Thirumalai, Dave

Publication with MATCHING institution:

Thirumalai D, Kumar A, Chakraborty D, ..., Mugnai ML (2023) Conformational fluctuations and phases in fused in sarcoma
(FUS) low-complexity domain. Biopolymers. [IF=0.522, Cited=0, 37399327].
Thirumalai D, Lorimer GH, Hyeon C (2019) Iterative annealing mechanism explains the functions of the GroEL and RNA
chaperones. Protein Science. [IF=1.97, Cited=21, 31800116].
Chakrabarti S, Jarzynski C, Thirumalai D (2019) Processivity, Velocity, and Universal Characteristics of Nucleic Acid
Unwinding by Helicases. Biophysical Journal. [IF=0.842, Cited=5, 31400912].
Mugnai ML, Caporizzo MA, Goldman YE, Thirumalai D (2020) Processivity and Velocity for Motors Stepping on Periodic
Tracks. Biophysical Journal. [IF=0.842, Cited=1, 32367805].
Houser JR, Cho HW, Hayden CC, ..., Stachowiak JC (2022) Molecular mechanisms of steric pressure generation and membrane
remodeling by disordered proteins. Biophysical Journal. [IF=0.842, Cited=5, 36016498].
Mugnai ML, Shin S, Thirumalai D (2023) Entropic contribution of ACE2 glycans to RBD binding. Biophysical Journal.
[IF=0.842, Cited=0, 37149733].
Dey A, Shi G, Takaki R, Thirumalai D (2023) Structural changes in chromosomes driven by multiple condensin motors during
mitosis. Cell Reports. [IF=1.738, Cited=2, 37027299].
Koculi E, Thirumalai D (2021) Retardation of Folding Rates of Substrate Proteins in the Nanocage of GroEL. Biochemistry.
[IF=0.753, Cited=2, 33464880].
Mugnai ML, Thirumalai D (2021) Molecular Transfer Model for pH Effects on Intrinsically Disordered Proteins: Theory and
Applications. Journal of Chemical Theory and Computation. [IF=1.512, Cited=2, 33566618].
Chakraborty D, Mondal B, Thirumalai D (2024) Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for
Simulations of DNA-Protein Complexes. Journal of Chemical Theory and Computation. [IF=1.512, Cited=1, 38241144].
Chakraborty D, Hori N, Thirumalai D (2018) Sequence-Dependent Three Interaction Site Model for Single- and Double-
Stranded DNA. Journal of Chemical Theory and Computation. [IF=1.512, Cited=20, 29870236].
Nguyen HT, Thirumalai D (2020) Charge Density of Cation Determines Inner versus Outer Shell Coordination to Phosphate in
RNA. Journal of Physical Chemistry B. [IF=0.893, Cited=7, 32342689].
Mugnai ML, Thirumalai D (2021) Step-Wise Hydration of Magnesium by Four Water Molecules Precedes Phosphate Release in a
Myosin Motor. Journal of Physical Chemistry B. [IF=0.893, Cited=3, 33481593].
Suvlu D, Thirumalai D, Rasaiah JC (2021) Water-Mediated Interactions Determine Helix Formation of Peptides in Open
Nanotubes. Journal of Physical Chemistry B. [IF=0.893, Cited=0, 33464101].
Hasnain S, Mugnai ML, Thirumalai D (2021) Effects of Gold Nanoparticles on the Stepping Trajectories of Kinesin. Journal
of Physical Chemistry B. [IF=0.893, Cited=2, 34499499].
Qin M, Denesyuk N, Liu Z, ..., Thirumalai D (2021) Temperature and Guanidine Hydrochloride Effects on the Folding
Thermodynamics of WW Domain and Variants. Journal of Physical Chemistry B. [IF=0.893, Cited=0, 34612657].
Liu Z, Thirumalai D (2022) Residue-Dependent Transition Temperatures and Denaturant Midpoints in the Folding of a
Multidomain Protein. Journal of Physical Chemistry B. [IF=0.893, Cited=0, 36512486].
Hinczewski M, Thirumalai D (2016) Noise Control in Gene Regulatory Networks with Negative Feedback. Journal of Physical
Chemistry B. [IF=0.893, Cited=2, 27095600].
Liu Z, Thirumalai D (2018) Denaturants Alter the Flux through Multiple Pathways in the Folding of PDZ Domain. Journal of
Physical Chemistry B. [IF=0.893, Cited=3, 29303586].
Baul U, Chakraborty D, Mugnai ML, ..., Thirumalai D (2019) Sequence Effects on Size, Shape, and Structural Heterogeneity
in Intrinsically Disordered Proteins. Journal of Physical Chemistry B. [IF=0.893, Cited=59, 30913885].
Kumar A, Chakraborty D, Mugnai ML, ..., Thirumalai D (2021) Sequence Determines the Switch in the Fibril Forming Regions
in the Low-Complexity FUS Protein and Its Variants. Journal of Physical Chemistry Letters. [IF=1.158, Cited=9, 34516126].
Suvlu D, Samaratunga S, Thirumalai D, Rasaiah JC (2017) Thermodynamics of Helix-Coil Transitions of Polyalanine in Open
Carbon Nanotubes. Journal of Physical Chemistry Letters. [IF=1.158, Cited=1, 28060517].
