UMD | IPST | CHEM

Thirumalai Group
University of Maryland
Institute for Physical Sciences and Technology, Building 085
College Park, MD 20742
Phone: 301.405.4803
Fax: 301.314.9404

Any complaints or random comments are encouraged to be addressed here. Helpful suggestions are to be directed here.

The old webpage can still be found here

Publication List

[ Chronological Order ] [ Printer Friendly Version ]


[ 2012 ] - [ 2011 ] - [ 2010 ]
[ 2009 ] - [ 2008 ] - [ 2007 ] - [ 2006 ] - [ 2005 ] - [ 2004 ] - [ 2003 ] - [ 2002 ] - [ 2001 ]
[ 2000 ] - [ 1990-1999 ] - [ 1980-1989 ]

2014

328. P.I. Zhuravlev, G. Reddy, J.E. Straub, and D. Thirumalai, "Propensity to Form Amyloid Fibrils Is Encoded as Excitations in the Free Energy Landscape of Monomeric Proteins", J. Mol. Biol. 426, 2653 (2014)
327. J. Yoon, J.C. Lin, and D. Thirumalai, "Dynamical Transition and Heterogeneous Hydration Dynamics in RNA", J. Phys. Chem. B. 118, 7910 (2014)
326. S. Chakrabarti, M. Hinczewski, and D. Thirumalai, "Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes", Proc. Natl. Acad. Sci. 111, 9048 (2014)
325. J.C. Lin, C. Hyeon, and D. Thirumalai, "Sequence-dependent folding landscapes of adenine riboswitch apatamers", Phys. Chem. Chem. Phys 16, 63766 (2014)
324. C. Hyeon, M. Hinczewski, and D. Thirumalai, "Evidence of disorder in biological molecules from single molecule pulling experiments", Phys. Rev. Lett. 112, 138101 (2014)
323. J.E. Straub and D. Thirumalai, "Membrane-protein interactions are key to understanding amyloid formation", J. Phys. Chem. Lett. 5, 633 (2014)
322. L. Domiinguez, S.C. Meredith, J.E. Straub, and D. Thirumalai, "Transmembrane fragment structures of amyloid precursor protein depend on membrane surface curvature", J. Am. Chem. Soc. 136, 854 (2014)

2013

321. E.J. Denning, D. Thirumalai, A.D. MacKerell Jr., "Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure", Biophys. Chem. 184, 8 (2013)
320. J.C. Lin and D. Thirumalai, "Kinetics of Allosteric Transitions in S-adenosymethionine Riboswitch are Accurately predicted from the folding landscape", J. Am. Chem. Soc. 135, 16641 (2013)
319. C. Hyeon and D. Thirumalai, "Generalized iterative annealing model for the action of RNA chaperones", J. Chem. Phys. 139, 121924 (2013)
318. H. Kang, T.R. Kirkpatrick and D. Thirumalai, "Manifestation of random first-order transition theory in Wigner Glasses", Phys. Rev. E 88, 042308 (2013)
317. D.L. Pincus and D. Thirumalai, "Force-Induced Unzipping Transitions in an Athermal Crowded Environment", J. Phys. Chem. B 117, 13107 (2013)
316. M. Hinzewski, R. Tehver and D. Thirumalai, "Design principles governing the motility of myosin V", Proc. Natl. Acad. Sci. 110, E4059 (2013)
315. M. Gruebele and D. Thirumalai, "Perspective: Reaches of chemical physics in biology", J. Chem. Phys. 139, 121701 (2013)
314. J. Yoon, D. Thirumalai and C. Hyeon, "Urea-Induced Denaturation of PreQ1-Riboswitch", J. Am. Chem. Soc. 135, 12112 (2013)
313. N. Denesyuk and D. Thirumalai, "Coarse-grained model for predicting RNA folding thermodynamics", J. Phys. Chem. B. 117, 4901 (2013)
312. M. Hinczewski, J. Chrostof M. Gebhardt, M. Rief and D. Thirumalai, "From mechanical folding trajectories to intrinsic energy landscapes of biopolymers", Proc. Natl. Acad. Sci. 110, 4500 (2013)
311. H.S. Samanta and D. Thirumalai, "Exact solution of the Zwanzig-Lauritzen model of polymer crystallization under tension", J. Chem. Phys. 138, 104901 (2013)
310. D. Thirumalai, Z. Liu, EP O'brien and G. Reddy, "Protein folding: from theory to practice", Curr. Opin. Struct. Biol. 23, 22 (2013)
309. J. Chen and D. Thirumalai, "Helices 2 and 3 Are the Initiation Sites in the PrPC -> PrPSC Transition", Biochemistry 52, 310 (2013)

2012

308. J. Lin, C. Hyeon and D. Thirumalai, "RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity", J. Phys. Chem. Lett. 3, 3616 (2012)
307. C. Hyeon, J. Lee, J. Yoon, S. Hohng and D. Thirumalai, "Hidden complexity in the isomerization dynamics of Holliday junctions", Nat. Chem. 4, 907 (2012)
306. J. Lin and D. Thirumalai, "Gene Regulation by Riboswitches with and without Negative Feedback Loop", Biophys. J. 103, 2330 (2012)
305. D. Thirumalai, G. Reddy and J. Straub, "Role of Water in Protein Aggregation and Amyloid Polymorphism", Acc. Chem. Res. 45, 83 (2012)
304. G. Reddy, Z. Liu and D. Thirumalai "Denaturant-dependent folding of GFP", Proc. Natl. Acad. Sci., 109, 17832 (2012)
303. E. Koculi, S.S. Cho, R. Desai, D. Thirumalai, S.A. Woodson "Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures", Nuc. Acid. Res., 40, 8011 (2012)
302. C. Hyeon and D. Thirumalai "Multiple barriers in forced rupture of protein complexes", J. Chem. Phys., 137, 055103 (2012)
301. A. Kudlay, M.S. Cheung and D. Thirumalai "Influence of the Shape of Crowding Particles on the Structural Transitions in a Polymer", J. Phys. chem. B, 116, 8513 (2012)
300. N.M. Toan and D. Thirumalai "On the origin of the unusual behavior in the stretching of single-stranded DNA", J. Chem. Phys., 136, 235103 (2012)
299. Z. Liu, G. Reddy and D. Thirumalai "Theory of the Molecular Transfer Model for Proteins with Applications to the Folding of the src-SH3 Domain", J. Phys. Chem. B, 116, 6707 (2012)
298. Z. Zhang and D. Thirumalai "Dissecting the Kinematics of the Kinesin Step", Structure, 20, 628 (2012)
297. C. Hyeon and D. Thirumalai "Chain Length Determines the Folding Rates of RNA", Biophys. J., 102, L11 (2012)
296. E.P. O'Brien, B. R. Brooks and D. Thirumalai "Effects of pH on Proteins: Predictions for Ensemble and Single- Molecule Pulling Experiments", J. Am. Chem. Soc. 134, 979 (2012)

2011

295. S. Biyun, S. Cho and D. Thirumalai "Folding of Human Telomerase RNA Pseudoknot Using Ion-Jump and Temperature-Quench Simulations", J. Am. Chem. Soc. 133, 20634 (2011)
294. G. Reddy and D. Thirumalai "Are native proteins metastable?", Nat. Chem. 3, 910 (2011)
293. S. Cho, G. Reddy, J. Straub and D. Thirumalai "Entropic Stabilization of Proteins by TMAO", J. Phys. Chem. B 115, 13401 (2011)
292. S. Vaitheeswaran, J. Chen and D. Thirumalai "Hydrophobic and Ionic-Interactions in Bulk and Confined Water with Implications for Collapse and Folding of Proteins", J. Stat. Phys. 145, 276 (2011)
291. C. Hyeon and D. Thirumalai "Capturing the essence of folding and functions of biomolecules using coarse-grained models", Nat. Comm. 2, 487 (2011)
290. E.P. O'Brien, J. Straub, B. R. Brooks and D. Thirumalai "Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide", J. Phys. Chem. Lett. 2, 1171 (2011)
289. N. Denesyuk and D. Thirumalai, "Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA", J. Amer. Chem. Soc. 133, 11858 (2011)
288. Z. Liu, G. Reddy, E.P. O'Brien, D. Thirumalai, "Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins", Proc. Natl. Acad. Sci. 108, 7787 (2011)
287. G. Morrison, C. Hyeon, M. Hinczewski, D. Thirumalai, "Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments", Phys. Rev. Lett. 106, 138102 (2011).

