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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/
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Year Citation  Score
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  0.589
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  0.578
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  0.556
2019 Kirkpatrick TR, Thirumalai D, Wolynes PG. Scaling concepts for the dynamics of viscous liquids near an ideal glassy state. Physical Review. a, General Physics. 40: 1045-1054. PMID 9902230 DOI: 10.1103/Physreva.40.1045  0.465
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  0.511
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  0.499
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  0.553
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  0.492
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  0.307
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  0.567
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  0.588
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  0.459
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  0.518
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  0.639
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  0.575
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  0.603
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  0.591
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  0.501
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  0.732
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  0.61
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  0.548
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  0.613
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  0.641
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  0.483
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  0.513
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  0.525
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  0.632
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  0.527
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  0.479
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  0.375
2014 Thirumalai D. Universal relations in the self-assembly of proteins and RNA. Physical Biology. 11: 053005. PMID 25292483 DOI: 10.1088/1478-3975/11/5/053005  0.315
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  0.622
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  0.62
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  0.585
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  0.598
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  0.605
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  0.709
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  0.579
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  0.502
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  0.575
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  0.479
2014 Holehouse AS, Lyle N, Vitalis A, Thirumalai D, Pappu RV. Parsing the Contributions of Polypeptide Backbones and Sidechains to Denaturation in Concentrated Aqueous Solutions of Urea and Guanidinium Chloride Biophysical Journal. 106: 484a. DOI: 10.1016/J.Bpj.2013.11.2731  0.337
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  0.624
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  0.589
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  0.625
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  0.384
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  0.342
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  0.634
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  0.668
2013 Hinczewski M, Tehver R, Thirumalai D. Searching, Stepping, and Stomping: What Polymer Theory can teach us about the Molecular Motor Myosin V Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.3553  0.629
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  0.618
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  0.572
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  0.551
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  0.311
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  0.307
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  0.554
2012 Kudlay A, Cheung MS, Thirumalai D. Influence of the shape of crowding particles on the structural transitions in a polymer. The Journal of Physical Chemistry. B. 116: 8513-22. PMID 22616622 DOI: 10.1021/Jp212535N  0.563
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  0.356
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  0.493
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  0.561
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  0.545
2012 Denning E, Thirumalai D, MacKerell AD. Impact of TMAO on the preQ1 RNA Riboswitch Studied using Molecular Dynamics Simulations Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.1529  0.37
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  0.564
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  0.68
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  0.563
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  0.491
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  0.796
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  0.314
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  0.598
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  0.553