Liu Z, Thirumalai D (2022) Cooperativity and Folding Kinetics in a Multidomain Protein with Interwoven Chain Topology.
ACS Central Science. [IF=2.363, Cited=3, 35756371].
Houser JR, Hayden CC, Thirumalai D, Stachowiak JC (2020) A Förster Resonance Energy Transfer-Based Sensor of Steric
Pressure on Membrane Surfaces. Journal of the American Chemical Society. [IF=2.573, Cited=9, 33237768].
Zeno WF, Baul U, Snead WT, ..., Stachowiak JC (2018) Synergy between intrinsically disordered domains and structured
proteins amplifies membrane curvature sensing. Nature Communications. [IF=3.268, Cited=51, 30297718].
Takaki R, Dey A, Shi G, Thirumalai D (2021) Theory and simulations of condensin mediated loop extrusion in DNA. Nature
Communications. [IF=3.268, Cited=10, 34620869].
Nguyen HT, Hori N, Thirumalai D (2022) Condensates in RNA repeat sequences are heterogeneously organized and exhibit
reptation dynamics. Nature Chemistry. [IF=3.667, Cited=15, 35501484].
Toan NM, Thirumalai D (2018) Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states.
Journal of Chemical Physics. [IF=1.184, Cited=2, 29604893].
Mugnai ML, Thirumalai D (2023) Allosteric communication between ACE2 active site and binding interface with SARS-CoV-2.
Journal of Chemical Physics. [IF=1.184, Cited=1, 37260139].
Nguyen HT, Hori N, Thirumalai D (2019) 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. [IF=2.765, Cited=25, 31570624].
Takaki R, Mugnai ML, Goldtzvik Y, Thirumalai D (2019) 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.
[IF=2.765, Cited=6, 31659052].
Chakraborty D, Straub JE, Thirumalai D (2020) Differences in the free energies between the excited states of Aβ40
and Aβ42 monomers encode their aggregation propensities. Proceedings of the National Academy of Sciences of the
United States of America. [IF=2.765, Cited=25, 32732434].
Takaki R, Mugnai ML, Thirumalai D (2022) Information flow, gating, and energetics in dimeric molecular motors.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=4, 36343226].
Song Y, Thirumalai D, Hyeon C (2022) Moderate activity of RNA chaperone maximizes the yield of self-spliced pre-RNA in
vivo. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=0, 36442111].
Maity H, Nguyen HT, Hori N, Thirumalai D (2023) Odd-even disparity in the population of slipped hairpins in RNA repeat
sequences with implications for phase separation. Proceedings of the National Academy of Sciences of the United States
of America. [IF=2.765, Cited=1, 37276412].
Shin S, Shi G, Cho HW, Thirumalai D (2024) Transcription-induced active forces suppress chromatin motion. Proceedings of
the National Academy of Sciences of the United States of America. [IF=2.765, Cited=2, 38489381].
Mugnai ML, Templeton C, Elber R, Thirumalai D (2020) Role of Long-range Allosteric Communication in Determining the
Stability and Disassembly of SARS-COV-2 in Complex with ACE2. None. [IF=None, Cited=0, 33299995].
Chakraborty D, Mondal B, Thirumalai D (2023) Brewing COFFEE: A sequence-specific coarse-grained energy function for
simulations of DNA-protein complexes. None. [IF=None, Cited=0, 37333386].
Samanta HS, Hinczewski M, Thirumalai D (2017) Optimal information transfer in enzymatic networks: A field theoretic
formulation. Physical Review E. [IF=0.912, Cited=1, 29347079].
Chakraborty D, Straub JE, Thirumalai D (2023) Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald's
rule of stages. Science advances. [IF=2.861, Cited=7, 36947617].
Morrison G, Thirumalai D (2024) Scaling regimes for wormlike chains confined to cylindrical surfaces under tension.
European Physical Journal E. [IF=0.567, Cited=0, 38252375].
Liu L, Shi G, Thirumalai D, Hyeon C (2018) Chain organization of human interphase chromosome determines the
spatiotemporal dynamics of chromatin loci. PLoS Computational Biology. [IF=1.278, Cited=33, 30507936].
Thirumalai D, Kumar A, Chakraborty D, ..., Mugnai ML (2023) Conformational Fluctuations and Phases in Fused in Sarcoma
(FUS) Low-Complexity Domain. None. [IF=None, Cited=0, 36945688].

Publication with MISMATCHING institution:

Ragavi SP, Thirumalai D, Asharani IV (2024) A Review on Small Organic Colorimetric and Fluorescent Hosts for the
Detection of Cobalt and Nickel Ion. Journal of Fluorescence. [IF=0.623, Cited=0, 38884827].
Denesyuk NA, Thirumalai D (2013) Entropic stabilization of the folded states of RNA due to macromolecular crowding.
Biophysical Reviews. [IF=1.227, Cited=11, 28510164].
Thirumalai D, Klimov DK (1999) Deciphering the timescales and mechanisms of protein folding using minimal off-lattice
models. Current Opinion in Structural Biology. [IF=1.4, Cited=88, 10322218].
Thirumalai D, Klimov DK (1998) Fishing for folding nuclei in lattice models and proteins. None. [IF=None, Cited=14, 9889171].
Lin JC, Yoon J, Hyeon C, Thirumalai D (2015) Using simulations and kinetic network models to reveal the dynamics and
functions of riboswitches. None. [IF=None, Cited=6, 25726468].