2010

286. G. Reddy, E. Straub, D. Thirumalai, "Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires", Proc. Natl. Acad. Sci. 107, 21459 (2010).
285. M. Li, N. Co, G. Reddy, C. Hu, E. Straub, D. Thirumalai, "Factors Governing Fibrillogenesis of Polypeptide Chains Revealed by Lattice Models", Phys. Rev. Lett. 105, 218101 (2010).
284. J. Chen, S. Darst, D. Thirumalai, "Promoter melting triggered by bacterial RNA polymerase occurs in three steps", Proc. Natl. Acad. Sci. 28, 12523 (2010).
283. D. Thirumalai, E.P. O'Brien, G. Morrison, C. Hyeon, "Theoretical perspectives on protein folding", Annu Rev Biophys 39, 159 (2010).
282. J.E. Straub, D. Thirumalai, "Principles governing oligomer formation in amyloidogenic peptides.", Curr Opin Struct Biol 20, 187 (2010).
281. N.M. Toan, D. Thirumalai, "Theory of Biopolymer Stretching at High Forces", Macromolecules 43, 4394 (2010).
280. R. Tehver, D. Thirumalai, "Rigor to Post-Rigor Transition in Myosin V: Link between the Dynamics and the Supporting Architecture", Structure 18, 471 (2010).

2009

279. U.D. Priyakumar, C. Hyeon, D. Thirumalai, A.D. MacKerell, Jr. "Urea Destabilizes RNA by Forming Stacking Interactions and Multiple Hydrogen Bonds with Nucleic Acid Bases", J. Amer. Chem. Soc. 131, 17759 (2009).
278. Z. Liu, J. Chen, D. Thirumalai, "On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: Illustrations using lattice model", Proteins 77, 823 (2009).
277. C. Hyeon, G. Morrison, D.L. Pincus, D. Thirumalai, "Refolding dynamics of stretched biopolymers upon force quench", Proc. Natl. Acad. Sci. 106, 20288 (2009).
276. S. Moghaddam, G. Caliskan, S. Chauhan, C. Hyeon, R.M. Briber, D. Thirumalai, S.A. Woodson, "Metal Ion Dependence of Cooperative Collapse Transitions in RNA", J. Mol. Biol. 393, 753 (2009).
275. E.P. O'Brien, Y. Okamoto, J.E. Straub, B.R. Brooks, D. Thirumalai, "Thermodynamic Perspective on the Dock−Lock Growth Mechanism of Amyloid Fibrils", J. Phys. Chem. 113, 14421 (2009).
274. S.S. Cho, D.L. Pincus, D. Thirumalai, "Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures", Proc. Natl. Acad. Sci. 106, 17349 (2009).
273. G. Reddy, J.E. Straub, D. Thirumalai, "Dynamics of locking of peptides onto growing amyloid fibrils", Proc. Natl. Acad. Sci. 106, 11948 (2009).
272. E. Rivera, J. Straub, D. Thirumalai, "Sequence and Crowding Effects in the Aggregation of a 10-Residue Fragment Derived from Islet Amyloid Polypeptide", Biophys. J. 96, 4552 (2009).
271. J.H. Roh, R.M. Briber, A. Damjanovic, D. Thirumalai, S.A. Woodson, A.P. Sokolov, "Dynamics of tRNA at Different Levels of Hydration", Biophys. J. 96, 2755 (2009).
270. E.P. O'Brien, B.R. Brooks, D. Thirumalai, "Molecular Origin of Constant m-Values, Denatured State Collapse, and Residue-Dependent Transition Midpoints in Globular Proteins ", Biochemistry 48, 3743 (2009).
269. E.P. O'Brien, G. Morrison, B.R. Brooks, D. Thirumalai, "How accurate are polymer models in the analysis of Forster resonance energy transfer experiments on proteins?", J. Chem. Phys. 130, 124903 (2009).
268. G. Morrison, D. Thirumalai, "Semiflexible Chains in Confined Spaces", Phys. Rev. E 79, 011924 (2009).
267. A. Kudlay, M.S. Cheung, D. Thirumalai, "Crowding Effects on the Structural Transitions in a Flexible Helical Homopolymer", Phys. Rev. Lett. 102, 118101 (2009).
266. W. Zheng, D. Thirumalai, "Coupling between Normal Modes Drives Protein Conformational Dynamics: Illustrations Using Allosteric Transitions in Myosin II", Biophys. J. 96, 2128–2137 (2009).
265. N. Miyashita, J.E. Straub, D. Thirumalai, Y. Sugita, "Transmembrane Structures of Amyloid Precursor Protein Dimer Predicted by Replica-Exchange Molecular Dynamics Simulations", J. Amer. Chem. Soc. 131, 3438-3439 (2009).
264. R. Tehver, J. Chen, D. Thirumalai, "Allostery Wiring Diagrams in the Transitions that Drive the GroEL Reaction Cycle", J. Mol. Biol. 387, 390–406 (2009).
263. S. Vaitheeswaran, G. Reddy, D. Thirumalai, "Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores", J. Chem. Phys. 130, 094502 (2009).
262. G. Reddy, J.E. Straub, D. Thirumalai, "Influence of Preformed Asp23-Lys28 Salt Bridge on the Conformational Fluctuations of Monomers and Dimers of A beta Peptides with Implications for Rates of Fibril Formation", J. Phys. Chem. B 113, 1162-1172 (2009).
261. D.L. Pincus, D. Thirumalai, "Crowding Effects on the Mechanical Stability and Unfolding Pathways of Ubiquitin", J. Phys. Chem. B 113, 359-368 (2009).
260. G. Ziv, D. Thirumalai, G. Haran, "Collapse transition in proteins", Phys. Chem. Chem. Phys. 11, 83-93 (2009).

2008

259. J. Chen, J.D. Bryngelson, D. Thirumalai, "Estimations of the Size of Nucleation Regions in Globular Proteins", J. Phys. Chem. B 112, 16115-16120 (2008).
258. E.P. O'Brien, G. Stan, D. Thirumalai, B.R. Brooks "Factors Governing Helix Formation in Peptides Confined to Carbon Nanotubes", Nano Lett. 8, 3702-3708 (2008).
257. M.S. Li, D.K. Klimov, J.E. Straub, D. Thirumalai, "Probing the mechanisms of fibril formation using lattice models", J. Chem. Phys. 129, 175101 (2008).
256. L. Hua, R. Zhou, D. Thirumalai, B.J. Berne, "Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding", Proc. Natl. Acad. Sci. 105, 16928–16933 (2008).
255. J. Lin, D. Thirumalai, "Relative Stability of Helices Determines the Folding Landscape of Adenine Riboswitch Aptamers", J. Am. Chem. Soc. 130, 14080–14081 (2008).
254. D.L. Pincus, S.S. Cho, C. Hyeon, D. Thirumalai, "Minimal Models for Protein and RNA: From Folding to Function", Chapter 6 in Progress in Molecular Biology and Translational Science edited by P. Michael Conn (2008) Academic Press, Vol. 84.
253. D. Thirumalai, C. Hyeon, "Theory of RNA Folding: From Hairpins to Ribozymes", Chapter 2 in Non-Protein Coding RNA's edited by Nils G. Walter, Sarah A. Woodson, and Rober T. Batey (2008) Springer Series in Biophysics, Vol. 13.
252. S. Vaitheeswaran, D. Thirumalai, "Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability", Proc. Natl. Acad. Sci. 105, 17636–17641 (2008).
251. S. Jun, D. Thirumalai, B.Y. Ha, "Compression and Stretching of a Self-Avoiding Chain in Cylindrical Nanopores", Phys. Rev. Lett. 101, 138101 (2008).
250. E. P. O'Brien, G. Ziv, G. Haran, B. R. Brooks, D. Thirumalai, "Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model", Proc. Natl. Acad. Sci. 105, 13403–13408 (2008).
249. C. Hyeon, G. Morrison, D. Thirumalai, "Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes", Proc. Natl. Acad. Sci. 105, 9604–9609 (2008).
248. V. Barsegov, G. Morrison, D. Thirumalai, "Role of Internal Chain Dynamics on the Rupture Kinetics of Adhesive Contacts ", Phys. Rev. Lett. 100, 248102 (2008).
247. D.L. Pincus, C. Hyeon, D. Thirumalai, "Effects of Trimethylamine N-Oxide (TMAO) and Crowding Agents on the Stability of RNA Hairpins", J. Amer. Chem. Soc. 130, 7364–7372 (2008).
246. B. Tarus, J.E. Straub, D. Thirumalai, "Structures and Free-Energy Landscapes of the Wild Type and Mutants of the Aβ21–30 Peptide Are Determined by an Interplay between Intrapeptide Electrostatic and Hydrophobic Interactions", J. Mol. Biol. 379, 815-829 (2008).
245. N.M. Toan, G. Morrison, C. Hyeon, D. Thirumalai, "Kinetics of Loop Formation in Polymer Chains", J. Phys. Chem. B 112, 6094-6106 (2008).
244. N.V. Buchete, J.E. Straub, D. Thirumalai, "Dissecting contact potentials for proteins: Relative contributions of individual amino acids", Proteins Struct. Funct. Bioinf. 70, 119-130 (2008).
243. C. Hyeon, D. Thirumalai, "Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins", J. Amer. Chem. Soc. 130, 1538-1539 (2008).
242. R. Tehver, D. Thirumalai, "Kinetic Model for the Coupling between Allosteric Transitions in GroEL and Substrate Protein Folding and Aggregation", J. Mol. Biol. 4, 1279-1295 (2008).

