PMID 30102042 DOI: 10.1021/acs.jpcb.8b06430  1
2018 Shi G, Liu L, Hyeon C, Thirumalai D. Interphase human chromosome exhibits out of equilibrium glassy dynamics. Nature Communications. 9: 3161. PMID 30089831 DOI: 10.1038/s41467-018-05606-6  1
2018 Litvinov RI, Kononova O, Zhmurov A, Marx KA, Barsegov V, Thirumalai D, Weisel JW. Regulatory element in fibrin triggers tension-activated transition from catch to slip bonds. Proceedings of the National Academy of Sciences of the United States of America. PMID 30087181 DOI: 10.1073/Pnas.1802576115  0.52
2018 Chakraborty D, Hori N, Thirumalai D. Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA. Journal of Chemical Theory and Computation. PMID 29870236 DOI: 10.1021/acs.jctc.8b00091  0.32
2018 Thirumalai D, Hyeon C. Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 373. PMID 29735736 DOI: 10.1098/rstb.2017.0182  1
2018 Pantelopulos GA, Straub JE, Thirumalai D, Sugita Y. Structure of APP-C99 and implications for role of extra-membrane domains in function and oligomerization. Biochimica Et Biophysica Acta. PMID 29702072 DOI: 10.1016/J.Bbamem.2018.04.002  1
2018 Toan NM, Thirumalai D. Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states. The Journal of Chemical Physics. 148: 123332. PMID 29604893 DOI: 10.1063/1.5011056  0.64
2018 Liu Z, Thirumalai D. Denaturants Alter the Flux Through Multiple Pathways in the Folding of PDZ Domain. The Journal of Physical Chemistry. B. PMID 29303586 DOI: 10.1021/acs.jpcb.7b11408  0.64
2017 Samanta HS, Hinczewski M, Thirumalai D. Optimal information transfer in enzymatic networks: A field theoretic formulation. Physical Review. E. 96: 012406. PMID 29347079 DOI: 10.1103/PhysRevE.96.012406  1
2017 Chakrabarti S, Hyeon C, Ye X, Lorimer GH, Thirumalai D. Molecular chaperones maximize the native state yield on biological times by driving substrates out of equilibrium. Proceedings of the National Academy of Sciences of the United States of America. PMID 29217641 DOI: 10.1073/pnas.1712962114  1
2017 Zhang Z, Goldtzvik Y, Thirumalai D. Parsing the roles of neck-linker docking and tethered head diffusion in the stepping dynamics of kinesin. Proceedings of the National Academy of Sciences of the United States of America. PMID 29087307 DOI: 10.1073/pnas.1706014114  1
2017 Lee Y, Thirumalai D, Hyeon C. Ultrasensitivity of water exchange kinetics to the size of metal ion. Journal of the American Chemical Society. PMID 28853881 DOI: 10.1021/jacs.7b04198  1
2017 Mugnai ML, Thirumalai D. Kinematics of the lever arm swing in myosin VI. Proceedings of the National Academy of Sciences of the United States of America. 114: E4389-E4398. PMID 28512223 DOI: 10.1073/pnas.1615708114  0.32
2017 Samanta HS, Zhuravlev PI, Hinczewski M, Hori N, Chakrabarti S, Thirumalai D. Protein collapse is encoded in the folded state architecture. Soft Matter. PMID 28447708 DOI: 10.1039/c7sm00074j  1
2017 Hyeon C, Thirumalai D. Ripping RNA by Force Using Gaussian Network Models. The Journal of Physical Chemistry. B. 121: 3515-3522. PMID 28423909 DOI: 10.1021/acs.jpcb.6b09402  1
2017 Reddy G, Thirumalai D. Collapse Precedes Folding in Denaturant-Dependent Assembly of Ubiquitin. The Journal of Physical Chemistry. B. PMID 28076957 DOI: 10.1021/Acs.Jpcb.6B13100  0.68
2017 Suvlu D, Samaratunga S, Thirumalai D, Rasaiah JC. Thermodynamics of Helix-Coil Transitions of Polyalanine in Open Carbon Nanotubes. The Journal of Physical Chemistry Letters. PMID 28060517 DOI: 10.1021/acs.jpclett.6b02620  0.84
2016 Thirumalai D, Shi G. Chromatin is Stretched But Intact When the Nucleus is Squeezed through Constrictions. Biophysical Journal. PMID 27989542 DOI: 10.1016/j.bpj.2016.11.902  0.76
2016 Vu HT, Chakrabarti S, Hinczewski M, Thirumalai D. Discrete Step Sizes of Molecular Motors Lead to Bimodal Non-Gaussian Velocity Distributions under Force. Physical Review Letters. 117: 078101. PMID 27564000 DOI: 10.1103/PhysRevLett.117.078101  1
2016 Dominguez L, Foster L, Straub JE, Thirumalai D. Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein. Proceedings of the National Academy of Sciences of the United States of America. PMID 27559086 DOI: 10.1073/Pnas.1606482113  1
2016 Hinczewski M, Hyeon C, Thirumalai D. Directly measuring single-molecule heterogeneity using force spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. PMID 27317744 DOI: 10.1073/pnas.1518389113  1
2016 Hori N, Denesyuk NA, Thirumalai D. Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension. Journal of Molecular Biology. 428: 2847-59. PMID 27315694 DOI: 10.1016/j.jmb.2016.06.002  0.52
2016 Zhuravlev PI, Hinczewski M, Chakrabarti S, Marqusee S, Thirumalai D. Reply to Alberti: Are in vitro folding experiments relevant in vivo? Proceedings of the National Academy of Sciences of the United States of America. PMID 27226292 DOI: 10.1073/Pnas.1603395113  1
2016 Hinczewski M, Thirumalai D. Noise Control in Gene Regulatory Networks with Negative Feedback. The Journal of Physical Chemistry. B. 120: 6166-77. PMID 27095600 DOI: 10.1021/acs.jpcb.6b02093  1
2016 Chakrabarti S, Hinczewski M, Thirumalai D. Phenomenological and microscopic theories for catch bonds. Journal of Structural Biology. PMID 27046010 DOI: 10.1016/j.jsb.2016.03.022  1
2016 Liu Z, Reddy G, Thirumalai D. Folding PDZ2 Domain Using the Molecular Transfer Model. The Journal of Physical Chemistry. B. PMID 26926418 DOI: 10.1021/Acs.Jpcb.6B00327  0.68
2016 Zhuravlev PI, Hinczewski M, Chakrabarti S, Marqusee S, Thirumalai D. Force-dependent switch in protein unfolding pathways and transition-state movements. Proceedings of the National Academy of Sciences of the United States of America. PMID 26818842 DOI: 10.1073/Pnas.1515730113  1
2015 Goldtzvik Y, Zhang Z, Thirumalai D. On the importance of hydrodynamic interactions in the stepping kinetics of kinesin. The Journal of Physical Chemistry. B. PMID 26702870 DOI: 10.1021/acs.jpcb.5b11153  1
2015 Kang H, Yoon YG, Thirumalai D, Hyeon C. Confinement-Induced Glassy Dynamics in a Model for Chromosome Organization. Physical Review Letters. 115: 198102. PMID 26588418 DOI: 10.1103/Physrevlett.115.198102  0.48