Pantelopulos GA, Straub JE, Thirumalai D, Sugita Y (2018) Structure of APP-C99_1-99 and implications for role
of extra-membrane domains in function and oligomerization. Biochimica et Biophysica Acta - Biomembranes. [IF=0.915,
Cited=19, 29702072].
Pincus DL, Chakrabarti S, Thirumalai D (2015) Helicase processivity and not the unwinding velocity exhibits universal
increase with force. Biophysical Journal. [IF=0.842, Cited=14, 26200858].
Thirumalai D, Shi G (2016) Chromatin Is Stretched but Intact When the Nucleus Is Squeezed through Constrictions.
Biophysical Journal. [IF=0.842, Cited=0, 27989542].
Hori N, Denesyuk NA, Thirumalai D (2019) Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent. Biophysical
Journal. [IF=0.842, Cited=11, 31130233].
Malmi-Kakkada AN, Sinha S, Li X, Thirumalai D (2022) Adhesion strength between cells regulate nonmonotonic growth by a
biomechanical feedback mechanism. Biophysical Journal. [IF=0.842, Cited=5, 35505608].
Katava M, Shi G, Thirumalai D (2022) Chromatin dynamics controls epigenetic domain formation. Biophysical Journal.
[IF=0.842, Cited=10, 35799447].
Zhuravlev PI, Reddy G, Straub JE, Thirumalai D (2014) Propensity to form amyloid fibrils is encoded as excitations in
the free energy landscape of monomeric proteins. Journal of Molecular Biology. [IF=1.281, Cited=22, 24846645].
Hori N, Denesyuk NA, Thirumalai D (2016) Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under
Tension. Journal of Molecular Biology. [IF=1.281, Cited=13, 27315694].
Chakrabarti S, Hinczewski M, Thirumalai D (2016) Phenomenological and microscopic theories for catch bonds. Journal of
Structural Biology. [IF=0.773, Cited=25, 27046010].
Thirumalai D, Liu Z, O'Brien EP, Reddy G (2012) Protein folding: from theory to practice. Current Opinion in Structural
Biology. [IF=1.4, Cited=19, 23266001].
Thirumalai D, Zhang Z (2010) Myosin VI: how do charged tails exert control? Structure. [IF=1.155, Cited=3, 21070937].
Goldtzvik Y, Mugnai ML, Thirumalai D (2018) Dynamics of Allosteric Transitions in Dynein. Structure. [IF=1.155,
Cited=4, 30270176].
Thirumalai D, Samanta HS, Maity H, Reddy G (2019) Universal Nature of Collapsibility in the Context of Protein Folding
and Evolution. Trends in Biochemical Sciences. [IF=2.462, Cited=17, 31153683].
Thirumalai D, Klimov DK, Dima RI (2003) Emerging ideas on the molecular basis of protein and peptide aggregation.
Current Opinion in Structural Biology. [IF=1.4, Cited=178, 12727507].
Thirumalai D, Woodson SA (2000) Maximizing RNA folding rates: a balancing act. RNA. [IF=0.956, Cited=35, 10864039].
Thirumalai D, Hyeon C, Zhuravlev PI, Lorimer GH (2019) Symmetry, Rigidity, and Allosteric Signaling: From Monomeric
Proteins to Molecular Machines. Chemical Reviews. [IF=11.712, Cited=30, 31017391].
Dutta S, Maity B, Thirumalai D, Koley D (2018) Computational Investigation of Carbene-Phosphinidenes: Correlation
between ³¹P Chemical Shifts and Bonding Features to Estimate the π-Backdonation of Carbenes. Inorganic
Chemistry. [IF=0.986, Cited=9, 29528628].
Goldtzvik Y, Thirumalai D (2021) Multiscale Coarse-Grained Model for the Stepping of Molecular Motors with Application
to Kinesin. Journal of Chemical Theory and Computation. [IF=1.512, Cited=2, 34251798].
Mondal B, Chakraborty D, Hori N, ..., Thirumalai D (2024) Competition between Stacking and Divalent Cation-Mediated
Electrostatic Interactions Determines the Conformations of Short DNA Sequences. Journal of Chemical Theory and
Computation. [IF=1.512, Cited=0, 38498914].
Mondal T, Dutta S, De S, ..., Koley D (2019) Donor Stabilized Diatomic Gr.14 E₂ (E = C-Pb) Molecule
D-E₂-D (D = NHC, aNHC, ^NNHC, NHSi, NHGe, cAAC, cAASi, cAAGe): A Theoretical Insight. Journal of
Physical Chemistry A. [IF=0.841, Cited=2, 30562460].
Kirmizialtin S, Pitici F, Cardenas AE, ..., Thirumalai D (2020) Dramatic Shape Changes Occur as Cytochrome c
Folds. Journal of Physical Chemistry B. [IF=0.893, Cited=1, 32840372].
Zhuravlev PI, Hinczewski M, Thirumalai D (2021) Low Force Unfolding of a Single-Domain Protein by Parallel Pathways.
Journal of Physical Chemistry B. [IF=0.893, Cited=0, 33565314].
Mondal B, Thirumalai D, Reddy G (2021) Energy Landscape of Ubiquitin Is Weakly Multidimensional. Journal of Physical
Chemistry B. [IF=0.893, Cited=0, 34319720].