2007

241. J. Chen, R. I. Dima, D. Thirumalai, "Allosteric Communication in Dihydrofolate Reductase: Signaling Network and Pathways for Closed to Occluded Transition and Back", J. Mol. Biol. 374, 250-266 (2007).
240. G. Morrison, C. Hyeon, N. M. Toan, B. Y. Ha, D. Thirumalai, "Stretching homopolymers", Macromolecules 40, 7343-7353 (2007).
239. W. Zheng, B. R. Brooks, D. Thirumalai, "Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations", Biophys. J. 93 2289-2299 (2007).
238. M. S. Cheung, D. Thirumalai, "Effects of crowding and confinement on the structures of the transition state ensemble in proteins", J. Phys. Chem. B 111 8250-8257 (2007).
237. E. P. O'Brien, R. I. Dima, B. Brooks, D. Thirumalai, "Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism", J. Amer. Chem. Soc. 129 7346-7353 (2007).
236. G. Stan, G. H. Lorimer, D. Thirumalai, B. R. Brooks, "Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein", Proc. Natl. Acad. Sci. 104, 8803-8808 (2007).
235. C. Hyeon, D. Thirumalai, "Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments", Journal of Physics-Condensed Matter 19, 113101 (2007).
234. E. Koculi, C. Hyeon, D. Thirumalai, S. A. Woodson, "Charge density of divalent metal cations determines RNA stability", J. Amer. Chem. Soc. 129, 2676-2682 (2007).
233. P. H. Nguyen, M. S. Li, G. Stock, J. E. Straub, D. Thirumalai, "Monomer adds to preformed structured oligomers of A beta-peptides by a two-stage dock-lock mechanism", Proc. Natl. Acad. Sci. 104, 111-116 (2007).
232. C. Hyeon, D. Thirumalai, "Mechanical unfolding of RNA: From hairpins to structures with internal multiloops", Biophys. J. 92 731-743 (2007).

2006

231. C. Hyeon, G. H. Lorimer, D. Thirumalai, "Dynamics of allosteric transitions in GroEL", Proc. Natl. Acad. Sci. 103, 18939-18944 (2006).
230. V. Barsegov, D. Thirumalai, "Dynamic competition between catch and slip bonds in selectins bound to ligands", J. Phys. Chem. B 110, 26403-26412 (2006).
229. B. Tarus, J. E. Straub, D. Thirumalai, "Dynamics of Asp23-Lys28 salt-bridge formation in A beta(10-35) monomers", J. Amer. Chem. Soc. 128 16159-16168 (2006).
228. C. Hyeon, R. I. Dima, D. Thirumalai, "Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins", Structure 14, 1633-1645 (2006).
227. C. Hyeon, R. I. Dima, D. Thirumalai. "Size, shape, and flexibility of RNA structures", J. Chem. Phys. 125, 194905 (2006).
226. S. Vaitheeswaran, D. Thirumalai, "Hydrophobic and ionic interactions in nanosized water droplets", J. Amer. Chem. Soc. 128, 13490-13496 (2006).
225. W. J. Zheng, B. R. Brooks, D. Thirumalai, "Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations", Proc. Natl. Acad. Sci. 103, 7664-7669 (2006).
224. E. Koculi, D. Thirumalai, S. A. Woodson, "Counterion charge density determines the position and plasticity of RNA folding transition states", J. Mol. Biol. 359, 446-454 (2006)
223. V. Barsegov, D. K. Klimov, D. Thirumalai, "Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy: Theory and applications", Biophys. J. 90, 3827-3841 (2006).
222. C. B. Hyeon, D. Thirumalai, "Forced-unfolding and force-quench refolding of RNA hairpins", Biophys, J. 90, 3410-3427, (2006)
221. G. Stan, B. R. Brooks, G. H. Lorimer, D. Thirumalai, "Residues in substrate proteins that interact witn GroEL in tne capture process are buried in the native state", Proc. Natl. Acad. Sci. 103, 4433-4438 (2006).
220. M. S. Cheung, D. Thirumalai, "Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces", J. Mol. Biol., 357, 632-643 (2006).
219. C. Hyeon, D. Thirumalai, "Kinetics of interior loop formation in semiflexible chains", J. Chem. Phys. 124, 104905 (2006).
218. Li M. S., Hu C. K., Klimov D. K., D. Thirumalai, "Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions" Proc. Natl. Acad. Sci. 103, 93-98 (2006).
217. M. Kouza, M. S. Li, E. P. O'Brien, C. K. Hu, D. Thirumalai, "Effect of finite size on cooperativity and rates of protein folding", J. Phys. Chem. A 110, 671-676 (2006).
216. R. I. Dima, D. Thirumalai, “Determination of Networks of Residues that Regulate Allostery in Protein Families Using Sequence Analysis”, Prot. Sci. 15, 258-268 (2006).
215. G. Caliskan, R. M. Briber, D. Thirumalai, V. Garcia-Sakai, S. A. Woodson, A. P. Sokolov, “Dynamic Transition in tRNA is Solvent Induced”, J. Amer. Chem. Soc. 128, 32-33 (2006).