2015 He J, Hu J, Thirumalai D, Schade R, Du E, Zhang X. Development of indirect competitive ELISA using egg yolk-derived immunoglobulin (IgY) for the detection of Gentamicin residues. Journal of Environmental Science and Health. Part. B, Pesticides, Food Contaminants, and Agricultural Wastes. 1-6. PMID 26513166 DOI: 10.1080/03601234.2015.1080479  0.64
2015 Denesyuk NA, Thirumalai D. How do metal ions direct ribozyme folding? Nature Chemistry. 7: 793-801. PMID 26391078 DOI: 10.1038/nchem.2330  0.52
2015 Qin M, Wang W, Thirumalai D. Protein folding guides disulfide bond formation. Proceedings of the National Academy of Sciences of the United States of America. PMID 26297249 DOI: 10.1073/pnas.1503909112  0.6
2015 Kang H, Toan NM, Hyeon C, Thirumalai D. Unexpected Swelling of Stiff DNA in a Polydisperse Crowded Environment. Journal of the American Chemical Society. 137: 10970-8. PMID 26267166 DOI: 10.1021/jacs.5b04531  1
2015 Pincus DL, Chakrabarti S, Thirumalai D. Helicase processivity and not the unwinding velocity exhibits universal increase with force. Biophysical Journal. 109: 220-30. PMID 26200858 DOI: 10.1016/j.bpj.2015.05.020  0.88
2015 Reddy G, Thirumalai D. Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model. The Journal of Physical Chemistry. B. PMID 26131594 DOI: 10.1021/Acs.Jpcb.5B03471  0.68
2015 Lin JC, Yoon J, Hyeon C, Thirumalai D. Using simulations and kinetic network models to reveal the dynamics and functions of riboswitches. Methods in Enzymology. 553: 235-58. PMID 25726468 DOI: 10.1016/Bs.Mie.2014.10.062  1
2015 Kang H, Pincus PA, Hyeon C, Thirumalai D. Effects of macromolecular crowding on the collapse of biopolymers. Physical Review Letters. 114: 068303. PMID 25723249 DOI: 10.1103/PhysRevLett.114.068303  1
2015 Lavanya M, Thirumalai D, Asharani IV, Aravindan PG. Domino synthesis of functionalized 1,6-naphthyridines and their in vitro anti-inflammatory and anti-oxidant efficacies Rsc Advances. 5: 86330-86336. DOI: 10.1039/c5ra11447k  0.56
2015 Pincus DL, Chakrabarti S, Thirumalai D. Helicase Processivity and Not the Unwinding Velocity Exhibits Universal Increase with Force Biophysical Journal. 109: 220-230. DOI: 10.1016/j.bpj.2015.05.020  0.88
2015 Saravanan D, Thirumalai D, Asharani IV. Anti-HIV flavonoids from natural products: A systematic review International Journal of Research in Pharmaceutical Sciences. 6: 248-255.  0.56
2014 Straub JE, Thirumalai D. Membrane-Protein Interactions Are Key to Understanding Amyloid Formation. The Journal of Physical Chemistry Letters. 5: 633-5. PMID 26276620 DOI: 10.1021/Jz500054D  1
2014 Vaitheeswaran S, Thirumalai D. Entropy and enthalpy of interaction between amino acid side chains in nanopores. The Journal of Chemical Physics. 141: 22D523. PMID 25494794 DOI: 10.1063/1.4901204  1
2014 Ramm B, Stigler J, Hinczewski M, Thirumalai D, Herrmann H, Woehlke G, Rief M. Sequence-resolved free energy profiles of stress-bearing vimentin intermediate filaments. Proceedings of the National Academy of Sciences of the United States of America. 111: 11359-64. PMID 25049381 DOI: 10.1073/pnas.1403122111  1
2014 He JX, Thirumalai D, Schade R, Zhang XY. Chronobiological studies of chicken IgY: monitoring of infradian, circadian and ultradian rhythms of IgY in blood and yolk of chickens. Veterinary Immunology and Immunopathology. 160: 266-72. PMID 24998020 DOI: 10.1016/j.vetimm.2014.05.016  0.64
2014 Chakrabarti S, Hinczewski M, Thirumalai D. Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes. Proceedings of the National Academy of Sciences of the United States of America. 111: 9048-53. PMID 24927549 DOI: 10.1073/Pnas.1405384111  1
2014 Dominguez L, Foster L, Meredith SC, Straub JE, Thirumalai D. Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection. Journal of the American Chemical Society. 136: 9619-26. PMID 24926593 DOI: 10.1021/Ja503150X  1
2014 Zhuravlev PI, Reddy G, Straub JE, Thirumalai D. Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins. Journal of Molecular Biology. 426: 2653-66. PMID 24846645 DOI: 10.1016/J.Jmb.2014.05.007  1
2014 Yoon J, Lin JC, Hyeon C, Thirumalai D. Dynamical transition and heterogeneous hydration dynamics in RNA. The Journal of Physical Chemistry. B. 118: 7910-9. PMID 24762118 DOI: 10.1021/Jp500643U  1
2014 Hyeon C, Hinczewski M, Thirumalai D. Evidence of disorder in biological molecules from single molecule pulling experiments. Physical Review Letters. 112: 138101. PMID 24745458 DOI: 10.1103/PhysRevLett.112.138101  1
2014 Wang Y, Tian Z, Thirumalai D, Zhang X. Neonatal Fc receptor (FcRn): a novel target for therapeutic antibodies and antibody engineering. Journal of Drug Targeting. 22: 269-78. PMID 24404896 DOI: 10.3109/1061186X.2013.875030  0.64
2014 Lin JC, Hyeon C, Thirumalai D. Sequence-dependent folding landscapes of adenine riboswitch aptamers. Physical Chemistry Chemical Physics : Pccp. 16: 6376-82. PMID 24366448 DOI: 10.1039/c3cp53932f  1
2014 Dominguez L, Meredith SC, Straub JE, Thirumalai D. Transmembrane fragment structures of amyloid precursor protein depend on membrane surface curvature. Journal of the American Chemical Society. 136: 854-7. PMID 24364734 DOI: 10.1021/Ja410958J  1
2014 Hinczewski M, Thirumalai D. Cellular signaling networks function as generalized Wiener-Kolmogorov filters to suppress noise Physical Review X. 4. DOI: 10.1103/Physrevx.4.041017  1
2014 Straub JE, Thirumalai D. Membrane-protein interactions are key to understanding amyloid formation Journal of Physical Chemistry Letters. 5: 633-635. DOI: 10.1021/jz500054d  1
2014 Hyeon C, Denesyuk NA, Thirumalai D. Development and applications of coarse-grained models for RNA Israel Journal of Chemistry. DOI: 10.1002/Ijch.201400029  1
2013 Kang H, Kirkpatrick TR, Thirumalai D. Manifestation of random first-order transition theory in Wigner glasses. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 88: 042308. PMID 24229173 DOI: 10.1103/PhysRevE.88.042308  0.52
2013 Hinczewski M, Tehver R, Thirumalai D. Design principles governing the motility of myosin V. Proceedings of the National Academy of Sciences of the United States of America. 110: E4059-68. PMID 24101499 DOI: 10.1073/pnas.1312393110  1