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  0.483
2011 Thirumalai D. Crowding Induced Conformational Switch Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.240  0.319
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  0.37
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  0.518
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  0.523
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  0.465
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  0.704
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  0.577
2010 Toan NM, Thirumalai D. Theory of biopolymer stretching at high forces Macromolecules. 43: 4394-4400. DOI: 10.1021/Ma902008Y  0.318
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  0.483
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  0.558
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  0.677
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  0.53
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  0.572
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  0.541
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  0.515
2009 Rivera E, Straub J, Thirumalai D. Sequence and crowding effects in the aggregation of a 10-residue fragment derived from islet amyloid polypeptide. Biophysical Journal. 96: 4552-60. PMID 19486677 DOI: 10.1016/J.Bpj.2009.03.039  0.513
2009 Kudlay A, Cheung MS, Thirumalai D. Crowding effects on the structural transitions in a flexible helical homopolymer. Physical Review Letters. 102: 118101. PMID 19392239 DOI: 10.1103/Physrevlett.102.118101  0.567
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  0.502
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  0.301
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  0.506
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  0.518
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  0.545
2009 Cho S, Thirumalai D. TMAO and Solvent Exposed RNA Bases Stabilizes Unfolded State via Hydrogen Bonding Biophysical Journal. 96: 576a. DOI: 10.1016/J.Bpj.2008.12.3009  0.579
2009 Valone SM, Thirumalai D, Truhlar DG. Dispersion-equation approach to obtaining complex optical potentials for electron scattering International Journal of Quantum Chemistry. 20: 341-353. DOI: 10.1002/Qua.560200836  0.377
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  0.697
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  0.536
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  0.381
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  0.788
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  0.406
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  0.495
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  0.695
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  0.574
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  0.557
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  0.672
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  0.621
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  0.521
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  0.601
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  0.326
2007 Cheung MS, Thirumalai D. Effects of crowding and confinement on the structures of the transition state ensemble in proteins. The Journal of Physical Chemistry. B. 111: 8250-7. PMID 17585794 DOI: 10.1021/Jp068201Y  0.609
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  0.343
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  0.551
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  0.574
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  0.638
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  0.634
2007 Morrison G, Hyeon C, Toan NM, Ha BY, Thirumalai D. Stretching homopolymers Macromolecules. 40: 7343-7353. DOI: 10.1021/ma071117b  0.479
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  0.561
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  0.528
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  0.57
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  0.583
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  0.341
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  0.572
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  0.361
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  0.592
2006 Cheung MS, Thirumalai D. Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces. Journal of Molecular Biology. 357: 632-43. PMID 16427652 DOI: 10.1016/J.Jmb.2005.12.048  0.588
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  0.395
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  0.523
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  0.302
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  0.448
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  0.329
2005 Thirumalai D, Hyeon C. RNA and protein folding: Common themes and variations Biochemistry. 44: 4957-4970. PMID 15794634 DOI: 10.1021/Bi047314+  0.596
2005 Cheung MS, Klimov D, Thirumalai D. Molecular crowding enhances native state stability and refolding rates of globular proteins. Proceedings of the National Academy of Sciences of the United States of America. 102: 4753-8. PMID 15781864 DOI: 10.1073/Pnas.0409630102  0.565
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  0.595
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  0.569
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  0.532