Thirumalai D (2021) Autobiography of Dave Thirumalai. Journal of Physical Chemistry B. [IF=0.893, Cited=0, 34965731].
Cho SS, Green AT, Hyeon C, Thirumalai D (2023) TMAO Destabilizes RNA Secondary Structure via Direct Hydrogen Bond
Interactions. Journal of Physical Chemistry B. [IF=0.893, Cited=1, 36602908].
Reddy G, Thirumalai D (2015) Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model. Journal of Physical
Chemistry B. [IF=0.893, Cited=14, 26131594].
Goldtzvik Y, Zhang Z, Thirumalai D (2016) Importance of Hydrodynamic Interactions in the Stepping Kinetics of Kinesin.
Journal of Physical Chemistry B. [IF=0.893, Cited=7, 26702870].
Liu Z, Reddy G, Thirumalai D (2016) Folding PDZ2 Domain Using the Molecular Transfer Model. Journal of Physical
Chemistry B. [IF=0.893, Cited=8, 26926418].
Hyeon C, Thirumalai D (2016) Ripping RNA by Force Using Gaussian Network Models. Journal of Physical Chemistry B.
[IF=0.893, Cited=1, 28423909].
Reddy G, Thirumalai D (2017) Collapse Precedes Folding in Denaturant-Dependent Assembly of Ubiquitin. Journal of
Physical Chemistry B. [IF=0.893, Cited=15, 28076957].
Chen J, Thirumalai D (2018) Interface Residues That Drive Allosteric Transitions Also Control the Assembly of l-Lactate
Dehydrogenase. Journal of Physical Chemistry B. [IF=0.893, Cited=1, 30102042].
Hori N, Denesyuk NA, Thirumalai D (2018) Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover. Journal of
Physical Chemistry B. [IF=0.893, Cited=2, 30179471].
Denesyuk NA, Hori N, Thirumalai D (2018) Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding.
Journal of Physical Chemistry B. [IF=0.893, Cited=11, 30468380].
Maity H, Nguyen HT, Hori N, Thirumalai D (2024) Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences.
Journal of Physical Chemistry Letters. [IF=1.158, Cited=0, 38557079].
Samanta HS, Mugnai ML, Kirkpatrick TR, Thirumalai D (2019) Giant Casimir Nonequilibrium Forces Drive Coil to Globule
Transition in Polymers. Journal of Physical Chemistry Letters. [IF=1.158, Cited=1, 31066561].
Thirumalai D, Reddy G, Straub JE (2011) Role of water in protein aggregation and amyloid polymorphism. Accounts of
Chemical Research. [IF=3.533, Cited=127, 21761818].
Perez-Salas UA, Rangan P, Krueger S, ..., Woodson SA (2004) Compaction of a bacterial group I ribozyme coincides with
the assembly of core helices. Biochemistry. [IF=0.753, Cited=42, 14769052].
Thirumalai D, Hyeon C (2005) RNA and protein folding: common themes and variations. Biochemistry. [IF=0.753, Cited=159, 15794634].
Chen J, Thirumalai D (2012) Helices 2 and 3 are the initiation sites in the PrP(C) → PrP(SC) transition. Biochemistry.
[IF=0.753, Cited=14, 23256626].
O'Brien EP, Brooks BR, Thirumalai D (2009) Molecular origin of constant m-values, denatured state collapse, and residue-
dependent transition midpoints in globular proteins. Biochemistry. [IF=0.753, Cited=34, 19278261].
Mountain RD, Thirumalai D (2003) Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in
water and aqueous urea solution. Journal of the American Chemical Society. [IF=2.573, Cited=46, 12580622].
Caliskan G, Briber RM, Thirumalai D, ..., Sokolov AP (2006) Dynamic transition in tRNA is solvent induced. Journal of
the American Chemical Society. [IF=2.573, Cited=53, 16390107].
Vaitheeswaran S, Thirumalai D (2006) Hydrophobic and ionic interactions in nanosized water droplets. Journal of the
American Chemical Society. [IF=2.573, Cited=30, 17031962].
Tarus B, Straub JE, Thirumalai D (2006) Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers. Journal of
the American Chemical Society. [IF=2.573, Cited=96, 17165769].
Koculi E, Hyeon C, Thirumalai D, Woodson SA (2007) Charge density of divalent metal cations determines RNA stability.
Journal of the American Chemical Society. [IF=2.573, Cited=86, 17295487].
O'Brien EP, Dima RI, Brooks B, Thirumalai D (2007) Interactions between hydrophobic and ionic solutes in aqueous
guanidinium chloride and urea solutions: lessons for protein denaturation mechanism. Journal of the American Chemical
Society. [IF=2.573, Cited=132, 17503819].
Hyeon C, Thirumalai D (2008) Multiple probes are required to explore and control the rugged energy landscape of RNA
hairpins. Journal of the American Chemical Society. [IF=2.573, Cited=31, 18186635].
Pincus DL, Hyeon C, Thirumalai D (2008) Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of
RNA hairpins. Journal of the American Chemical Society. [IF=2.573, Cited=35, 18479134].
Denesyuk NA, Thirumalai D (2011) Crowding promotes the switch from hairpin to pseudoknot conformation in human
telomerase RNA. Journal of the American Chemical Society. [IF=2.573, Cited=46, 21736319].