2013 Hyeon C, Thirumalai D. Generalized iterative annealing model for the action of RNA chaperones. The Journal of Chemical Physics. 139: 121924. PMID 24089736 DOI: 10.1063/1.4818594  1
2013 Lin JC, Thirumalai D. Kinetics of allosteric transitions in S-adenosylmethionine riboswitch are accurately predicted from the folding landscape. Journal of the American Chemical Society. 135: 16641-50. PMID 24087850 DOI: 10.1021/Ja408595E  0.52
2013 Denning EJ, Thirumalai D, MacKerell AD. Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure. Biophysical Chemistry. 184: 8-16. PMID 24012912 DOI: 10.1016/J.Bpc.2013.08.002  0.72
2013 Yoon J, Thirumalai D, Hyeon C. Urea-induced denaturation of preQ1-riboswitch. Journal of the American Chemical Society. 135: 12112-21. PMID 23863126 DOI: 10.1021/Ja406019S  1
2013 Pincus DL, Thirumalai D. Force-induced unzipping transitions in an athermal crowded environment. The Journal of Physical Chemistry. B. 117: 13107-14. PMID 23789729 DOI: 10.1021/jp402922q  0.88
2013 Denesyuk NA, Thirumalai D. Coarse-grained model for predicting RNA folding thermodynamics. The Journal of Physical Chemistry. B. 117: 4901-11. PMID 23527587 DOI: 10.1021/jp401087x  0.52
2013 Samanta HS, Thirumalai D. Exact solution of the Zwanzig-Lauritzen model of polymer crystallization under tension. The Journal of Chemical Physics. 138: 104901. PMID 23514513 DOI: 10.1063/1.4794154  0.68
2013 Hinczewski M, Gebhardt JC, Rief M, Thirumalai D. From mechanical folding trajectories to intrinsic energy landscapes of biopolymers. Proceedings of the National Academy of Sciences of the United States of America. 110: 4500-5. PMID 23487746 DOI: 10.1073/Pnas.1214051110  1
2013 Thirumalai D, Liu Z, O'Brien EP, Reddy G. Protein folding: from theory to practice. Current Opinion in Structural Biology. 23: 22-9. PMID 23266001 DOI: 10.1016/J.Sbi.2012.11.010  0.84
2013 Chen J, Thirumalai D. Helices 2 and 3 are the initiation sites in the PrP(C) → PrP(SC) transition. Biochemistry. 52: 310-9. PMID 23256626 DOI: 10.1021/bi3005472  1
2013 Denesyuk NA, Thirumalai D. Entropic stabilization of the folded states of RNA due to macromolecular crowding Biophysical Reviews. 5: 225-232. DOI: 10.1007/s12551-013-0119-x  0.52
2013 Asharani IV, Thirumalai D, Paridhavi M, Gowtham M. Physiochemical, pharmacognostical and phytochemical evaluation of Premna latifolia International Journal of Pharmacy and Pharmaceutical Sciences. 5: 309-317.  0.56
2013 Thirumalai D, Paridhavi M, Gowtham M. Evaluation of physiochemical, pharmacognostical and phytochemical parameters of Premna Herbacea Asian Journal of Pharmaceutical and Clinical Research. 6: 173-181.  0.56
2012 Lin JC, Hyeon C, Thirumalai D. RNA under tension: Folding Landscapes, Kinetic partitioning Mechanism, and Molecular Tensegrity. The Journal of Physical Chemistry Letters. 3: 3616-3625. PMID 23336034 DOI: 10.1021/Jz301537T  1
2012 Lin JC, Thirumalai D. Gene regulation by riboswitches with and without negative feedback loop. Biophysical Journal. 103: 2320-30. PMID 23283231 DOI: 10.1016/j.bpj.2012.10.026  0.52
2012 Hyeon C, Lee J, Yoon J, Hohng S, Thirumalai D. Hidden complexity in the isomerization dynamics of Holliday junctions. Nature Chemistry. 4: 907-14. PMID 23089865 DOI: 10.1038/nchem.1463  1
2012 Hyeon C, Thirumalai D. Multiple barriers in forced rupture of protein complexes. The Journal of Chemical Physics. 137: 055103. PMID 22894385 DOI: 10.1063/1.4739747  1
2012 Toan NM, Thirumalai D. On the origin of the unusual behavior in the stretching of single-stranded DNA. The Journal of Chemical Physics. 136: 235103. PMID 22779622 DOI: 10.1063/1.4729371  0.64
2012 Reddy G, Liu Z, Thirumalai D. Denaturant-dependent folding of GFP. Proceedings of the National Academy of Sciences of the United States of America. 109: 17832-8. PMID 22778437 DOI: 10.1073/Pnas.1201808109  0.68
2012 Koculi E, Cho SS, Desai R, Thirumalai D, Woodson SA. Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures. Nucleic Acids Research. 40: 8011-20. PMID 22641849 DOI: 10.1093/Nar/Gks468  0.92
2012 Liu Z, Reddy G, Thirumalai D. Theory of the molecular transfer model for proteins with applications to the folding of the src-SH3 domain. The Journal of Physical Chemistry. B. 116: 6707-16. PMID 22497652 DOI: 10.1021/Jp211941B  0.68
2012 Zhang Z, Thirumalai D. Dissecting the kinematics of the kinesin step. Structure (London, England : 1993). 20: 628-40. PMID 22483110 DOI: 10.1016/J.Str.2012.02.013  1
2012 Hyeon C, Thirumalai D. Chain length determines the folding rates of RNA. Biophysical Journal. 102: L11-3. PMID 22325296 DOI: 10.1016/j.bpj.2012.01.003  1
2012 O'Brien EP, Brooks BR, Thirumalai D. Effects of pH on proteins: predictions for ensemble and single-molecule pulling experiments. Journal of the American Chemical Society. 134: 979-87. PMID 22148729 DOI: 10.1021/Ja206557Y  0.84
2012 Thirumalai D, Reddy G, Straub JE. Role of water in protein aggregation and amyloid polymorphism. Accounts of Chemical Research. 45: 83-92. PMID 21761818 DOI: 10.1021/Ar2000869  1
2012 Asharani IV, Thirumalai D. Synthesis of dendrimer-encapsulated silver nanoparticles and its catalytic activity on the reduction of 4-nitrophenol Journal of the Chinese Chemical Society. 59: 1455-1460. DOI: 10.1002/jccs.201100734  0.56
2012 Toan NM, Ha BY, Thirumalai D. Polyelectrolyte and Polyampholyte Effects in Synthetic and Biological Macromolecules Ionic Interactions in Natural and Synthetic Macromolecules. 91-119. DOI: 10.1002/9781118165850.ch4  0.64
2011 Thirumalai D, Reddy G. Protein thermodynamics: Are native proteins metastable? Nature Chemistry. 3: 910-1. PMID 22109266 DOI: 10.1038/nchem.1207  0.68
2011 Biyun S, Cho SS, Thirumalai D. Folding of human telomerase RNA pseudoknot using ion-jump and temperature-quench simulations. Journal of the American Chemical Society. 133: 20634-43. PMID 22082261 DOI: 10.1021/Ja2092823  0.92
2011 Cho SS, Reddy G, Straub JE, Thirumalai D. Entropic stabilization of proteins by TMAO. The Journal of Physical Chemistry. B. 115: 13401-7. PMID 21985427 DOI: 10.1021/Jp207289B  1