2005

214. D. M. Dunlavy D. P. O’Leary, D. Klimov, D. Thirumalai, “HOPE: A Homotopy Optimization Method for Protein Structure Prediction”, J. Computational Bio. 12, 1275-1288 (2005).
213. G. Ziv, G. Haran, D. Thirumalai, "Ribosome Exit Tunnel Can Entropically Stabilize Alpha-Helices", Proc. Nat. Acad. Sci. 102, 18956-18961 (2005).
212. G. Caliskan, C. Hyeon, U. Perez-Salas, R. M. Briber, S. A. Woodson, D. Thirumalai, "Persistence Length Changes Dramatically as RNA Folds", Phys. Rev. Lett. 95, 268303 (2005).
211. D. K. Klimov, D. Thirumalai, "Symmetric Connectivity of Secondary Structure Elements Enhances the Diversity of Folding Pathways", J. Mol. Bio. 353, 1171-1186 (2005).
210. S. Chauhan, G. Caliskan, R. M. Briber, U. Perez-Salas, P. Rangan, D. Thirumalai, S. A. Woodson, "RNA Tertiary Interactions Mediate Native Collapse of a Bacterial Group I Ribozyme", J. Mol. Bio. 353, 1199-1209 (2005).
209. V. Barsegov, D. Thirumalai, "Probing Protein-Protein Interactions by Dynamic Force Correlation Spectroscopy", Phys. Rev. Lett. 95, 168302 (2005).
208. G. Stan, B. R. Brooks, D. Thirumalai, "Probing the 'Annealing' Mechanism of GroEL Mini-Chaperone Using Molecular Dynamics Simulations", J. Mol. Bio. 350, 817-829 (2005).
207. G. Morrison, D. Thirumalai, "The Shape of a Flexible Polymer in a Cylindrical Pore", J. Chem. Phys. 122, 194907 (2005).
206. Hyeon C., Thirumalai D. "Mechanical unfolding of RNA hairpins" Proc. Natl. Acad. Sci. 102 (19): 6789-6794 2005
205. Zheng W. J., Brooks B. R., Doniach S., Thirumalai D., "Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved" Structure 13 (4): 565-577 (2005)
204. Thirumalai D., Hyeon C. "RNA and protein folding: Common themes and variations" Biochemistry 44 (13): 4957-4970 (2005)
203. Cheung M. S., Klimov D., Thirumalai D. "Molecular crowding enhances native state stability and refolding rates of globular proteins" Proc. Natl. Acad. Sci. 102 (13): 4753-4758 (2005)
202. Li M. S., Klimov D. K., Thirumalai D. "Finite size effects on calorimetric cooperativity of two-state proteins" Physica A - Statistical Mechanics and its Applications 350 (1): 38-44 (2005)
201. Dima R. I., Hyeon C., Thirumalai D. "Extracting stacking interaction parameters for RNA from the data set of native structures" J. Mol. Biol. 347 (1): 53-69 (2005).
200. Barsegov V., Thirumalai D. "Dynamics of unbinding of cell adhesion molecules: Transition from catch to slip bonds" Proc. Natl. Acad. Sci. 102 (6): 1835-1839 (2005)
199. Tarus B., Straub J. E., Thirumalai D. "Probing the initial stage of aggregation of the A beta(10-35)-protein: Assessing the propensity for peptide dimerization" J. Mol. Biol. 345 (5): 1141-1156 (2005)
198. Stan G., Brooks B. R., Lorimer G. H., Thirumalai D., "Identifying natural substrates for chaperonins using a sequence-based approach" Prot. Sci. 14 (1): 193-201 (2005)

2004

197. Li M. S., Klimov D. K., Thirumalai D. "Finite size effects on thermal denaturation of globular proteins" Phys. Rev. Lett. 93 (26): Art. No. 268107 (2004)
196. Mountain R. D., Thirumalai D. "Alterations in water structure induced by guanidinium and sodium ions" J. Phys. Chem. B 108 (51): 19711-19716 2004
195. Klimov D. K., Thirumalai D. "Progressing from folding trajectories to transition state ensemble in proteins" Chem. Phys. 307 (2-3): 251-258 (2004)
194. Dima R. I., Thirumalai D. "Probing the instabilities in the dynamics of helical fragments from mouse PrPc" Proc. Natl. Acad. Sci. 101 (43): 15335-15340 (2004)
193. Klimov D. K., Straub J. E., Thirumalai D. "Aqueous urea solution destabilizes A beta(16-22) oligomers" Proc. Natl. Acad. Sci. 101 (41): 14760-14765 (2004)
192. Dima R. I., Thirumalai D. "Proteins associated with diseases show enhanced sequence correlation between charged residues" Bioinformatics 20 (15): 2345-2354 (2004)
191. Koculi E., Lee N. K., Thirumalai D, Woodson S. A., "Folding of the Tetrahymena ribozyme by polyamines: Importance of counterion valence and size" J. Mol. Biol. 341 (1): 27-36 (2004)
190. Dima R. I., Thirumalai D. "Asymmetry in the shapes of folded and denatured states of proteins" J. Phys. Chem. B 108 (21): 6564-6570 (2004)
189. Mountain R. D., Thirumalai D. "Importance of excluded volume on the solvation of urea in water" J. Phys. Chem. B 108 (21): 6826-6831 (2004)
188. Buchete N. V., Straub J. E., Thirumalai D. "Development of novel statistical potentials for protein fold recognition" Curr. Opin. Struct. Biol. 14 (2): 225-232 (2004)
187. Buchete N. V., Straub J. E., Thirumalai D. "Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis" J. Molecular Graphics & Modelling 22 (5): 441-450 Sp. Iss. (2004)
186. Lee N. K., Thirumalai D. "Pulling-speed-dependent force-extension profiles for semiflexible chains" Biophys. J. 86 (5): 2641-2649 (2004)
185. Buchete N. V., Straub J. E., Thirumalai D. "Orientational potentials extracted from protein structures improve native fold recognition" Prot. Sci. 13 (4): 862-874 (2004)
184. Perez-Salas U. A., 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 (6): 1746-1753 (2004)
183. Li M. S., Klimov D. K., Thirumalai D. "Thermal denaturation and folding rates of single domain proteins: size matters" Polymer 45 (2): 573-579 (2004)
182. Buchete N. V., Straub J. E., Thirumalai D. "Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases" Polymer 45 (2): 597-608 (2004)

2003

181. Ha B. Y., Thirumalai D. "Bending rigidity of stiff polyelectrolyte chains: A single chain and a bundle of multichains" Macromolecules 36 (25): 9658-9666 (2003)
180. Thirumalai D., Klimov D. K., Lorimer G. H. "Caging helps proteins fold" Proc. Natl. Acad. Sci. 100 (20): 11195-11197 (2003)
179. Hyeon C. B., Thirumalai D. "Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments?" Proc. Natl. Acad. Sci. 100 (18): 10249-10253 (2003)
178. Thirumalai D., Klimov D. K., Dima R. I. "Emerging ideas on the molecular basis of protein and peptide aggregation" Curr. Opin. Struct. Biol. 13 (2): 146-159 (2003)
177. Buchete N. V., Straub J. E., Thirumalai D. "Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures" J. Chem. Phys. 118 (16): 7658-7671 (2003)
176. Klimov D. K., Thirumalai D., "Dissecting the assembly of A beta(16-22) amyloid peptides into antiparallel beta sheets" Structure 11 (3): 295-307 (2003)
175. Tobi D., Elber R., Thirumalai D., "The dominant interaction between peptide and urea is electrostatic in nature: A molecular dynamics simulation study" Biopolymers 68 (3): 359-369 (2003)
174. Thirumalai D., "The Dominant Interaction Between Peptide and Urea is Electrostatic in Nature: A Molecular Dynamics Simulation Study", Biopolymers 68, 359-369 (2003)
173. Mountain R. D., Thirumalai D. "Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution" J. Amer. Chem. Soc. 125 (7): 1950-1957 (2003)
172. Li M. S., Klimov D. K., Thirumalai D. "Folding in lattice models with side chains" Comp. Phys. Comm. 147 (1-2): 625-628 (2002)
171. G. Stan, D. Thirumalai, G. H. Lorimer, and B. R. Brooks, "Annealing Function of GroEL: Structural and Bioinformatic Analysis", Biophys. Chem. 100, 453-467 (2003).

2002

170. M. R. Betancourt and D. Thirumalai, "Designing Fast Folding Protein Sequences by Tuning the Energy Landscape", in "Recent Developments in Protein Folding, Stability and Design", edited by M. Gromika and S. Selvaraj, (World Scientific, 2002).
169. Li M. S., Klimov D. K., Thirumalai D. "Dependence of folding rates on protein length" J. Phys. Chem. B 106 (33): 8302-8305 (2002)
168. Thirumalai D., Klimov D. K., Dima R. I. "Insights into specific problems in protein folding using simple concepts" Adv. Chem. Phys. 120: 35-76 (2002)
167. Massi F., Klimov D., Thirumalai D., Straub J. E., "Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant" Prot. Sci. 11 (7): 1639-1647 (2002).
166. R. I. Dima, D. Thirumalai, "Exploring the Propensities of Helices in PrPc to Form ?-Sheet Using NMR Structures and Sequence Alignments", Biophys. J. 83, 1268-1280 (2002).
165. R. I. Dima, D. Thirumalai, "Exploring Protein Aggregation and Self-Propagation Using Lattice-Models: Phase Diagram and Kinetics", Prot. Sci. 11, 1036-1049 (2002).
164. Klimov D. K., Newfield D., Thirumalai D. "Simulations of beta-hairpin folding confined to spherical pores using distributed computing" Proc. Natl. Acad. Sci. 99 (12): 8019-8024 (2002)
163. Klimov D.K., Thirumalai D., "Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in S" J. Mol. Biol. 317 (5): 721-737 (2002)
162. Dima R. I., Thirumalai D. "Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics", Prot. Sci. 11 (5): 1036-1049 (2002)
161. Perez-Salas U. A., Krueger S., Woodson S., Rangan P., Georgieva E., Thirumalai D., Briber R. M., "Folding pathways of RNA by cation binding" Biophys. J. 82 (1): 644 Part 2 (2002)
160. Betancourt M. R., Thirumalai D., "Protein sequence design by energy landscaping" J. Phys. Chem. B 106 (3): 599-609 (2002)
159. Thirumalai D., "Kinetic partitioning mechanism in protein folding." J. Phys Chem. B 106 (3): 599-609 (2002)
158. D. K. Klimov, D. Thirumalai, "Is There a Unique Melting Temperature for Two-State Proteins?", J. Comp. Chem., 23, 161-165 (2002).