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  0.516
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  0.387
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  0.565
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  0.539
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  0.336
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  0.597
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  0.605
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  0.383
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  0.613
2003 Tobi D, Elber R, Thirumalai D. The dominant interaction between peptide and urea is electrostatic in nature: a molecular dynamics simulation study. Biopolymers. 68: 359-69. PMID 12601795 DOI: 10.1002/Bip.10290  0.335
2003 Mountain RD, Thirumalai D. Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. Journal of the American Chemical Society. 125: 1950-7. PMID 12580622 DOI: 10.1021/Ja020496F  0.334
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  0.577
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  0.388
2002 Betancourt MR, Thirumalai D. Protein sequence design by energy landscaping Journal of Physical Chemistry B. 106: 599-609. DOI: 10.1021/Jp012014C  0.741
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  0.37
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  0.362
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  0.403
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  0.372
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  0.371
1999 Betancourt MR, Thirumalai D. Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity Journal of Molecular Biology. 287: 627-644. PMID 10092464 DOI: 10.1006/Jmbi.1999.2591  0.765
1999 Betancourt MR, Thirumalai D. Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes Protein Science. 8: 361-369. PMID 10048329 DOI: 10.1110/Ps.8.2.361  0.745
1999 Lidar DA, Thirumalai D, Elber R, Gerber RB. Fractal analysis of protein potential energy landscapes Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 59: 2231-2243. DOI: 10.1103/Physreve.59.2231  0.337
1999 Lee N, Thirumalai D. Stretching DNA: Role of electrostatic interactions European Physical Journal B. 12: 599-605. DOI: 10.1007/S100510051043  0.332
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  0.747
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  0.414
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  0.371
1998 Klimov DK, Thirumalai D. Linking rates of folding in lattice models of proteins with underlying thermodynamic characteristics Journal of Chemical Physics. 109: 4119-4125. DOI: 10.1063/1.477012  0.381
1997 Mohanty D, Elber R, Thirumalai D, Beglov D, Roux B. Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. Journal of Molecular Biology. 272: 423-42. PMID 9325101 DOI: 10.1006/Jmbi.1997.1246  0.373
1997 Veitshans T, Klimov D, Thirumalai D. Protein folding kinetics: Timescales, pathways and energy landscapes in terms of sequence-dependent properties Folding and Design. 2: 1-22. PMID 9080195 DOI: 10.1016/S1359-0278(97)00002-3  0.439
1997 Bussemaker HJ, Thirumalai D, Bhattacharjee JK. Thermodynamic Stability of Folded Proteins against Mutations Physical Review Letters. 79: 3530-3533. DOI: 10.1103/Physrevlett.79.3530  0.323
1996 Thirumalai D, Ashwin VV, Bhattacharjee J. Dynamics of Random Hydrophobic-Hydrophilic Copolymers with Implications for Protein Folding. Physical Review Letters. 77: 5385-5388. PMID 10062790 DOI: 10.1103/Physrevlett.77.5385  0.305
1996 Thirumalai D, Woodson SA. Kinetics of Folding of Proteins and RNA Accounts of Chemical Research. 29: 433-439. DOI: 10.1021/Ar9500933  0.434
1995 Thirumalai D. From Minimal Models to Real Proteins: Time Scales for Protein Folding Kinetics Journal De Physique I. 5: 1457-1467. DOI: 10.1051/Jp1:1995209  0.393
1995 Guo Z, Thirumalai D. Kinetics Of Protein Folding: Nucleation Mechanism, Time Scales, And Pathways Biopolymers. 36: 83-102. DOI: 10.1002/Bip.360360108  0.42
1995 Thirumalai D, Guo Z. Nucleation mechanism for protein folding and theoretical predictions for hydrogen‐exchange labeling experiments Biopolymers. 35: 137-140. DOI: 10.1002/Bip.360350114  0.31
1994 Straub JE, Rashkin AB, Thirumalai D. Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease A Journal of the American Chemical Society. 116: 2049-2063. DOI: 10.1021/Ja00084A051  0.572
1992 Honeycutt JD, Thirumalai D. The nature of folded states of globular proteins. Biopolymers. 32: 695-709. PMID 1643270 DOI: 10.1002/Bip.360320610  0.425
1991 Thirumalai D, Berne BJ. Methods for simulating time correlation functions in quantum systems Computer Physics Communications. 63: 415-426. DOI: 10.1016/0010-4655(91)90266-N  0.496
1989 Kirkpatrick TR, Thirumalai D. Random solutions from a regular density functional Hamiltonian: a static and dynamical theory for the structural glass transition Journal of Physics a: Mathematical and General. 22: L149-L155. DOI: 10.1088/0305-4470/22/5/003  0.314
1988 Thirumalai D, Kirkpatrick TR. Mean-field Potts glass model: Initial-condition effects on dynamics and properties of metastable states Physical Review B. 38: 4881-4892. DOI: 10.1103/Physrevb.38.4881  0.305
1987 Mountain RD, Thirumalai D. Molecular-dynamics study of glassy and supercooled states of a binary mixture of soft spheres. Physical Review A. 36: 3300-3311. PMID 9899249 DOI: 10.1103/Physreva.36.3300  0.303