2011 Hyeon C, Thirumalai D. Capturing the essence of folding and functions of biomolecules using coarse-grained models. Nature Communications. 2: 487. PMID 21952221 DOI: 10.1038/ncomms1481  1
2011 Denesyuk NA, Thirumalai D. Crowding promotes the switch from hairpin to pseudoknot conformation in human telomerase RNA. Journal of the American Chemical Society. 133: 11858-61. PMID 21736319 DOI: 10.1021/ja2035128  0.52
2011 O'Brien EP, Straub JE, Brooks BR, Thirumalai D. Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide. The Journal of Physical Chemistry Letters. 2: 1171-1177. PMID 21691423 DOI: 10.1021/Jz200330K  1
2011 Morrison G, Hyeon C, Hinczewski M, Thirumalai D. Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments. Physical Review Letters. 106: 138102. PMID 21517423 DOI: 10.1103/Physrevlett.106.138102  1
2011 Liu Z, Reddy G, O'Brien EP, Thirumalai D. Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins. Proceedings of the National Academy of Sciences of the United States of America. 108: 7787-92. PMID 21512127 DOI: 10.1073/Pnas.1019500108  0.84
2011 Xia F, Thirumalai D, Gräter F. Minimum energy compact structures in force-quench polyubiquitin folding are domain swapped. Proceedings of the National Academy of Sciences of the United States of America. 108: 6963-8. PMID 21482804 DOI: 10.1073/pnas.1018177108  0.36
2011 Straub JE, Thirumalai D. Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Annual Review of Physical Chemistry. 62: 437-63. PMID 21219143 DOI: 10.1146/Annurev-Physchem-032210-103526  1
2011 Patro R, Ip CY, Bista S, Thirumalai D, Cho SS, Varshney A. MDMap: A system for data-driven layout and exploration of molecular dynamics simulations Ieee Symposium On Biological Data Visualization 2011, Biovis 2011 - Proceedings. 111-118. DOI: 10.1109/BioVis.2011.6094055  0.92
2011 Vaitheeswaran S, Chen J, Thirumalai D. Hydrophobic and Ionic-Interactions in Bulk and Confined Water with Implications for Collapse and Folding of Proteins Journal of Statistical Physics. 145: 276-292. DOI: 10.1007/S10955-011-0313-9  1
2011 Saraswathi VS, Thirumalai D, Malipeddi H, Saranya M, Yadav PK. Detection of metals present in leaves of Lagerstroemia speciosa International Journal of Pharmacy and Pharmaceutical Sciences. 3: 297-298.  0.56
2010 Li MS, Co NT, Reddy G, Hu CK, Straub JE, Thirumalai D. Factors governing fibrillogenesis of polypeptide chains revealed by lattice models. Physical Review Letters. 105: 218101. PMID 21231356 DOI: 10.1103/Physrevlett.105.218101  1
2010 Reddy G, Straub JE, Thirumalai D. Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires. Proceedings of the National Academy of Sciences of the United States of America. 107: 21459-64. PMID 21098298 DOI: 10.1073/Pnas.1008616107  1
2010 Thirumalai D, Zhang Z. Myosin VI: how do charged tails exert control? Structure (London, England : 1993). 18: 1393-4. PMID 21070937 DOI: 10.1016/j.str.2010.10.004  1
2010 Chen J, Darst SA, Thirumalai D. Promoter melting triggered by bacterial RNA polymerase occurs in three steps. Proceedings of the National Academy of Sciences of the United States of America. 107: 12523-8. PMID 20615963 DOI: 10.1073/Pnas.1003533107  1
2010 Tehver R, Thirumalai D. Rigor to post-rigor transition in myosin V: link between the dynamics and the supporting architecture. Structure (London, England : 1993). 18: 471-81. PMID 20399184 DOI: 10.1016/j.str.2010.01.019  0.64
2010 Thirumalai D, O'Brien EP, Morrison G, Hyeon C. Theoretical perspectives on protein folding. Annual Review of Biophysics. 39: 159-83. PMID 20192765 DOI: 10.1146/annurev-biophys-051309-103835  1
2010 Straub JE, Thirumalai D. Principles governing oligomer formation in amyloidogenic peptides. Current Opinion in Structural Biology. 20: 187-95. PMID 20106655 DOI: 10.1016/J.Sbi.2009.12.017  1
2010 Chen WT, Thirumalai D, Shih TT, Chen RC, Tu SY, Lin CI, Yang PC. Dynamic contrast-enhanced folate-receptor-targeted MR imaging using a Gd-loaded PEG-dendrimer-folate conjugate in a mouse xenograft tumor model. Molecular Imaging and Biology : Mib : the Official Publication of the Academy of Molecular Imaging. 12: 145-54. PMID 19636639 DOI: 10.1007/s11307-009-0248-6  0.56
2010 Toan NM, Thirumalai D. Theory of biopolymer stretching at high forces Macromolecules. 43: 4394-4400. DOI: 10.1021/Ma902008Y  0.64
2009 Miyashita N, Straub JE, Thirumalai D. Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase. Journal of the American Chemical Society. 131: 17843-52. PMID 19995075 DOI: 10.1021/Ja905457D  1
2009 Priyakumar UD, Hyeon C, Thirumalai D, Mackerell AD. Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases. Journal of the American Chemical Society. 131: 17759-61. PMID 19919063 DOI: 10.1021/ja905795v  1
2009 Hyeon C, Morrison G, Pincus DL, Thirumalai D. Refolding dynamics of stretched biopolymers upon force quench. Proceedings of the National Academy of Sciences of the United States of America. 106: 20288-93. PMID 19915145 DOI: 10.1073/pnas.0905764106  1
2009 O'Brien EP, Okamoto Y, Straub JE, Brooks BR, Thirumalai D. Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils. The Journal of Physical Chemistry. B. 113: 14421-30. PMID 19813700 DOI: 10.1021/Jp9050098  1
2009 Cho SS, Pincus DL, Thirumalai D. Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures. Proceedings of the National Academy of Sciences of the United States of America. 106: 17349-54. PMID 19805055 DOI: 10.1016/J.Bpj.2009.12.2573  0.92
2009 Moghaddam S, Caliskan G, Chauhan S, Hyeon C, Briber RM, Thirumalai D, Woodson SA. Metal ion dependence of cooperative collapse transitions in RNA. Journal of Molecular Biology. 393: 753-64. PMID 19712681 DOI: 10.1016/J.Jmb.2009.08.044  1
2009 Liu Z, Chen J, Thirumalai D. On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: illustrations using lattice model. Proteins. 77: 823-31. PMID 19639636 DOI: 10.1002/prot.22498  1
2009 Reddy G, Straub JE, Thirumalai D. Dynamics of locking of peptides onto growing amyloid fibrils. Proceedings of the National Academy of Sciences of the United States of America. 106: 11948-53. PMID 19581575 DOI: 10.1073/Pnas.0902473106  1