O'Brien EP, Brooks BR, Thirumalai D (2011) Effects of pH on proteins: predictions for ensemble and single-molecule
pulling experiments. Journal of the American Chemical Society. [IF=2.573, Cited=36, 22148729].
Biyun S, Cho SS, Thirumalai D (2011) Folding of human telomerase RNA pseudoknot using ion-jump and temperature-quench
simulations. Journal of the American Chemical Society. [IF=2.573, Cited=21, 22082261].
Yoon J, Thirumalai D, Hyeon C (2013) Urea-induced denaturation of preQ1-riboswitch. Journal of the American Chemical
Society. [IF=2.573, Cited=19, 23863126].
Lin JC, Thirumalai D (2013) Kinetics of allosteric transitions in S-adenosylmethionine riboswitch are accurately
predicted from the folding landscape. Journal of the American Chemical Society. [IF=2.573, Cited=13, 24087850].
Dominguez L, Foster L, Meredith SC, ..., Thirumalai D (2014) Structural heterogeneity in transmembrane amyloid precursor
protein homodimer is a consequence of environmental selection. Journal of the American Chemical Society. [IF=2.573,
Cited=21, 24926593].
Lin JC, Thirumalai D (2008) Relative stability of helices determines the folding landscape of adenine riboswitch
aptamers. Journal of the American Chemical Society. [IF=2.573, Cited=46, 18828635].
Miyashita N, Straub JE, Thirumalai D, Sugita Y (2009) Transmembrane structures of amyloid precursor protein dimer
predicted by replica-exchange molecular dynamics simulations. Journal of the American Chemical Society. [IF=2.573,
Cited=46, 19275251].
Miyashita N, Straub JE, Thirumalai D (2009) 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. [IF=2.573, Cited=50, 19995075].
Priyakumar UD, Hyeon C, Thirumalai D, Mackerell AD (2009) Urea destabilizes RNA by forming stacking interactions and
multiple hydrogen bonds with nucleic acid bases. Journal of the American Chemical Society. [IF=2.573, Cited=35, 19919063].
Kang H, Toan NM, Hyeon C, Thirumalai D (2015) Unexpected Swelling of Stiff DNA in a Polydisperse Crowded Environment.
Journal of the American Chemical Society. [IF=2.573, Cited=13, 26267166].
Lee Y, Thirumalai D, Hyeon C (2017) Ultrasensitivity of Water Exchange Kinetics to the Size of Metal Ion. Journal of the
American Chemical Society. [IF=2.573, Cited=16, 28853881].
Kouza M, Li MS, O'brien EP, ..., Thirumalai D (2006) Effect of finite size on cooperativity and rates of protein
folding. Journal of Physical Chemistry A. [IF=0.841, Cited=32, 16405339].
Barsegov V, Thirumalai D (2005) Influence of surface interactions on folding and forced unbinding of semiflexible
chains. Journal of Physical Chemistry B. [IF=0.893, Cited=2, 16853856].
Barsegov V, Thirumalai D (2006) Dynamic competition between catch and slip bonds in selectins bound to ligands. Journal
of Physical Chemistry B. [IF=0.893, Cited=19, 17181300].
Cheung MS, Thirumalai D (2007) Effects of crowding and confinement on the structures of the transition state ensemble in
proteins. Journal of Physical Chemistry B. [IF=0.893, Cited=40, 17585794].
Toan NM, Morrison G, Hyeon C, Thirumalai D (2008) Kinetics of loop formation in polymer chains. Journal of Physical
Chemistry B. [IF=0.893, Cited=43, 18269274].
Cho SS, Reddy G, Straub JE, Thirumalai D (2011) Entropic stabilization of proteins by TMAO. Journal of Physical
Chemistry B. [IF=0.893, Cited=64, 21985427].
Kudlay A, Cheung MS, Thirumalai D (2012) Influence of the shape of crowding particles on the structural transitions in a
polymer. Journal of Physical Chemistry B. [IF=0.893, Cited=12, 22616622].
Denesyuk NA, Thirumalai D (2013) Coarse-grained model for predicting RNA folding thermodynamics. Journal of Physical
Chemistry B. [IF=0.893, Cited=67, 23527587].
Pincus DL, Thirumalai D (2013) Force-induced unzipping transitions in an athermal crowded environment. Journal of
Physical Chemistry B. [IF=0.893, Cited=4, 23789729].
Yoon J, Lin JC, Hyeon C, Thirumalai D (2014) Dynamical transition and heterogeneous hydration dynamics in RNA. Journal
of Physical Chemistry B. [IF=0.893, Cited=12, 24762118].
Chen J, Bryngelson JD, Thirumalai D (2008) Estimations of the size of nucleation regions in globular proteins. Journal
of Physical Chemistry B. [IF=0.893, Cited=7, 19367923].
Pincus DL, Thirumalai D (2009) Crowding effects on the mechanical stability and unfolding pathways of ubiquitin. Journal
of Physical Chemistry B. [IF=0.893, Cited=18, 19072020].
Reddy G, Straub JE, Thirumalai D (2009) 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. Journal of
Physical Chemistry B. [IF=0.893, Cited=75, 19125574].
O'Brien EP, Okamoto Y, Straub JE, ..., Thirumalai D (2009) Thermodynamic perspective on the dock-lock growth mechanism
of amyloid fibrils. Journal of Physical Chemistry B. [IF=0.893, Cited=48, 19813700].