1987 Coker DF, Berne BJ, Thirumalai D. Path integral Monte Carlo studies of the behavior of excess electrons in simple fluids The Journal of Chemical Physics. 86: 5689-5702. DOI: 10.1063/1.452495  0.663
1987 Wallqvist A, Thirumalai D, Berne BJ. Path integral Monte Carlo study of the hydrated electron The Journal of Chemical Physics. 86: 6404-6418. DOI: 10.1063/1.452429  0.493
1986 Berne BJ, Thirumalai D. On the Simulation of Quantum Systems: Path Integral Methods Annual Review of Physical Chemistry. 37: 401-424. DOI: 10.1146/Annurev.Pc.37.100186.002153  0.46
1986 Thirumalai D, Wallqvist A, Berne BJ. Path-integral Monte Carlo simulations of electron localization in water clusters Journal of Statistical Physics. 43: 973-984. DOI: 10.1007/Bf02628324  0.499
1986 Wallqvist A, Thirumalai D, Berne BJ. Localization of an excess electron in water clusters The Journal of Chemical Physics. 85: 1583-1591. DOI: 10.1002/Chin.198642001  0.441
1985 Thirumalai D, Bruskin EJ, Berne BJ. On the use of semiclassical dynamics in determining electronic spectra of Br2in an Ar matrix The Journal of Chemical Physics. 83: 230-238. DOI: 10.1063/1.449813  0.487
1985 Thirumalai D, Garrett BC, Berne BJ. Evaluation of microcanonical rate constants for bimolecular reactions by path integral techniques The Journal of Chemical Physics. 83: 2972-2975. DOI: 10.1063/1.449200  0.621
1985 Thirumalai D, Berne B. Path integral methods for simulating electronic spectra Chemical Physics Letters. 116: 471-473. DOI: 10.1016/0009-2614(85)85196-4  0.473
1984 Thirumalai D, Hall RW, Berne BJ. A path integral Monte Carlo study of liquid neon and the quantum effective pair potential The Journal of Chemical Physics. 81: 2523-2527. DOI: 10.1063/1.447985  0.637
1984 Thirumalai D, Berne BJ. Time correlation functions in quantum systems The Journal of Chemical Physics. 81: 2512-2513. DOI: 10.1063/1.447913  0.443
1984 Thirumalai D, Thompson TC, Truhlar DG. Rational fraction analytic continuation method for complex resonance energies in multidimensional systems The Journal of Chemical Physics. 80: 5864-5865. DOI: 10.1063/1.446616  0.388
1983 Schwenke DW, Thirumalai D, Truhlar DG. Accurate, smooth, local, energy-dependent optical potentials for electron scattering Physical Review A. 28: 3258-3267. DOI: 10.1103/Physreva.28.3258  0.402
1983 Staszewska G, Schwenke DW, Thirumalai D, Truhlar DG. Quasifree-scattering model for the imaginary part of the optical potential for electron scattering Physical Review A. 28: 2740-2751. DOI: 10.1103/Physreva.28.2740  0.38
1983 Thirumalai D, Truhlar DG. Tests of the semiclassical polarization approximation for electron scattering by helium and neon Physical Review A. 27: 158-166. DOI: 10.1103/Physreva.27.158  0.406
1983 Staszewska G, Schwenke DW, Thirumalai D, Truhlar DG. Non-empirical model for the imaginary part of the optical potential for electron scattering Journal of Physics B: Atomic and Molecular Physics. 16: L281-L287. DOI: 10.1088/0022-3700/16/9/006  0.373
1983 Thirumalai D, Bruskin EJ, Berne BJ. An iterative scheme for the evaluation of discretized path integrals The Journal of Chemical Physics. 79: 5063-5069. DOI: 10.1063/1.445601  0.482
1983 Thirumalai D, Berne BJ. On the calculation of time correlation functions in quantum systems: Path integral techniquesa) The Journal of Chemical Physics. 79: 5029-5033. DOI: 10.1063/1.445597  0.481
1983 Schwenke DW, Thirumalai D, Truhlar DG, Coltrin ME. Tests of the quasiclassical trajectory cross‐correlation moment method against accurate quantum dynamics for V–V energy transfer in HF–HF collisions The Journal of Chemical Physics. 78: 3078-3083. DOI: 10.1063/1.445221  0.397
1983 Abusalbi N, Eades RA, Nam T, Thirumalai D, Dixon DA, Truhlar DG, Dupuis M. Electron scattering by methane: Elastic scattering and rotational excitation cross sections calculated withab initiointeraction potentials The Journal of Chemical Physics. 78: 1213-1227. DOI: 10.1002/Chin.198319041  0.359
1982 Thirumalai D, Truhlar DG. Energy-dependent polarization potential, dispersion-relation absorption potential, and matrix effective potential for electron-neon scattering at 10 — 100 eV Physical Review A. 26: 793-807. DOI: 10.1103/Physreva.26.793  0.401
1982 Thirumalai D, Truhlar DG. Application of the matrix-effective-potential formalism to electron-neon scattering at 150 - 700-eV impact energy and comparison to optical-potential calculations Physical Review A. 25: 3058-3071. DOI: 10.1103/Physreva.25.3058  0.385
1982 Valone SM, Truhlar DG, Thirumalai D. Localized second-order optical potential for electron scattering in terms of imaginary-frequency susceptibilities Physical Review A. 25: 3003-3014. DOI: 10.1103/Physreva.25.3003  0.416
1982 Thirumalai D, Truhlar DG, Brandt MA, Eades RA, Dixon DA. Polarization and absorption effects in electron-helium scattering at 30-400 eV Physical Review A. 25: 2946-2958. DOI: 10.1103/Physreva.25.2946  0.385
1982 Thirumalai D, Truhlar DG. Rapid convergence of V–V energy transfer calculated using adiabatic basis functions. I. An accurate two‐state model for low‐energy resonant V–V energy transfer. II. The Journal of Chemical Physics. 76: 5287-5294. DOI: 10.1063/1.442926  0.402
1982 Thirumalai D, Truhlar DG. Full‐response pseudochannels: A new method for converging coupled‐channels scattering calculations. Theory and examples The Journal of Chemical Physics. 76: 385-389. DOI: 10.1063/1.442733  0.392