2009 Zheng W, Brooks BR, Thirumalai D. Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks. Current Protein & Peptide Science. 10: 128-32. PMID 19355980 DOI: 10.2174/138920309787847608  0.56
2009 Roh JH, Briber RM, Damjanovic A, Thirumalai D, Woodson SA, Sokolov AP. Dynamics of tRNA at different levels of hydration. Biophysical Journal. 96: 2755-62. PMID 19348758 DOI: 10.1016/J.Bpj.2008.12.3895  0.52
2009 O'Brien EP, Morrison G, Brooks BR, Thirumalai D. How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins? The Journal of Chemical Physics. 130: 124903. PMID 19334885 DOI: 10.1063/1.3082151  1
2009 Zheng W, Thirumalai D. Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II. Biophysical Journal. 96: 2128-37. PMID 19289039 DOI: 10.1016/J.Bpj.2008.12.3897  0.36
2009 O'Brien EP, Brooks BR, Thirumalai D. Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins. Biochemistry. 48: 3743-54. PMID 19278261 DOI: 10.1021/bi8021119  0.84
2009 Vaitheeswaran S, Reddy G, Thirumalai D. Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores. The Journal of Chemical Physics. 130: 094502. PMID 19275404 DOI: 10.1063/1.3080720  1
2009 Miyashita N, Straub JE, Thirumalai D, Sugita Y. Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations. Journal of the American Chemical Society. 131: 3438-9. PMID 19275251 DOI: 10.1021/Ja809227C  1
2009 Morrison G, Thirumalai D. Semiflexible chains in confined spaces. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 79: 011924. PMID 19257086 DOI: 10.1103/PhysRevE.79.011924  1
2009 Reddy G, Straub JE, Thirumalai D. Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation. The Journal of Physical Chemistry. B. 113: 1162-72. PMID 19125574 DOI: 10.1021/Jp808914C  1
2009 Tehver R, Chen J, Thirumalai D. Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle. Journal of Molecular Biology. 387: 390-406. PMID 19121324 DOI: 10.1016/j.jmb.2008.12.032  1
2009 Pincus DL, Thirumalai D. Crowding effects on the mechanical stability and unfolding pathways of ubiquitin. The Journal of Physical Chemistry. B. 113: 359-68. PMID 19072020 DOI: 10.1021/jp807755b  0.88
2008 Chen J, Bryngelson JD, Thirumalai D. Estimations of the size of nucleation regions in globular proteins. The Journal of Physical Chemistry. B. 112: 16115-20. PMID 19367923 DOI: 10.1021/jp806161k  1
2008 Pincus DL, Cho SS, Hyeon C, Thirumalai D. Minimal models for proteins and RNA from folding to function. Progress in Molecular Biology and Translational Science. 84: 203-50. PMID 19121703 DOI: 10.1016/S0079-6603(08)00406-6  1
2008 Li MS, Klimov DK, Straub JE, Thirumalai D. Probing the mechanisms of fibril formation using lattice models. The Journal of Chemical Physics. 129: 175101. PMID 19045373 DOI: 10.1063/1.2989981  1
2008 Vaitheeswaran S, Thirumalai D. Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability. Proceedings of the National Academy of Sciences of the United States of America. 105: 17636-41. PMID 19004772 DOI: 10.1073/Pnas.0803990105  1
2008 Hua L, Zhou R, Thirumalai D, Berne BJ. Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proceedings of the National Academy of Sciences of the United States of America. 105: 16928-33. PMID 18957546 DOI: 10.1073/Pnas.0808427105  0.84
2008 Jun S, Thirumalai D, Ha BY. Compression and stretching of a self-avoiding chain in cylindrical nanopores. Physical Review Letters. 101: 138101. PMID 18851496 DOI: 10.1103/PhysRevLett.101.138101  0.64
2008 Lin JC, Thirumalai D. Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. Journal of the American Chemical Society. 130: 14080-1. PMID 18828635 DOI: 10.1021/Ja8063638  0.52
2008 O'Brien EP, Stan G, Thirumalai D, Brooks BR. Factors governing helix formation in peptides confined to carbon nanotubes. Nano Letters. 8: 3702-8. PMID 18817452 DOI: 10.1021/Nl8019328  0.84
2008 O'Brien EP, Ziv G, Haran G, Brooks BR, Thirumalai D. Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model. Proceedings of the National Academy of Sciences of the United States of America. 105: 13403-8. PMID 18757747 DOI: 10.1073/Pnas.0802113105  0.84
2008 Barsegov V, Morrison G, Thirumalai D. Role of internal chain dynamics on the rupture kinetic of adhesive contacts. Physical Review Letters. 100: 248102. PMID 18643632 DOI: 10.1103/Physrevlett.100.248102  1
2008 Hyeon C, Morrison G, Thirumalai D. Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes. Proceedings of the National Academy of Sciences of the United States of America. 105: 9604-9. PMID 18621721 DOI: 10.1073/Pnas.0802484105  1
2008 Tarus B, Straub JE, Thirumalai D. Structures and free-energy landscapes of the wild type and mutants of the Abeta(21-30) peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions. Journal of Molecular Biology. 379: 815-29. PMID 18479708 DOI: 10.1016/J.Jmb.2008.04.028  1
2008 Pincus DL, Hyeon C, Thirumalai D. Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins. Journal of the American Chemical Society. 130: 7364-72. PMID 18479134 DOI: 10.1021/ja078326w  1
2008 Tehver R, Thirumalai D. Kinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation. Journal of Molecular Biology. 377: 1279-95. PMID 18313071 DOI: 10.1016/j.jmb.2008.01.059  0.64
2008 Toan NM, Morrison G, Hyeon C, Thirumalai D. Kinetics of loop formation in polymer chains. The Journal of Physical Chemistry. B. 112: 6094-106. PMID 18269274 DOI: 10.1021/jp076510y  1
2008 Hyeon C, Thirumalai D. Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins. Journal of the American Chemical Society. 130: 1538-9. PMID 18186635 DOI: 10.1021/Ja0771641  1
2008 Buchete NV, Straub JE, Thirumalai D. Dissecting contact potentials for proteins: relative contributions of individual amino acids. Proteins. 70: 119-30. PMID 17640067 DOI: 10.1002/Prot.21538  1
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  1
2007 Chen J, Dima RI, Thirumalai D. Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back. Journal of Molecular Biology. 374: 250-66. PMID 17916364 DOI: 10.1016/J.Jmb.2007.08.047  1