Lin JC, Hyeon C, Thirumalai D (2012) RNA under tension: Folding Landscapes, Kinetic partitioning Mechanism, and
Molecular Tensegrity. Journal of Physical Chemistry Letters. [IF=1.158, Cited=7, 23336034].
Straub JE, Thirumalai D (2014) Membrane-Protein Interactions Are Key to Understanding Amyloid Formation. Journal of
Physical Chemistry Letters. [IF=1.158, Cited=13, 26276620].
Toan NM, Thirumalai D (2010) Theory of Biopolymer Stretching at High Forces. Macromolecules. [IF=1.262, Cited=6, 29225374].
O'Brien EP, Stan G, Thirumalai D, Brooks BR (2008) Factors governing helix formation in peptides confined to carbon
nanotubes. Nano Letters. [IF=1.873, Cited=16, 18817452].
Denesyuk NA, Thirumalai D (2015) How do metal ions direct ribozyme folding? Nature Chemistry. [IF=3.667, Cited=51, 26391078].
Shi G, Liu L, Hyeon C, Thirumalai D (2018) Interphase human chromosome exhibits out of equilibrium glassy dynamics.
Nature Communications. [IF=3.268, Cited=69, 30089831].
Shi G, Thirumalai D (2019) Conformational heterogeneity in human interphase chromosome organization reconciles the FISH
and Hi-C paradox. Nature Communications. [IF=3.268, Cited=18, 31467267].
Shi G, Thirumalai D (2023) A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise
distances with applications to interphase chromosomes and structural variants. Nature Communications. [IF=3.268,
Cited=3, 36854665].
Samanta HS, Zhuravlev PI, Hinczewski M, ..., Thirumalai D (2017) Protein collapse is encoded in the folded state
architecture. Soft Matter. [IF=0.97, Cited=12, 28447708].
Sinha S, Malmi-Kakkada AN, Li X, ..., Thirumalai D (2020) Spatially heterogeneous dynamics of cells in a growing tumor
spheroid: comparison between theory and experiments. Soft Matter. [IF=0.97, Cited=8, 32462163].
Sinha S, Malmi-Kakkada AN, Li X, ..., Thirumalai D (2020) Correction: Spatially heterogeneous dynamics of cells in a
growing tumor spheroid: comparison between theory and experiments. Soft Matter. [IF=0.97, Cited=0, 32602498].
Sinha S, Samanta H, Thirumalai D (2023) Observe without disturbing: tracer particles sense local stresses in cell
collectives without affecting the cancer cell dynamics. Soft Matter. [IF=0.97, Cited=0, 37417272].
Morrison G, Thirumalai D (2005) The shape of a flexible polymer in a cylindrical pore. Journal of Chemical Physics.
[IF=1.184, Cited=17, 16161617].
Hyeon C, Thirumalai D (2006) Kinetics of interior loop formation in semiflexible chains. Journal of Chemical Physics.
[IF=1.184, Cited=33, 16542102].
Hyeon C, Dima RI, Thirumalai D (2006) Size, shape, and flexibility of RNA structures. Journal of Chemical Physics.
[IF=1.184, Cited=68, 17129165].
Li MS, Klimov DK, Straub JE, Thirumalai D (2008) Probing the mechanisms of fibril formation using lattice models.
Journal of Chemical Physics. [IF=1.184, Cited=46, 19045373].
Vaitheeswaran S, Reddy G, Thirumalai D (2009) Water-mediated interactions between hydrophobic and ionic species in
cylindrical nanopores. Journal of Chemical Physics. [IF=1.184, Cited=1, 19275404].
O'Brien EP, Morrison G, Brooks BR, Thirumalai D (2009) How accurate are polymer models in the analysis of Förster
resonance energy transfer experiments on proteins? Journal of Chemical Physics. [IF=1.184, Cited=52, 19334885].
Toan NM, Thirumalai D (2012) On the origin of the unusual behavior in the stretching of single-stranded DNA. Journal of
Chemical Physics. [IF=1.184, Cited=13, 22779622].
Hyeon C, Thirumalai D (2012) Multiple barriers in forced rupture of protein complexes. Journal of Chemical Physics.
[IF=1.184, Cited=14, 22894385].
Samanta HS, Thirumalai D (2013) Exact solution of the Zwanzig-Lauritzen model of polymer crystallization under tension.
Journal of Chemical Physics. [IF=1.184, Cited=0, 23514513].
Hyeon C, Thirumalai D (2013) Generalized iterative annealing model for the action of RNA chaperones. Journal of Chemical
Physics. [IF=1.184, Cited=9, 24089736].
Gruebele M, Thirumalai D (2013) Perspective: Reaches of chemical physics in biology. Journal of Chemical Physics.
[IF=1.184, Cited=8, 24089712].
Vaitheeswaran S, Thirumalai D (2014) Entropy and enthalpy of interaction between amino acid side chains in nanopores.
Journal of Chemical Physics. [IF=1.184, Cited=0, 25494794].
Samanta HS, Chakraborty D, Thirumalai D (2018) Charge fluctuation effects on the shape of flexible polyampholytes with
applications to intrinsically disordered proteins. Journal of Chemical Physics. [IF=1.184, Cited=22, 30384718].
Sinha S, Thirumalai D (2020) Self-generated persistent random forces drive phase separation in growing tumors. Journal
of Chemical Physics. [IF=1.184, Cited=1, 33261486].