2001

157. Klimov D. K., Thirumalai D. "Lattice model studies of force-induced unfolding of proteins", J. Phys. Chem. B 105 (28): 6648-6654 (2001)
156. Pechukas P., Thirumalai D., "Bruce Berne Festschrift - Foreword" J. Phys. Chem. B 105 (28): 6453-6454 (2001)
155. Lee N., Thirumalai D., "Dynamics of collapse of flexible polyelectrolytes in poor solvents", Macromolecules, 34 (10): 3446-3457 (2001)
154. Straub J. E., Buchete N. V., Thirumalai D., "Protein threading using novel inter-residue contact potentials" Biophys. J. 80(1): 2514 Part 2 (2001)
153. S. L. Heilman-Miller, J. Pan, D. Thirumalai, S.A. Woodson "Role of Counterion Condensation in Folding of the Tetrahymena Ribozyme II. Counterion-dependence of Folding Kinetics", J. Mol. Biol. 309, 57-68 (2001)
152. S. L. Heilman-Miller, D. Thirumalai, S. A. Woodson, "Role of Counterion Condensation in the Folding of Tetrahymena Ribozyme I. Equilibrium Stabilization by Cations", J. Mol. Biol. 306, 1157-1166 (2001).
151. M. S. Li, D. K. Klimov, D. Thirumalai, "Lattice Model Studies of Force-Induced Unfolding of Proteins", J. Phys. Chem. B, 6648-6654 (2001)
150. D. K. Klimov, D. Thirumalai, "Multiple protein folding nuclei and the transition state ensemble in two state proteins", Proteins Struct. Funct. Gen., 43, 465-475 (2001)
149. D. Thirumalai, N. Lee, S. A. Woodson, D. K. Klimov, "Early Events in RNA Folding", Ann. Rev. Phys. Chem. 52, 751-762 (2001).
148. D. Thirumalai, G. H. Lorimer, "Chaperonin-Mediated Protein Folding", Ann. Rev. Biophys. Biomol. Struct. 30, 245-269 (2001).

2000

147. D. Mohanty, R. Elber, D. Thirumalai, "Probing the Role of Local Propensity in Peptide Turn Formation", Int. J. Quant. Chem., 80, 1125-1128 (2000).
146. D. E. Sagnella, J. E. Straub, and D. Thirumalai, "Time Scales and Pathways for Kinetic Energy Relaxation in Solvated Proteins: Applicating to Carbonmonoxy Myoglobin", J. Chem. Phys. 113, 7702-7711 (2000).
145. D. Thirumalai, S. A. Woodson, "Maximizing RNA Folding: A Balancing Act", RNA 6, 790-794 (2000).
144. D. Thirumalai and D. K. Klimov "Introducing Protein Folding Using Lattice Models", in "Encyclopedia of Chemical Physics and Physical Chemistry, Vol. III: Applications" (Institute for Physics Publishing, Bristol and Philadelphia), 2345-2366 (2002).
143. D. Thirumalai, "Two Landmarks in Polymer Physics", Theor. Chem. Acc. 103, 242-293 (2000).
142. D. K. Klimov, D. Thirumalai, "Native topology determines force-induced unfolding pathways in globular proteins", Proc. Natl. Acad. Sci. 97, 7254-7259 (2000)
141. N. Lee, D. Thirumalai, "Dynamics of Collapse of Flexible Polyampholytes", J. Chem. Phys. 133, 5126-5129 (2000).
140. D. K. Klimov, D. Thirumalai, "Mechanisms and Kinetics of beta-Hairpin Formation", Proc. Natl. Acad. Sci. 97, 2544-2549 (2000)
139. D. Thirumalai, D. K. Klimov, "Emergence of Stable and Fast Folding Protein Structures", in Stochastic Dynamics and Pattern Formation in Biological and Complex Systems edited by S. Kim, K. J. Lu and W. Song, (American Institute of Physics) 95-111 (2000).