2007 Zheng W, Brooks BR, Thirumalai D. Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophysical Journal. 93: 2289-99. PMID 17557788 DOI: 10.1529/Biophysj.107.105270  0.56
2007 O'Brien EP, Dima RI, Brooks B, Thirumalai D. Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism Journal of the American Chemical Society. 129: 7346-7353. PMID 17503819 DOI: 10.1021/Ja069232+  0.84
2007 Stan G, Lorimer GH, Thirumalai D, Brooks BR. Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein Proceedings of the National Academy of Sciences of the United States of America. 104: 8803-8808. PMID 17496143 DOI: 10.1073/Pnas.0700607104  0.68
2007 Koculi E, Hyeon C, Thirumalai D, Woodson SA. Charge density of divalent metal cations determines RNA stability. Journal of the American Chemical Society. 129: 2676-82. PMID 17295487 DOI: 10.1021/Ja068027R  1
2007 Nguyen PH, Li MS, Stock G, Straub JE, Thirumalai D. Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism. Proceedings of the National Academy of Sciences of the United States of America. 104: 111-6. PMID 17190811 DOI: 10.1073/Pnas.0607440104  1
2007 Hyeon C, Thirumalai D. Mechanical unfolding of RNA: From hairpins to structures with internal multiloops Biophysical Journal. 92: 731-743. PMID 17028142 DOI: 10.1529/Biophysj.106.093062  1
2007 Thirumalai D, Klimov DK. Intermediates and transition states in protein folding Methods in Molecular Biology (Clifton, N.J.). 350: 277-303. PMID 16957328  0.4
2007 Hyeon C, Thirumalai D. Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments Journal of Physics Condensed Matter. 19. DOI: 10.1088/0953-8984/19/11/113101  1
2007 Morrison G, Hyeon C, Toan NM, Ha BY, Thirumalai D. Stretching homopolymers Macromolecules. 40: 7343-7353. DOI: 10.1021/ma071117b  1
2006 Tarus B, Straub JE, Thirumalai D. Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers. Journal of the American Chemical Society. 128: 16159-68. PMID 17165769 DOI: 10.1021/Ja064872Y  1
2006 Hyeon C, Lorimer GH, Thirumalai D. Dynamics of allosteric transitions in GroEL Proceedings of the National Academy of Sciences of the United States of America. 103: 18939-18944. PMID 17135353 DOI: 10.1073/Pnas.0608759103  1
2006 Hyeon C, Dima RI, Thirumalai D. Size, shape, and flexibility of RNA structures Journal of Chemical Physics. 125. PMID 17129165 DOI: 10.1063/1.2364190  1
2006 Hyeon C, Dima RI, Thirumalai D. Pathways and Kinetic Barriers in Mechanical Unfolding and Refolding of RNA and Proteins Structure. 14: 1633-1645. PMID 17098189 DOI: 10.1016/j.str.2006.09.002  1
2006 Han CC, Balakumar R, Thirumalai D, Chung MT. The different electronic natures displayed by the alkylthio groups in simple and higher conjugated aniline systems. Organic & Biomolecular Chemistry. 4: 3511-6. PMID 17036147 DOI: 10.1039/b609506b  0.56
2006 Vaitheeswaran S, Thirumalai D. Hydrophobic and ionic interactions in nanosized water droplets Journal of the American Chemical Society. 128: 13490-13496. PMID 17031962 DOI: 10.1021/ja063445h  1
2006 Zheng W, Brooks BR, Thirumalai D. Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proceedings of the National Academy of Sciences of the United States of America. 103: 7664-9. PMID 16682636 DOI: 10.1073/Pnas.0510426103  0.56
2006 Koculi E, Thirumalai D, Woodson SA. Counterion charge density determines the position and plasticity of RNA folding transition states. Journal of Molecular Biology. 359: 446-54. PMID 16626736 DOI: 10.1016/J.Jmb.2006.03.031  0.52
2006 Hyeon C, Thirumalai D. Kinetics of interior loop formation in semiflexible chains Journal of Chemical Physics. 124. PMID 16542102 DOI: 10.1063/1.2178805  1
2006 Stan G, Brooks BR, Lorimer GH, Thirumalai D. Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state Proceedings of the National Academy of Sciences of the United States of America. 103: 4433-4438. PMID 16537402 DOI: 10.1073/Pnas.0600433103  0.68
2006 Barsegov V, Klimov DK, Thirumalai D. Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy: Theory and applications Biophysical Journal. 90: 3827-3841. PMID 16533852 DOI: 10.1529/Biophysj.105.075937  0.52
2006 Hyeon C, Thirumalai D. Forced-unfolding and force-quench refolding of RNA hairpins Biophysical Journal. 90: 3410-3427. PMID 16473903 DOI: 10.1529/biophysj.105.078030  1
2006 Dima RI, Thirumalai D. Determination of network of residues that regulate allostery in protein families using sequence analysis Protein Science. 15: 258-268. PMID 16434743 DOI: 10.1110/ps.051767306  0.72
2006 Kouza M, Li MS, O'brien EP, Hu CK, Thirumalai D. Effect of finite size on cooperativity and rates of protein folding. The Journal of Physical Chemistry. A. 110: 671-6. PMID 16405339 DOI: 10.1021/jp053770b  0.84
2006 Caliskan G, Briber RM, Thirumalai D, Garcia-Sakai V, Woodson SA, Sokolov AP. Dynamic transition in tRNA is solvent induced. Journal of the American Chemical Society. 128: 32-3. PMID 16390107 DOI: 10.1021/ja056444i  0.52
2006 Li MS, Hu CK, Klimov DK, Thirumalai D. Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions. Proceedings of the National Academy of Sciences of the United States of America. 103: 93-8. PMID 16373511 DOI: 10.1073/Pnas.0503758103  0.4
2006 Aruna S, Senthilvelan A, Thirumalai D, Muthusamy S, Ramakrishnan VT. Synthesis and photocyclization of 1,2,4-triazole-3-thiones Synthesis. 3841-3848. DOI: 10.1055/s-2006-950301  0.56
2006 Barsegov V, Thirumalai D. Dynamic competition between catch and slip bonds in selectins bound to ligands Journal of Physical Chemistry B. 110: 26403-26412. DOI: 10.1021/Jp0653306  0.52
2006 Thirumalai D, Murugan P, Ramakrishnan VT. Synthesis of 4-aryl-5-oxo-1H,4H-5,6,7,8-tetrahydroquinoline and 4-aryl-5-oxo-1H-4,5,6,7-tetrahydrocyclopenteno[b]pyridine derivatives by ultrasound irradiation and by conventional methods Indian Journal of Chemistry - Section B Organic and Medicinal Chemistry. 45: 335-338.  0.56
2005 Barsegov V, Thirumalai D. Influence of surface interactions on folding and forced unbinding of semiflexible chains Journal of Physical Chemistry B. 109: 21979-21988. PMID 16853856 DOI: 10.1021/Jp053803N  0.52