Sinha S, Li X, Das R, Thirumalai D (2022) Mechanical feedback controls the emergence of dynamical memory in growing
tissue monolayers. Journal of Chemical Physics. [IF=1.184, Cited=2, 35778098].
Dima RI, Thirumalai D (2004) Probing the instabilities in the dynamics of helical fragments from mouse PrPC. Proceedings
of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=67, 15494440].
Klimov DK, Straub JE, Thirumalai D (2004) Aqueous urea solution destabilizes Abeta(16-22) oligomers. Proceedings of the
National Academy of Sciences of the United States of America. [IF=2.765, Cited=65, 15465917].
Barsegov V, Thirumalai D (2005) 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. [IF=2.765, Cited=98, 15701706].
Hyeon C, Thirumalai D (2005) Mechanical unfolding of RNA hairpins. Proceedings of the National Academy of Sciences of
the United States of America. [IF=2.765, Cited=106, 15749822].
Cheung MS, Klimov D, Thirumalai D (2005) 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. [IF=2.765,
Cited=258, 15781864].
Li MS, Hu CK, Klimov DK, Thirumalai D (2005) 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.
[IF=2.765, Cited=36, 16373511].
Ziv G, Haran G, Thirumalai D (2005) Ribosome exit tunnel can entropically stabilize alpha-helices. Proceedings of the
National Academy of Sciences of the United States of America. [IF=2.765, Cited=81, 16357202].
Zheng W, Brooks BR, Thirumalai D (2006) 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. [IF=2.765, Cited=154, 16682636].
Stan G, Brooks BR, Lorimer GH, Thirumalai D (2006) 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. [IF=2.765, Cited=28, 16537402].
Nguyen PH, Li MS, Stock G, ..., Thirumalai D (2006) 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.
[IF=2.765, Cited=188, 17190811].
Hyeon C, Lorimer GH, Thirumalai D (2006) Dynamics of allosteric transitions in GroEL. Proceedings of the National
Academy of Sciences of the United States of America. [IF=2.765, Cited=91, 17135353].
Stan G, Lorimer GH, Thirumalai D, Brooks BR (2007) 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. [IF=2.765,
Cited=25, 17496143].
Mickler M, Dima RI, Dietz H, ..., Rief M (2007) 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. [IF=2.765, Cited=89, 18079292].
Klimov DK, Newfield D, Thirumalai D (2002) Simulations of beta-hairpin folding confined to spherical pores using
distributed computing. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765,
Cited=103, 12060748].
O'Brien EP, Ziv G, Haran G, ..., Thirumalai D (2008) 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. [IF=2.765, Cited=87, 18757747].
Hyeon C, Morrison G, Thirumalai D (2008) 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.
[IF=2.765, Cited=45, 18621721].
Vaitheeswaran S, Thirumalai D (2008) 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.
[IF=2.765, Cited=17, 19004772].
Hua L, Zhou R, Thirumalai D, Berne BJ (2008) 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.
[IF=2.765, Cited=192, 18957546].
Reddy G, Straub JE, Thirumalai D (2009) Dynamics of locking of peptides onto growing amyloid fibrils. Proceedings of the
National Academy of Sciences of the United States of America. [IF=2.765, Cited=62, 19581575].
Hyeon C, Morrison G, Pincus DL, Thirumalai D (2009) Refolding dynamics of stretched biopolymers upon force quench.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=20, 19915145].
Cho SS, Pincus DL, Thirumalai D (2009) 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.
[IF=2.765, Cited=53, 19805055].
Chen J, Darst SA, Thirumalai D (2010) Promoter melting triggered by bacterial RNA polymerase occurs in three steps.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=35, 20615963].
Reddy G, Straub JE, Thirumalai D (2010) 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.
[IF=2.765, Cited=39, 21098298].
Xia F, Thirumalai D, Gräter F (2011) 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. [IF=2.765, Cited=9, 21482804].
Liu Z, Reddy G, O'Brien EP, Thirumalai D (2011) 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.
[IF=2.765, Cited=34, 21512127].
Reddy G, Liu Z, Thirumalai D (2012) Denaturant-dependent folding of GFP. Proceedings of the National Academy of Sciences
of the United States of America. [IF=2.765, Cited=31, 22778437].
Hinczewski M, Gebhardt JCM, Rief M, Thirumalai D (2013) From mechanical folding trajectories to intrinsic energy
landscapes of biopolymers. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765,
Cited=50, 23487746].
Hinczewski M, Tehver R, Thirumalai D (2013) Design principles governing the motility of myosin V. Proceedings of the
National Academy of Sciences of the United States of America. [IF=2.765, Cited=19, 24101499].
Ramm B, Stigler J, Hinczewski M, ..., Rief M (2014) Sequence-resolved free energy profiles of stress-bearing vimentin
intermediate filaments. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765,
Cited=9, 25049381].
Chakrabarti S, Hinczewski M, Thirumalai D (2014) Plasticity of hydrogen bond networks regulates mechanochemistry of cell
adhesion complexes. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765,
Cited=26, 24927549].
Qin M, Wang W, Thirumalai D (2015) Protein folding guides disulfide bond formation. Proceedings of the National Academy
of Sciences of the United States of America. [IF=2.765, Cited=55, 26297249].