1981 Thirumalai D, Truhlar DG. Improved calculation of the cross section for excitation of the asymmetric stretch of CO2 by electron impact The Journal of Chemical Physics. 75: 5207-5209. DOI: 10.1063/1.441876  0.367
1981 Thirumalai D, Onda K, Truhlar DG. Electron scattering by CO2: Elastic scattering, rotational excitation, and excitation of the asymmetric stretch at 10 eV impact energy The Journal of Chemical Physics. 74: 6792-6805. DOI: 10.1063/1.441086  0.406
1981 Thirumalai D, Onda K, Truhlar DG. Elastic scattering and rotational excitation of a polyatomic molecule by electron impact: Acetylene The Journal of Chemical Physics. 74: 526-534. DOI: 10.1063/1.440804  0.394
1980 Thirumalai D, Onda K, Truhlar DG. Excitation of the asymmetric stretch mode of CO2by electron impact Journal of Physics B: Atomic and Molecular Physics. 13: L619-L622. DOI: 10.1088/0022-3700/13/20/003  0.392
1980 Thirumalai D, Truhlar DG. Comparison of convergence for the schwinger, optimized anomaly-free, and optimized minimum-norm variational methods for potential scattering Chemical Physics Letters. 70: 330-335. DOI: 10.1016/0009-2614(80)85345-0  0.361
Low-probability matches (unlikely to be authored by this person)
1998 Wallqvist A, Covell DG, Thirumalai D. Hydrophobic Interactions In Aqueous Urea Solutions With Implications For The Mechanism Of Protein Denaturation Journal of the American Chemical Society. 120: 427-428. DOI: 10.1021/Ja972053V  0.299
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  0.298
2003 Klimov DK, Thirumalai D. Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets. Structure (London, England : 1993). 11: 295-307. PMID 12623017 DOI: 10.1016/S0969-2126(03)00031-5  0.295
1988 Bagchi B, Thirumalai D. Freezing of a colloidal liquid subject to shear flow. Physical Review. A. 37: 2530-2538. PMID 9899961 DOI: 10.1103/Physreva.37.2530  0.293
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  0.292
1996 Guo Z, Thirumalai D. Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. Journal of Molecular Biology. 263: 323-43. PMID 8913310 DOI: 10.1006/jmbi.1996.0578  0.291
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  0.29
1987 Kirkpatrick TR, Thirumalai D. P-spin-interaction spin-glass models: Connections with the structural glass problem Physical Review B. 36: 5388-5397. DOI: 10.1103/Physrevb.36.5388  0.289
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  0.288
2007 Thirumalai D, Klimov DK. Intermediates and transition states in protein folding Methods in Molecular Biology (Clifton, N.J.). 350: 277-303. PMID 16957328  0.282
1995 Camacho CJ, Thirumalai D. Modeling the role of disulfide bonds in protein folding: entropic barriers and pathways. Proteins. 22: 27-40. PMID 7675784 DOI: 10.1002/Prot.340220105  0.28
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  0.278
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  0.275
2013 Gruebele M, Thirumalai D. Perspective: Reaches of chemical physics in biology. The Journal of Chemical Physics. 139: 121701. PMID 24089712 DOI: 10.1063/1.4820139  0.275
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  0.272
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  0.272
1993 Camacho CJ, Thirumalai D. Kinetics and thermodynamics of folding in model proteins. Proceedings of the National Academy of Sciences of the United States of America. 90: 6369-72. PMID 8327519 DOI: 10.1073/Pnas.90.13.6369  0.271
1993 Mountain RD, Thirumalai D. Relationship between the fluctuation metric and the non-ergodicity parameter: incoherent scattering function Physica a-Statistical Mechanics and Its Applications. 192: 543-549. DOI: 10.1016/0378-4371(93)90106-E  0.27
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  0.27
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  0.269
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  0.269
2018 Roca J, Hori N, Baral S, Velmurugu Y, Narayanan R, Narayanan P, Thirumalai D, Ansari A. Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot. Proceedings of the National Academy of Sciences of the United States of America. PMID 30012621 DOI: 10.1073/Pnas.1717582115  0.268
2018 Hori N, Denesyuk NA, Thirumalai D. Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover. The Journal of Physical Chemistry. B. 122: 11279-11288. PMID 30179471 DOI: 10.1021/acs.jpcb.8b07129  0.266
2009 Roh JH, Behrouzi R, Briber RM, Guo L, Thirumalai D, Woodson SA. Kinetics and Mechanism of RNA Folding studied by SAXS Biophysical Journal. 96: 575a. DOI: 10.1016/J.Bpj.2008.12.3001  0.264
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  0.263
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  0.263
2009 Ziv G, Thirumalai D, Haran G. Collapse transition in proteins. Physical Chemistry Chemical Physics : Pccp. 11: 83-93. PMID 19081910 DOI: 10.1039/B813961J  0.261
1996 Camacho CJ, Thirumalai D. Denaturants can accelerate folding rates in a class of globular proteins. Protein Science : a Publication of the Protein Society. 5: 1826-32. PMID 8880906 DOI: 10.1002/Pro.5560050908  0.259
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  0.254
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  0.254
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  0.25
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  0.249
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  0.247
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  0.246