2005 Caliskan G, Hyeon C, Perez-Salas U, Briber RM, Woodson SA, Thirumalai D. Persistence length changes dramatically as RNA folds. Physical Review Letters. 95: 268303. PMID 16486414 DOI: 10.1103/PhysRevLett.95.268303  1
2005 Barsegov V, Thirumalai D. Probing protein-protein interactions by dynamic force correlation spectroscopy Physical Review Letters. 95. PMID 16241846 DOI: 10.1103/Physrevlett.95.168302  0.52
2005 Klimov DK, Thirumalai D. Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways Journal of Molecular Biology. 353: 1171-1186. PMID 16219323 DOI: 10.1016/J.Jmb.2005.09.029  0.4
2005 Chauhan S, Caliskan G, Briber RM, Perez-Salas U, Rangan P, Thirumalai D, Woodson SA. RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme. Journal of Molecular Biology. 353: 1199-209. PMID 16214167 DOI: 10.1016/J.Jmb.2005.09.015  0.52
2005 Morrison G, Thirumalai D. The shape of a flexible polymer in a cylindrical pore The Journal of Chemical Physics. 122: 194907. PMID 16161617 DOI: 10.1063/1.1903923  1
2005 Stan G, Brooks BR, Thirumalai D. Probing the "annealing" mechanism of GroEL minichaperone using molecular dynamics simulations Journal of Molecular Biology. 350: 817-829. PMID 15967467 DOI: 10.1016/J.Jmb.2005.05.012  0.56
2005 Zheng W, Brooks BR, Doniach S, Thirumalai D. Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure (London, England : 1993). 13: 565-77. PMID 15837195 DOI: 10.1016/J.Str.2005.01.017  0.56
2005 Thirumalai D, Hyeon C. RNA and protein folding: Common themes and variations Biochemistry. 44: 4957-4970. PMID 15794634 DOI: 10.1021/bi047314+  1
2005 Hyeon C, Thirumalai D. Mechanical unfolding of RNA hairpins Proceedings of the National Academy of Sciences of the United States of America. 102: 6789-6794. PMID 15749822 DOI: 10.1073/pnas.0408314102  1
2005 Dima RI, Hyeon C, Thirumalai D. Extracting stacking interaction parameters for RNA from the data set of native structures Journal of Molecular Biology. 347: 53-69. PMID 15733917 DOI: 10.1016/j.jmb.2004.12.012  1
2005 Thiagarajan V, Ramamurthy P, Thirumalai D, Ramakrishnan VT. A novel colorimetric and fluorescent chemosensor for anions involving PET and ICT pathways Organic Letters. 7: 657-660. PMID 15704918 DOI: 10.1021/ol047463k  0.56
2005 Barsegov V, Thirumalai D. Dynamics of unbinding of cell adhesion molecules: Transition from catch to slip bonds Proceedings of the National Academy of Sciences of the United States of America. 102: 1835-1839. PMID 15701706 DOI: 10.1073/Pnas.0406938102  0.52
2005 Tarus B, Straub JE, Thirumalai D. Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing the propensity for peptide dimerization. Journal of Molecular Biology. 345: 1141-56. PMID 15644211 DOI: 10.1016/J.Jmb.2004.11.022  1
2005 Stan G, Brooks BR, Lorimer GH, Thirumalai D. Identifying natural substrates for chaperonins using a sequence-based approach Protein Science. 14: 193-201. PMID 15576562 DOI: 10.1110/Ps.04933205  0.68
2005 Murugan P, Hwang KC, Thirumalai D, Ramakrishnan VT. Facile and simple route to the synthesis of condensed acridine systems Synthetic Communications. 35: 1781-1788. DOI: 10.1081/SCC-200063947  0.56
2005 Senthilvelan A, Thirumalai D, Ramakrishnan VT. Photochemical synthesis of benzoxazolo[3,2-b]isoquinolin-11-one and isoquinolino[3,2-b][1,3]benzoxazin-11-one under basic conditions Tetrahedron. 61: 4213-4220. DOI: 10.1016/j.tet.2005.02.068  0.56
2005 Li MS, Klimov DK, Thirumalai D. Finite size effects on calorimetric cooperativity of two-state proteins Physica a: Statistical Mechanics and Its Applications. 350: 38-44. DOI: 10.1016/j.physa.2004.11.029  0.4
2005 Palani K, Thirumalai D, Ambalavanan P, Ponnuswamy MN, Ramakrishnan VT. Synthesis and characterization of 9-(4-nitrophenyl)-3,3,6,6-tetramethyl-3, 4,6,7,9,10-hexahydro-1,8(2H,5H) acridinedione and its methoxyphenyl derivative Journal of Chemical Crystallography. 35: 751-760. DOI: 10.1007/s10870-005-3880-2  0.56
2004 Li MS, Klimov DK, Thirumalai D. Finite size effects on thermal denaturation of globular proteins Physical Review Letters. 93. PMID 15698029 DOI: 10.1103/PhysRevLett.93.268107  0.4
2004 Dima RI, Thirumalai D. 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: 15335-15340. PMID 15494440 DOI: 10.1073/pnas.0404235101  0.72
2004 Klimov DK, Straub JE, Thirumalai D. Aqueous urea solution destabilizes Abeta(16-22) oligomers. Proceedings of the National Academy of Sciences of the United States of America. 101: 14760-5. PMID 15465917 DOI: 10.1073/Pnas.0404570101  1
2004 Koculi E, Lee NK, Thirumalai D, Woodson SA. Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size. Journal of Molecular Biology. 341: 27-36. PMID 15312760 DOI: 10.1016/J.Jmb.2004.06.008  0.52
2004 Buchete NV, Straub JE, Thirumalai D. Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis. Journal of Molecular Graphics & Modelling. 22: 441-50. PMID 15099839 DOI: 10.1016/J.Jmgm.2003.12.010  1
2004 Buchete NV, Straub JE, Thirumalai D. Development of novel statistical potentials for protein fold recognition. Current Opinion in Structural Biology. 14: 225-32. PMID 15093838 DOI: 10.1016/j.sbi.2004.03.002  1
2004 Dima RI, Thirumalai D. Proteins associated with diseases show enhanced sequence correlation between charged residues Bioinformatics. 20: 2345-2354. PMID 15073020 DOI: 10.1093/Bioinformatics/Bth245  0.72
2004 Buchete NV, Straub JE, Thirumalai D. Orientational potentials extracted from protein structures improve native fold recognition. Protein Science : a Publication of the Protein Society. 13: 862-74. PMID 15044723 DOI: 10.1110/Ps.03488704  1
2004 Perez-Salas UA, Rangan P, Krueger S, Briber RM, Thirumalai D, Woodson SA. Compaction of a bacterial group I ribozyme coincides with the assembly of core helices. Biochemistry. 43: 1746-53. PMID 14769052 DOI: 10.1021/Bi035642O  0.52
2004 Senthilvelan A, Thirumalai D, Ramakrishnan VT. Photochemical synthesis of triazolo[3,4-b]-1,3(4H)-benzothiazines: A detailed mechanistic study on photocyclization/photodesulfurisation of triazole-3-thiones Tetrahedron. 60: 851-860. DOI: 10.1016/j.tet.2003.11.053  0.56
2004 Buchete NV, Straub JE, Thirumalai D. Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases Polymer. 45: 597-608. DOI: 10.1016/J.Polymer.2003.10.093  1