1990-1999

138. N. K. Lee, D. Thirumalai, "Stretching DNA: Effect of electrostatic interactions", Europhys. J.B. 12, 599-605 (1999).
137. D. Thirumalai, "Time Scales for the Formation of the Most Probable Contacts in Proteins with Applications to Cytochrome C", J. Phys. Chem. B 103, 608-610 (1999).
136. B. Y. Ha, D. Thirumalai, "Persistence Length of Flexible Polyelectrolyte Chains;", J. Chem. Phys. 110, 7533-7541 (1999).
135. D.K. Klimov, D. Thirumalai, "Stretching Single Domain Proteins: Phase diagram and kinetics of force-induced unfolding", Proc. Natl. Acad. Sci. 96, 6166-6170 (1999).
134. J. Pan, D. Thirumalai, S. Woodson, "Magnesium-Dependent Folding of Self-Splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics", Proc. Natl. Acad. Sci. 96, 6149-6154 (1999).
133. D. Thirumalai, D. K. Klimov, "Deciphering the Time Scales and Mechanisms of Protein Folding Using Minimal Off-Lattice Models", Curr. Opin. Struct. Biol. 9, 197-207 (1999).
132. D. A. Lidar, D. Thirumalai, R. Elber, R. B. Gerber, "Fractal Analysis of Protein Potential Energy Landscapes", Phys. Rev. E 59, 2231-2243 (1999).
131. M. R. Betancourt, D. Thirumalai, "Pair Potentials for Protein Folding: Choice of Reference States and Sensitivity of Predicted Motive States to Variations in the Interaction Schemes", Protein Science 8, 361-389 (1999).
130. M. R. Betancourt, D. Thirumalai, "Exploring the Kinetic Requirements for Enhancement of Protein Folding Rates in the GroEL Cavity", J. Mol. Biol. 287, 627-644 (1999).
129. D. K. Klimov, D. Thirumalai, "Linking Rates of Folding in Lattice Models of Proteins with Underlying Thermodynamic Characteristics", J. Chem. Phys. 109, 4119-4125 (1998).
128. D. K. Klimov, D. Thirumalai, "Lattice Models for Proteins Reveal Multiple Folding Nuclei for Nucleation-Collapse Mechanism", J. Mol. Biol. 282, 471-492 (1998).
127. D. Thirumalai, B.-Y. Ha, "Statistical Mechanics of Stiff Chains", in Theoretical and Mathematical Methods in Polymer Research edited by A. Y. Grosberg (Academic Press, New York), 1-35, (1998).
126. D. Thirumalai, "Native Secondary Structure Formation in RNA may be Slave to Tertiary Folding", Proc. Natl. Acad. Sci. 95, 11506-11508 (1998).
125. D. Thirumalai, D. K. Klimov, "Fishing for Folding Nuclei in Lattice Models and Proteins", Folding & Design, 3, R112-R118 (1998).
124. D. K. Klimov, M. R. Betancourt, D. Thirumalai, "Virtual Atom Representation of Hydrogen Bonds in Minimal Off-lattice models of α-Helices: Effect on Stability, Cooperativity, and Kinetics", Folding & Design, 3, 481-496 (1998).
123. R. D. Mountain, D. Thirumalai, "Hydration for Series of Hydrocarbons", Proc. Natl. Acad. Sci., (USA) 95, 8436-8440 (1998).
122. D. Thirumalai, D. K. Klimov, M. R. Betancourt "Exploring the Folding Mechanisms in Proteins Using Lattice Models", in Monte Carlo Approach to Biopolymers and Protein Folding edited by P. Grasssberger, G. J. Barkema and H. Nadler (World Scientific),19-28 (1998).
121. D. K. Klimov, D. Thirumalai, "Cooperativity in Protein Folding: From Lattice Models with Side Chains to Real Proteins", Folding & Design, 3, 127-139 (1998).
120. A. Wallqvist, D. G. Covell, D. Thirumalai, "Hydrophobic Interactions in Aqueous Urea Solutions with Implications for Mechanisms of Protein Denaturation", J. Am. Chem. Soc., 120, 427-428 (1998).
119. H. J. Bussemaker, D. Thirumalai, J. K. Bhattacharjee, "Thermodynamic Stability of Folded Proteins Against Mutations", Phys. Rev. Lett., 79, 3530-3533 (1997).
118. Zhuyan Guo, D. Thirumalai, "The Nucleation-Collapse Mechanism in Protein Folding: Evidence for the Non-Uniqueness of the Folding Nucleus", Folding & Design, 2, 277-341 (1997).
117. D. Mohanty, R. Elber, D. Thirumalai, D. Beglov, B. Roux, "Kinetics of Peptide Folding: Computer Simulations of SYPFDU and Peptide Variants in Water", J. Mol. Biol., 272, 423-442 (1997).
116. J. Pan, D. Thirumalai, S. A. Woodson, "Folding of RNA Involves Parallel Pathways", J. Mol. Biol., 273, 7-13 (1997).
115. D. Thirumalai, D. K. Klimov, S. A. Woodson, "Kinetic Partitioning Mechanism as a Unifying Theme in the Folding of Biomolecules", Theoretical Chemistry Accounts, 1, 23-30 (1997).
114. D. K. Klimov, D. Thirumalai, "Viscosity Dependence of Folding Rates of Protein", Phys. Rev. Lett., 79, 317-320 (1997).
113. B. Y. Ha, D. Thirumalai, "Semiflexible Chains Under Tension", J. Chem. Phys.106, 4243-4247 (1997).
112. H. Orland, D. Thirumalai, "A Kinetic Model for Chaperonin Assisted Folding of Protein", J. Phys. I (France) 7, 553-560 (1997).
111. B. Y. Ha, D. Thirumalai, "Persistence Length of Intrinsically Stiff Polyampholyte Chain", J. Phys. II (France) 7, 887-902 (1997).
110. C. Cordeiro, M. Molisana, D. Thirumalai, "Shapes of Confined Polymer Chains", J. Phys. II (France) 7, 433-447 (1997).
109. T. Veitshans, D. K. Klimov, D. Thirumalai, "Protein Folding Kinetics: Time Scales, Pathways, and Energy Landscapes in Terms of Sequence-Dependent Properties", Folding & Design, 2, 1-22 (1997).
108. M. J. Todd, G. H. Lorimer, D. Thirumalai, "Chaperonins-Facilitated Protein Folding: Optimization of Rate and Yield by an Iterative Annealing Mechanism", Proc. Natl. Acad. Sci. (USA), 93, 4030-4075 (1996).
107. C. J. Camacho, D. Thirumalai, "A Criterion that Determines Fast Folding of Proteins: A Model Study", Europhys. Lett., 35, 627-632 (1996).
106. D. Thirumalai, J. K. Bhattacharjee, "Polymer Induced Drag Reduction in Turbulent Flows", Phys. Rev. E, 53, 546-551 (1996).
105. C. J. Camacho, D. Thirumalai, "Denaturants Can Accelerate Folding in a Class of Globular Proteins", Protein Science, 5, 1826-1832 (1996).
104. Z. Guo, D. Thirumalai, "Kinetics and Thermodynamics of Folding of a de novo Designed four Helix Bundle", J. Mol. Biol., 263, 323-343 (1996).
103. D. Thirumalai, V. Ashwin, J. K. Bhattacharjee, "Dynamics of Random Hydrophobic-Hydrophilic Copolymers with Implications for Protein Folding", Phys. Rev. Lett. 77, 5385-5388 (1996).
102. D. Thirumalai, "Energy Landscape Perspective of in Vitro and in Vivo Protein Folding", J. de Physique I 6, 51-53 (1996).
101. D. K. Klimov, D. Thirumalai, "Factors Governing the Foldability of Proteins", Proteins: Structure, Function, and Genetics, 26, 411-441 (1996).