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  0.245
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  0.243
2004 Lee NK, Thirumalai D. Pulling-Speed-Dependent Force-Extension Profiles for Semiflexible Chains Biophysical Journal. 86: 2641-2649. PMID 15111385  0.241
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  0.241
2005 Dunlavy DM, O'Leary DP, Klimov D, Thirumalai D. HOPE: a homotopy optimization method for protein structure prediction. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 1275-88. PMID 16379534 DOI: 10.1089/Cmb.2005.12.1275  0.239
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  0.238
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  0.237
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  0.234
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  0.233
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  0.232
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  0.231
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  0.23
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  0.229
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  0.228
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  0.227
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  0.227
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  0.225
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  0.224
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  0.223
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  0.223
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  0.222
1995 Camacho CJ, Thirumalai D. Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor. Proceedings of the National Academy of Sciences of the United States of America. 92: 1277-81. PMID 7533290 DOI: 10.1073/Pnas.92.5.1277  0.221
2005 Ziv G, Haran G, Thirumalai D. Ribosome exit tunnel can entropically stabilize alpha-helices. Proceedings of the National Academy of Sciences of the United States of America. 102: 18956-61. PMID 16357202 DOI: 10.1073/Pnas.0508234102  0.219
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  0.219
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  0.218
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  0.217
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  0.214
1998 Klimov DK, Thirumalai D. Cooperativity in protein folding: from lattice models with sidechains to real proteins. Folding & Design. 3: 127-39. PMID 9565757 DOI: 10.1016/S1359-0278(98)00018-2  0.214
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  0.209
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  0.208
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  0.208
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  0.207
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  0.207
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  0.207
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  0.205
1998 Thirumalai D. Native secondary structure formation in RNA may be a slave to tertiary folding. Proceedings of the National Academy of Sciences of the United States of America. 95: 11506-8. PMID 9751694 DOI: 10.1073/pnas.95.20.11506  0.205
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  0.205
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  0.204
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  0.202
2004 Dima RI, Thirumalai D. Asymmetry in the shapes of folded and denatured states of proteins Journal of Physical Chemistry B. 108: 6564-6570.  0.202
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+  0.201
2018 Mugnai ML, Thirumalai D. Hydration of Magnesium is Required for Myosin VI Phosphate Release Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.1788  0.198
2019 Nguyen HT, Hori N, Thirumalai D. Theory and simulations for RNA folding in mixtures of monovalent and divalent cations. Proceedings of the National Academy of Sciences of the United States of America. PMID 31570624 DOI: 10.1073/pnas.1911632116  0.197
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  0.19
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  0.19
2018 Goldtzvik Y, Mugnai ML, Thirumalai D. Dynamics of Allosteric Transitions in Dynein. Structure (London, England : 1993). 26: 1664-1677.e5. PMID 30270176 DOI: 10.1016/j.str.2018.08.005  0.19
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  0.189
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  0.187
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  0.186
1998 Mountain RD, Thirumalai D. Hydration for a series of hydrocarbons. Proceedings of the National Academy of Sciences of the United States of America. 95: 8436-40. PMID 9671695 DOI: 10.1073/pnas.95.15.8436  0.186
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  0.185
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  0.183
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  0.182
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  0.179
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  0.179
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  0.174
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  0.172
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  0.171
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  0.169
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  0.168
2019 Hori N, Denesyuk NA, Thirumalai D. Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent. Biophysical Journal. 116: 2400-2410. PMID 31130233 DOI: 10.1016/j.bpj.2019.04.037  0.166