2004 Li MS, Klimov DK, Thirumalai D. Thermal denaturation and folding rates of single domain proteins: Size matters Polymer. 45: 573-579. DOI: 10.1016/j.polymer.2003.10.066  0.4
2004 Klimov DK, Thirumalai D. Progressing from folding trajectories to transition state ensemble in proteins Chemical Physics. 307: 251-258. DOI: 10.1016/j.chemphys.2004.06.071  0.4
2004 Dima RI, Thirumalai D. Asymmetry in the shapes of folded and denatured states of proteins Journal of Physical Chemistry B. 108: 6564-6570.  0.72
2003 Thirumalai D, Klimov DK, Lorimer GH. Caging helps proteins fold Proceedings of the National Academy of Sciences of the United States of America. 100: 11195-11197. PMID 14506295 DOI: 10.1073/Pnas.2035072100  0.68
2003 Hyeon C, Thirumalai D. Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? Proceedings of the National Academy of Sciences of the United States of America. 100: 10249-53. PMID 12934020 DOI: 10.1073/Pnas.1833310100  1
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  0.72
2003 Stan G, Thirumalai D, Lorimer GH, Brooks BR. Annealing function of GroEL: Structural and bioinformatic analysis Biophysical Chemistry. 100: 453-467. PMID 12646383 DOI: 10.1016/S0301-4622(02)00298-3  0.68
2003 Buchete NV, Straub JE, Thirumalai D. Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures Journal of Chemical Physics. 118: 7658-7671. DOI: 10.1063/1.1561616  1
2003 Ha BY, Thirumalai D. Bending rigidity of stiff polyelectrolyte chains: A single chain and a bundle of multichains Macromolecules. 36: 9658-9666. DOI: 10.1021/ma021226k  0.64
2002 Dima RI, Thirumalai D. Exploring the propensities of helices in PrPC to form β sheet using NMR structures and sequence alignments Biophysical Journal. 83: 1268-1280. PMID 12202354 DOI: 10.1016/S0006-3495(02)73899-X  0.72
2002 Klimov DK, Newfield D, Thirumalai D. Simulations of β-hairpin folding confined to spherical pores using distributed computing Proceedings of the National Academy of Sciences of the United States of America. 99: 8019-8024. PMID 12060748 DOI: 10.1073/pnas.072220699  0.4
2002 Dima RI, Thirumalai D. Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics Protein Science. 11: 1036-1049. PMID 11967361 DOI: 10.1110/Ps.4220102  0.72
2002 Klimov DK, Thirumalai D. Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains Journal of Molecular Biology. 317: 721-737. PMID 11955020 DOI: 10.1006/jmbi.2002.5453  0.4
2001 Heilman-Miller SL, Pan J, Thirumalai D, Woodson SA. Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics. Journal of Molecular Biology. 309: 57-68. PMID 11491301 DOI: 10.1006/Jmbi.2001.4660  0.52
2001 Klimov DK, Thirumalai D. Multiple protein folding nuclei and the transition state ensemble in two-state proteins Proteins: Structure, Function and Genetics. 43: 465-475. PMID 11340662 DOI: 10.1002/prot.1058  0.4
2001 Thirumalai D, Lee N, Woodson SA, Klimov D. Early events in RNA folding. Annual Review of Physical Chemistry. 52: 751-62. PMID 11326079 DOI: 10.1146/annurev.physchem.52.1.751  0.52
2001 Heilman-Miller SL, Thirumalai D, Woodson SA. Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. Journal of Molecular Biology. 306: 1157-66. PMID 11237624 DOI: 10.1006/Jmbi.2001.4437  0.52
2000 Thirumalai D, Woodson SA. Maximizing RNA folding rates: a balancing act. Rna (New York, N.Y.). 6: 790-4. PMID 10864039 DOI: 10.1017/S1355838200000522  0.52
2000 Klimov DK, Thirumalai D. Native topology determines force-induced unfolding pathways in globular proteins Proceedings of the National Academy of Sciences of the United States of America. 97: 7254-7259. PMID 10860990 DOI: 10.1073/Pnas.97.13.7254  0.4
2000 Klimov DK, Thirumalai D. Mechanisms and kinetics of β-hairpin formation Proceedings of the National Academy of Sciences of the United States of America. 97: 2544-2549. PMID 10716988 DOI: 10.1073/Pnas.97.6.2544  0.4
1999 Klimov DK, Thirumalai D. Stretching single-domain proteins: Phase diagram and kinetics of force- induced unfolding Proceedings of the National Academy of Sciences of the United States of America. 96: 6166-6170. PMID 10339559 DOI: 10.1073/pnas.96.11.6166  0.4
1999 Pan J, Thirumalai D, Woodson SA. Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics. Proceedings of the National Academy of Sciences of the United States of America. 96: 6149-54. PMID 10339556 DOI: 10.1073/Pnas.96.11.6149  0.52
1999 Thirumalai D, Klimov DK. Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models Current Opinion in Structural Biology. 9: 197-207. PMID 10322218 DOI: 10.1016/S0959-440X(99)80028-1  0.4
1998 Thirumalai D, Klimov DK. Fishing for folding nuclei in lattice models and proteins Folding and Design. 3. PMID 9889171 DOI: 10.1016/S1359-0278(98)00057-1  0.4
1998 Klimov DK, Betancourt MR, Thirumalai D. Virtual atom representation of hydrogen bonds in minimal off-lattice models of α helices: Effect on stability, cooperativity and kinetics Folding and Design. 3: 481-496. PMID 9889160 DOI: 10.1016/S1359-0278(98)00065-0  0.4
1998 Klimov DK, Thirumalai D. Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism Journal of Molecular Biology. 282: 471-492. PMID 9735420 DOI: 10.1006/Jmbi.1998.1997  0.4
1998 Guo Z, Thirumalai D. The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus. Folding & Design. 2: 377-91. PMID 9427012 DOI: 10.1016/S1359-0278(97)00052-7  0.32
1997 Pan J, Thirumalai D, Woodson SA. Folding of RNA involves parallel pathways. Journal of Molecular Biology. 273: 7-13. PMID 9367740 DOI: 10.1006/jmbi.1997.1311  0.52
1996 Klimov DK, Thirumalai D. Factors governing the foldability of proteins Proteins: Structure, Function and Genetics. 26: 411-441. PMID 8990496 DOI: 10.1002/(SICI)1097-0134(199612)26:4<411::AID-PROT4>3.0.CO;2-E  0.4
1996 Todd MJ, Lorimer GH, Thirumalai D. Chaperonin-facilitated protein folding: Optimization of rate and yield by an iterative annealing mechanism Proceedings of the National Academy of Sciences of the United States of America. 93: 4030-4035. PMID 8633011 DOI: 10.1073/Pnas.93.9.4030  0.68
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