100. D. Thirumalai, S. A. Woodson, "Kinetics of Folding of Proteins and RNA", Acc. Chem. Res. 29, 433-439 (1996).
99. D. Klimov, D. Thirumalai, "A Criterion That Determines the Foldability of Protein", Phys. Rev. Lett. 76, 4070-4073 (1996).
98. J. D. Bryngelson, D. Thirumalai, "Internal Constraints Induce Localization in an Isolated Polymer Molecule", Phys. Rev. Lett. 76, 542-545 (1996).
97. T. Garel, H. Orland, D. Thirumalai, "Analytical Theories of Protein Folding", in New Developments in Theoretical Studies of Protein Folding edited by R. Elber (World Scientific, in press, 1996) pp. 197-268.
96. Z. Guo, D. Thirumalai, "Energy Landscape and Folding Mechanisms in Proteins", In Protein Folds: a distance based approach edited by H. Bohr and S. Brunak (CRC Press, Boca Raton, FL, 1995) 233-239.
95. B. Y. Ha, D. Thirumalai, "A Mean Field Model for Semiflexible Chains", J. Chem. Phys., 103, 9408-9412 (1995).
94. P. G. Wolynes, J. Onuchic,, D. Thirumalai, "Navigating the Folding Routes", Science, 267, 1619-1620 (1995).
93. D. Thirumalai, "From Minimal Models to Proteins: Time Scales for Protein Folding Kinetics", J. Physique (Paris), 5, 1457-1467 (1995).
92. T. R. Kirkpatrick, D. Thirumalai, "Are Disordered Spin Models Relevant for the Structural Glass Problem?", Transp. Theory and Stat. Mech., 24 927-945 (1995).
91. T. R. Kirkpatrick, D. Thirumalai, "The Cavity Approach to Metastable Glassy States Near Random First Order Phase Transition", J. Physique I 5, 771-786 (1995).
90. B. Ha, D. Thirumalai, "Electrostatic Persistence Length of a Polyelectrolyte Chain", Macromolecules 28, 577-581 (1995).
89. Z. Guo, D. Thirumalai, "Kinetics of Protein Folding: Nucleation Mechanism, Time Scales, and Pathways", Biopolymers, 36, 83-102 (1995).
88. C. J. Camacho, D. Thirumalai, "Modelling Disulfide Bonds in Globular Proteins: Entropic Barriers and Pathways", Proteins: Structure, Function and Genetics, 22. 28-40 (1995).
87. D. Thirumalai, Z. Guo, "Nucleation Mechanism for Protein Folding and Theoretical Predictions for Hydrogen-Exchange Labelling Experiments", Biopolymers (Research Communications 37, 137-140 (1995)).
86. C. J. Camacho, D. Thirumalai, "Theoretical Predictions of Folding Pathways Using the Proximity Rule with Applications to BPTI", Proc. Nat'l. Acad. Sci. 92, 1277 (1995).
85. R. D. Mountain, D. Thirumalai, "Quantitative Measure of Efficiency of Monte Carlo Simulations", Physica A 210, 453-460 (1994).
84. D. Thirumalai, "Theoretical Perspectives on in vitro and in vivo Protein Folding", in Statistical Mechanics, Protein Structure, and Protein Substrate Interactions, edited by S. Doniach p. 115-134, (Plenum Press, NY, 1994).
83. D. Thirumalai, "Rotational Relaxation of a Spherocylinder and a Semirigid Molecule in Concentrated Solutions", J. Phys. Chem. 98, 9265-9269 (1994).
82. J. E. Straub, A. B. Rashkin,, D. Thirumalai, "Dynamics in Rugged Energy Landscapes with Applications to the S-peptide and Ribonuclease A", J. Am. Chem. Soc. 116, 2049-2063 (1994).
81. D. Thirumalai, "Minimum Energy Compact Structures of Random Sequences of Heteropolymers", Phys. Rev. Lett. 71, 2505-2508 (1993).
80. D. Thirumalai, R. D. Mountain, "Activated Dynamics, Loss of Ergodicity, and Transport in Supercooled Liquids", Phys. Rev. E 47, 479-489 (1993).
79. R. D. Mountain, D. Thirumalai, "Relationship Between the Fluctuation Metric and the Non-ergodicity Parameter: Incoherent Scattering Function", Physica A 192, 543-549 (1993).
78. J. E. Straub, D. Thirumalai, "Exploring the Energy Landscape in Proteins", Proc. Natl. Acad. Sci. (USA) 90, 809-813 (1993).
77. C. J. Camacho, D. Thirumalai, "Kinetics and Thermodynamics of Folding in Model Proteins", Proc. Natl. Acad. Sci. 90, 6369-6372 (1993).
76. J. E. Straub, D. Thirumalai, "Theoretical Probes of Conformational Fluctuations in Proteins with Applications to S. Peptide and RNase A/3' - UMP Enzyme/Product Complex", Proteins: Structure, Function, and Genetics 15, 360-373 (1993).
75. B.-Y. Ha, D. Thirumalai, "Conformations of Polyelectrolyte Chain", Phys. Rev. A 46, R3012-R3015 (1992).
74. Z. Guo, D. Thirumalai, J. D. Honeycutt, "Folding Kinetics of Proteins: A Model Study", J. Chem. Phys. 97, 525-535 (1992).
73. R. D. Mountain, D. Thirumalai, "Loss in Ergodicity in Supercooled Liquids", "Slow Dynamics in Condensed Matter", edited by K. Kawazaki, T. Kawakatsu, and M. Tokuyama, AIP Conference Proceedings, 256, 165-172 (1992).
72. R. D. Mountain, D. Thirumalai, "Ergodicity and Activated Dynamics in Supercooled Liquids", Phys. Rev. A 45, R3380-R3383 (1992).
71. J. D. Honeycutt, D. Thirumalai, "The Nature of Folded States of Globular Proteins", Biopolymers 32, 695-709 (1992).
70. D. Thirumalai, "Topologically Entangled Polymers", Theor. Chem. Acta. 82, 407-417 (1992).
69. M. R. Shaw, D. Thirumalai, "Free Polymer in a Colloidal Solution", Phys. Rev. A 44, R4797-R4800 (1991).
68. D. Thirumalai, B. J. Berne, "Methods for Simulating Time Correlation Functions in Quantum Systems", Comp. Phys. Comm. 63, 415-426 (1991).
67. R. D. Mountain, D. Thirumalai, "Ergodic Measures for the Simulation of Dielectric Properties of Water", Comp. Phys. Comm. 62, 352-359 (1991).
66. J. K. Bhattacharjee, D. Thirumalai, "Drag Reduction in Turbulent Flows by Polymers", Phys. Rev. Lett. 67, 196-199 (1991).
65. J. D. Honeycutt, D. Thirumalai, "Influence of Optimal Cavity Shapes on the Size of Polymer Molecules in Random Media", J. Chem. Phys. 93, 6851-6858 (1990).
64. D. Thirumalai, R. D. Mountain, "Ergodic Convergence Properties of Supercooled Liquids and Glasses", Phys. Rev. A 42, 4574-4587 (1990).
63. V. Dobrosavljevic, D. Thirumalai, "1/p Expansions for p-Spin Interaction Model in a Transverse Field", J. Phys. A 23, L767-L774 (1990).
62. R. D. Mountain, D. Thirumalai, "Ergodic Convergences in Liquids and Glasses", Int. J. Mod. Phys. C 1, 77-89 (1990).
61. M. R. Shaw, D. Thirumalai, "Variational Theories for Localized States of an Excess Electron in Fluids", J. Chem. Phys. 93, 3460-3470 (1990).
60. J. D. Honeycutt, D. Thirumalai, "Metastability of the Folded States of Globular Proteins", Proc. Natl. Acad. Sci. 87, 3526-3529 (1990).
59. R. D. Mountain, D. Thirumalai, "Dynamical Aspects of Anisotropic Correlations in Supercooled Liquids", J. Chem. Phys. 92, 6116-6122 (1990).