2011 Thirumalai D, Reddy G. Protein thermodynamics: Are native proteins metastable? Nature Chemistry. 3: 910-1. PMID 22109266 DOI: 10.1038/nchem.1207  0.166
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  0.162
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  0.162
1999 Lidar DA, Thirumalai D, Elber R, Gerber RB. Fractal analysis of protein potential energy landscapes Physical Review E. 59: 2231-2243. DOI: 10.1103/PhysRevE.59.2231  0.161
2019 Takaki R, Mugnai ML, Goldtzvik Y, Thirumalai D. How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kinetics. Proceedings of the National Academy of Sciences of the United States of America. 116: 23091-23099. PMID 31659052 DOI: 10.1073/pnas.1913650116  0.159
2020 Nguyen HT, Thirumalai D. Charge Density of Cation Determines Inner Versus Outer Shell Coordination to Phosphate in RNA. The Journal of Physical Chemistry. B. PMID 32342689 DOI: 10.1021/acs.jpcb.0c02371  0.157
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  0.152
2015 Denesyuk NA, Thirumalai D. How do metal ions direct ribozyme folding? Nature Chemistry. 7: 793-801. PMID 26391078 DOI: 10.1038/nchem.2330  0.152
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  0.146
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  0.146
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  0.145
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  0.144
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  0.141
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  0.14
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  0.133
2019 Mugnai ML, Caporizzo MA, Goldman YE, Thirumalai D. Kinetic Model for Myosin Gating and Backward Stepping Mechanisms Biophysical Journal. 116: 260a-261a. DOI: 10.1016/J.Bpj.2018.11.1418  0.129
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  0.109
2012 Kirkpatrick TR, Thirumalai D. Random First-Order Phase Transition Theory of the Structural Glass Transition Structural Glasses and Supercooled Liquids: Theory, Experiment, and Applications. 223-236. DOI: 10.1002/9781118202470.ch6  0.109
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  0.096
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  0.095
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  0.092
2005 Welch BJ, Kanaujia SO, Seetharam A, Thirumalai D, Dean AG. Supporting demanding hard-real-time systems with STI Ieee Transactions On Computers. 54: 1188-1202. DOI: 10.1109/Tc.2005.169  0.09
2019 Zeno WF, Baul U, Snead WT, DeGroot AC, Wang L, Lafer EM, Thirumalai D, Stachowiak JC. Intrinsically Disordered Proteins Sense Membrane Curvature Biophysical Journal. 116: 21a. DOI: 10.1016/J.Bpj.2018.11.153  0.085
2004 Mountain RD, Thirumalai D. Alterations in water structure induced by guanidinium and sodium ions Journal of Physical Chemistry B. 108: 19711-19716. DOI: 10.1021/jp046607  0.081
2004 Mountain RD, Thirumalai D. Importance of excluded volume on the solvation of urea in water Journal of Physical Chemistry B. 108: 6826-6831.  0.077
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  0.075
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  0.072
2017 Mugnai ML, Thirumalai D. Kinematics of the Lever Arm Swing in Myosin VI Biophysical Journal. 112: 265a. DOI: 10.1016/j.bpj.2016.11.1439  0.064
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  0.063
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  0.06
2017 Thirumalai D. Theory and computations in biology: Kamal's legacy. Physical Biology. 14: 010401. PMID 28177933 DOI: 10.1088/1478-3975/aa5564  0.056
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  0.055
2020 Dey A, Shi G, Thirumalai D. Predicting the Organization of Mitotic Chromosomes using the Generalized Rouse Model Biophysical Journal. 118: 551a. DOI: 10.1016/j.bpj.2019.11.3013  0.048
2015 Thirumalai D. 48 Design principles governing the motility of myosin motors. Journal of Biomolecular Structure & Dynamics. 33: 33. PMID 26103260 DOI: 10.1080/07391102.2015.1032597  0.041
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  0.039
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  0.037
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  0.034
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  0.028
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  0.023
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  0.021
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  0.02
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  0.02
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.  0.02
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.  0.017
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  0.014
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.  0.013
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.  0.013
2014 Thirumalai DPR. A critical review of future materials for wind turbine blades International Journal of Materials Engineering Innovation. 5: 81-99. DOI: 10.1504/IJMATEI.2014.060339  0.01
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.  0.01
2010 James A, Fosnacht KJ, Stolzenberg EB, Thirumalai D. Identifying patterns of doctoral attrition across academic fields International Encyclopedia of Education. 827-837. DOI: 10.1016/B978-0-08-044894-7.01742-5  0.01
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