1980-1989

58. R. D. Mountain, D. Thirumalai, "Measures of Effective Ergodic Convergence in Liquids", J. Phys. Chem. 93, 6975-6979 (1989).
57. D. Thirumalai, Q. Li, T. R. Kirkpatrick, "Infinite Range Ising Spin Glass in a Transverse Field", J. Phys. A 22, 3339-3349 (1989).
56. D. Thirumalai, R. D. Mountain, "Probes of Equipartition in Nonlinear Hamiltonian Systems", J. Stat. Phys. 57, 789-801 (1989).
55. R. O. Rosenberg, D. Thirumalai, R. D. Mountain, "Liquid, Crystalline and Glassy States of Binary Charged Colloidal Suspensions", J. Phys. Condensed Matter 1, 2109-2114 (1989).
54. T. R. Kirkpatrick, D. Thirumalai, P. G. Wolynes, "Scaling and Droplet Notions for the Dynamics of Viscous Liquids Near an Ideal Glassy State", Phys. Rev. A 40, 1045-1054 (1989).
53. D. Thirumalai, "Liquid and Crystalline States of Monodisperse Charged Colloidal Particles", J. Phys. Chem. 93. 5637-5644 (1989).
52. J. D. Honeycutt, D. Thirumalai, "Static Properties of Polymer Chains in Porous Media", J. Chem. Phys. 90, 4542-4559 (1989).
51. D. Thirumalai, R. D. Mountain, T. R. Kirkpatrick, "Ergodic Behavior in Supercooled Liquids and in Glasses", Phys. Rev. A 39, 3563-3574 (1989).
50. J. D. Honeycutt, D. Thirumalai, D. K. Klimov, "Polymer Chains in Porous Media", J. Phys. A 22, L169-L175 (1989).
49. T. R. Kirkpatrick, D. Thirumalai, "Random Solutions From a Regular Density Functional Hamiltonian: A Static and Dynamical Theory for the Structural Glass Transition", J. Phys. A 22, L149-L159 (1989).
48. D. Thirumalai, T. R. Kirkpatrick, "Mean Field Potts Glass Model: Initial Condition Effects on Dynamics and Properties of Metastable States", Phys. Rev. B 38, 4881-4892 (1988).
47. T. R. Kirkpatrick, D. Thirumalai, "A Comparison Between Dynamical Theories and Metastable States in Regular and Glassy Mean Field Spin Models with Underlying First Order Like Transitions", Phys. Rev. A 38, 4439-4448 (1988).
46. D. Thirumalai, "Electron Localization by Atomic and Molecular Clusters", in Large Finite Systems, 231-240, eds. J. Jortner and B. Pullman (Reidel Publishing, 1988).
45. B. Bagchi, D. Thirumalai, "Freezing of a Colloidal Liquid Subject to Shear Flow", Phys. Rev. A 37, 2530-2538 (1988).
44. D. Thirumalai, "Isolated Polymer Molecule in a Random Environment", Phys. Rev. A 37, 269-276 (1988).
43. T. R. Kirkpatrick, D. Thirumalai, "A Mean Field Soft Spin Potts Glass Model: Statics and Dynamics", Phys. Rev. B 37, 5342-5350 (1988).
42. T. R. Kirkpatrick, D. Thirumalai, "p-Spin Interaction Model: Connections with the Structural Glass Problem", Phys. Rev B 36, 5388-5397 (1987).
41. R. O. Rosenberg, D. Thirumalai, "Order-Disorder Transition in Colloidal Suspensions", Phys. Rev. A 36, 5690-5700 (1987).
40. R. D. Mountain, D. Thirumalai, "Molecular Dynamics Study of Glassy and Supercooled States of a Binary Mixture of Soft Spheres", Phys. Rev. A 36, 3300-3311 (1987).
39. D. F. Coker, D. Thirumalai, B. J. Berne, "Path Integral Monte Carlo Studies of the Behavior of Excess Electrons in Simple Fluids", J. Chem. Phys. 86, 5689-5702 (1987).
38. T. R. Kirkpatrick, D. Thirumalai, "Dynamics of the Structural Glass Transition and the p-Spin Interaction Spin Glass Model", Phys. Rev. Lett. 58, 2091-2094 (1987).
37. A. Wallqvist, D. Thirumalai, B. J. Berne, "Path Integral Monte Carlo Study of the Hydrated Electron", J. Chem. Phys. 86, 6404-6418 (1987).
36. D. Thirumalai, R. D. Mountain, "Relaxation of Anisotropic Correlations in (Two Component) Supercooled Liquids", J. Phys. C 20, L399-L405 (1987).
35. C. A. Condat, D. Thirumalai, "Flow Induced Transitions in Smectic Liquid Crystals", J. Chem. Phys. 86, 4548-4554 (1987).
34. D. Thirumalai, G. Staszewska,, D. G. Truhlar, "On the Use of Dispersion Relations in Obtaining Local Optical Model Potential for Electron Scattering", Comm. At. Mol. Phys. 20, 217-243 (1987).
33. B. J. Berne, D. Thirumalai, "On the Simulation of Quantum Systems: Path Integral Methods", Ann. Rev. Phys. Chem. 37, 401-424 (1986).
32. D. Thirumalai, "Lifshitz Tails in a Spatially Correlated Random Potential", J. Phys. C 19, L397-L401 (1986).
31. R. O. Rosenberg, D. Thirumalai, "Structure and Dynamics of Screened Coulomb Colloidal Liquids", Phys. Rev. A 33, 4473-4476 (1986) (Rapid Communication).
30. A. Wallqvist, D. Thirumalai, B. J. Berne, "Localization of an Electron in Water Clusters", J. Chem. Phys. 85, 1583-1591 (1986).
29. D. Thirumalai, "Effect of Elongational Flow on the Isotropic Nematic Phase Transitions in Rod-like Systems", J. Chem. Phys. 84, 5869-5873 (1986).
28. D. Thirumalai, A. Wallqvist, B. J. Berne, "Path Integral Monte Carlo Simulations of Electron Localization in Water Clusters", J. Stat. Phys. 43, 973-984 (1986).
27. D. Thirumalai, B. C. Garrett, B. J. Berne, "Evaluation of Microcanonical Rate Constants for Bimolecular Reactions by Path Integral Techniques", J. Chem. Phys. 83, 2972-2975 (1985).
26. D. Thirumalai, B. J. Berne, "Path Integral Methods for Simulating Electronic Spectra", Chem. Phys. Lett. 116, 471-473 (1985).
25. D. Thirumalai, E. J. Bruskin, B. J. Berne, "On the Use of Semiclassical Dynamics in Determining Electronic Spectra of Br2 in Ar Matrix", J. Chem. Phys. 83, 230-238 (1985).
24. B. C. Garrett, D. W. Schwenke, R. T. Skodje, D. Thirumalai, T. C. Thompson, D. G. Truhlar, "Adiabatic and Nonadiabatic Methods for Energies, Lifetimes, and Branching Probabilities of Bimolecular Reactive Collisions", A. C. S. Symposia Series 263, 375-400 (1984).
23. D. Thirumalai, R. W. Hall, B. J. Berne, "A Path Integral Monte Carlo Study of Liquid Neon and the Quantum Effective Pair Potential", J. Chem. Phys. 80, 5864-5865 (1984).
22. D. Thirumalai, B. J. Berne, "Time Correlation Functions in Quantum Systems", J. Chem. Phys. 81, 2512-2513 (1984).
21. D. Thirumalai, T. C. Thompson, D. G. Truhlar, "Rational Fraction Analytic Continuation Method for Complex Resonance Energies in Multidimensional Systems", J. Chem. Phys. 80, 5864-5865 (1984).
20. D. W. Schwenke, D. Thirumalai, D. G. Truhlar, "Accurate, Smooth, Local, Energy Dependent Optical Potentials for Electron Scattering", Phys. Rev. A 28, 3258-3267 (1983).
19. G. Staszewska, D. W. Schwenke, D. Thirumalai, D. G. Truhlar, "Quasifree Scattering Model for the Imaginary Part of the Optical Potential for Electron Scattering", Phys. Rev. A 28, 2740-2751 (1983).
18. D. Thirumalai, E. J. Bruskin, B. J. Berne, "An Iterative Scheme for the Evaluation of Discretized Path Integrals", J. Chem. Phys. 79, 5063-5069 (1983).
17. D. Thirumalai, B. J. Berne, "On the Calculation of Time Correlation Functions in Quantum Systems: Path Integral Techniques", J. Chem. Phys. 79, 5029-5033 (1983).
16. G. Staszewska, D. W. Schwenke, D. Thirumalai, D. G. Truhlar, "Non-Empirical Model for Imaginary Part of the Optical Potential for Electron Scattering", J. Phys. B 16, L281-L287 (1983).
15. D. W. Schwenke, D. Thirumalai, D. G. Truhlar, M. E. Coltrin, "Tests of Quasiclassical Trajectory Cross-Correlation Moment Method Against Accurate Quantum Dynamics for V-V Energy Transfer in HF-HF Collisions", J. Chem. Phys. 78, 3078-3083 (1983).
14. N. Abusalbi, R. A. Eades, T. Nam, D. Thirumalai, D. A. Dixon, D. G. Truhlar, M. Dupuis, "Electron Scattering by Methane. Elastic Scattering and Rotational Excitation Cross Sections by ab-Initio Potential", J. Chem. Phys. 78, 1213-1227 (1983).
13. D. Thirumalai, D. G. Truhlar, "Tests of Semiclassical Polarization Approximation foe Electron Scattering by Helium and Neon", Phys. Rev. A 27, 158-166 (1982).
12. D. Thirumalai, D. G. Truhlar, "Energy Dependent Polarization Potential, Dispersion Relation Absorption Potential and Matrix Effective Potential for Electron-Neon Scattering at 10-100 eV", Phys. Rev. A 26, 793-807 (1982).
11. D. Thirumalai, D. G. Truhlar, "Rapid Convergence of V-V Energy Transfer Calculations Using Adiabatic Basis Functions. I. An Accurate Two State Model for Low-Energy Resonant V-V Energy Transfer. II.", J. Chem. Phys. 76, 5287-5294 (1982).
10. D. Thirumalai, D. G. Truhlar, "Application of Variational Matrix Effective Potential Formalism for e-Ne Scattering and Comparisons to Optical Potential Calculations", Phys. Rev. A 25, 3058-3071 (1982).
9. S. M. Valone, D. G. Truhlar, D. Thirumalai, "A Localized Second-Order Optical Potential for Electron Scattering in Terms of Imaginary Frequency Susceptibilities", Phys. Rev. A 25, 3003-3014 (1982).
8. D. Thirumalai, D. G. Truhlar, M. A. Brandt, R. A. Eades, D. A. Dixon, "Polarization and Absorption Effects in e-He Scattering at 30-400 eV", Phys. Rev. A 25, 2946-2958 (1982).
7. D. Thirumalai, D. G. Truhlar, "Full Response Pseudo Channels: A New Method for Converging Coupled-Channel Scattering Calculations: Theory and Examples", J. Chem. Phys. 76, 385-389 (1982).
6. S. M. Valone, D. Thirumalai, D. G. Truhlar, "Dispersion-Equation Approach to Obtaining Complex Potentials for Electron Scattering", Int. J. Quant. Chem. Symp. 15, 341 (1981).
5. D. Thirumalai, D. G. Truhlar, "Improved Calculation of the Cross Section for Excitation of the Asymmetric Stretch of CO2 by Electron Impact", J. Chem. Phys. 75, 5207-5209 (1981).
4. D. Thirumalai, K. Onda, D. G. Truhlar, "Electron Scattering by CO2: Elastic Scattering, Rotational Excitation and Excitation of the Asymmetric Stretch at 10 eV Impact Energy", J. Chem. Phys. 4, 6792-6805 (1981).
3. D. Thirumalai, K. Onda, D. G. Truhlar, "Elastic Scattering and Rotational Excitation of a Polyatomic Molecule by Electron Impact: Acetylene", J. Chem. Phys. 74, 526-534 (1981).
2. D. Thirumalai, K. Onda, D. G. Truhlar, "Excitation of the Asymmetric Stretch of CO2 by Electron Impact", J. Phys. B 13, L619-L622 (1980).
1. D. Thirumalai, D. G. Truhlar, "Comparison of Convergence for the Schwinger, Optimized Anomaly-Free and Optimized Minimum-Norm Variational Methods for Potential Scattering", Chem. Phys. Lett. 70, 330-335 (1980).