Zhuravlev PI, Hinczewski M, Chakrabarti S, ..., Thirumalai D (2016) Force-dependent switch in protein unfolding pathways
and transition-state movements. Proceedings of the National Academy of Sciences of the United States of America.
[IF=2.765, Cited=25, 26818842].
Hinczewski M, Hyeon C, Thirumalai D (2016) Directly measuring single-molecule heterogeneity using force spectroscopy.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=14, 27317744].
Zhuravlev PI, Hinczewski M, Chakrabarti S, ..., Thirumalai D (2016) Reply to Alberti: Are in vitro folding experiments
relevant in vivo? Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=0, 27226292].
Dominguez L, Foster L, Straub JE, Thirumalai D (2016) 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. [IF=2.765, Cited=33, 27559086].
Mugnai ML, Thirumalai D (2017) Kinematics of the lever arm swing in myosin VI. Proceedings of the National Academy of
Sciences of the United States of America. [IF=2.765, Cited=6, 28512223].
Zhang Z, Goldtzvik Y, Thirumalai D (2017) 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.
[IF=2.765, Cited=18, 29087307].
Chakrabarti S, Hyeon C, Ye X, ..., Thirumalai D (2017) 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. [IF=2.765, Cited=19, 29217641].
Roca J, Hori N, Baral S, ..., Ansari A (2018) 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. [IF=2.765, Cited=9, 30012621].
Litvinov RI, Kononova O, Zhmurov A, ..., Weisel JW (2018) 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.
[IF=2.765, Cited=12, 30087181].
Hyeon C, Thirumalai D (2003) 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. [IF=2.765,
Cited=67, 12934020].
Hori N, Denesyuk NA, Thirumalai D (2021) Shape changes and cooperativity in the folding of the central domain of the 16S
ribosomal RNA. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=9, 33658370].
Thirumalai D, Klimov DK, Lorimer GH (2003) Caging helps proteins fold. Proceedings of the National Academy of Sciences
of the United States of America. [IF=2.765, Cited=45, 14506295].
Pantelopulos GA, Matsuoka D, Hutchison JM, ..., Thirumalai D (2022) Formation of extramembrane β-strands controls
dimerization of transmembrane helices in amyloid precursor protein C99. Proceedings of the National Academy of Sciences
of the United States of America. [IF=2.765, Cited=0, 36538482].
Honeycutt JD, Thirumalai D (1990) Metastability of the folded states of globular proteins. Proceedings of the National
Academy of Sciences of the United States of America. [IF=2.765, Cited=147, 2333297].
Camacho CJ, Thirumalai D (1993) Kinetics and thermodynamics of folding in model proteins. Proceedings of the National
Academy of Sciences of the United States of America. [IF=2.765, Cited=202, 8327519].
Straub JE, Thirumalai D (1993) Exploring the energy landscape in proteins. Proceedings of the National Academy of
Sciences of the United States of America. [IF=2.765, Cited=35, 8430090].
Camacho CJ, Thirumalai D (1995) 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. [IF=2.765, Cited=53, 7533290].
Todd MJ, Lorimer GH, Thirumalai D (1996) 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.
[IF=2.765, Cited=151, 8633011].
Mountain RD, Thirumalai D (1998) Hydration for a series of hydrocarbons. Proceedings of the National Academy of Sciences
of the United States of America. [IF=2.765, Cited=16, 9671695].
Thirumalai D (1998) 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. [IF=2.765, Cited=30, 9751694].
Pan J, Thirumalai D, Woodson SA (1999) 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. [IF=2.765, Cited=54, 10339556].
Klimov DK, Thirumalai D (1999) 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. [IF=2.765, Cited=57, 10339559].
Klimov DK, Thirumalai D (2000) Native topology determines force-induced unfolding pathways in globular proteins.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=108, 10860990].
Klimov DK, Thirumalai D (2000) Mechanisms and kinetics of beta-hairpin formation. Proceedings of the National Academy of
Sciences of the United States of America. [IF=2.765, Cited=144, 10716988].
Thirumalai D (2014) Universal relations in the self-assembly of proteins and RNA. Physical Biology. [IF=0.648, Cited=2, 25292483].
Dunlavy DM, O'Leary DP, Klimov D, Thirumalai D (2005) HOPE: a homotopy optimization method for protein structure
prediction. Journal of Computational Biology. [IF=0.499, Cited=7, 16379534].
Dima RI, Thirumalai D (2004) Proteins associated with diseases show enhanced sequence correlation between charged
residues. Bioinformatics. [IF=1.954, Cited=14, 15073020].
Reddy G, Thirumalai D (2021) Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a
nucleosome. Nucleic Acids Research. [IF=4.663, Cited=3, 33877361].
Hori N, Thirumalai D (2023) Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and
topological frustration one molecule at a time. Nucleic Acids Research. [IF=4.663, Cited=2, 37758176].
Li X, Thirumalai D (2019) Share, but unequally: a plausible mechanism for emergence and maintenance of intratumour
heterogeneity. Journal of the Royal Society Interface. [IF=1.305, Cited=6, 30958159].
Li X, Thirumalai D (2022) A mathematical model for phenotypic heterogeneity in breast cancer with implications for
therapeutic strategies. Journal of the Royal Society Interface. [IF=1.305, Cited=5, 35078336].
Thirumalai D, Hyeon C (2018) Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL:
implications for iterative annealing of misfolded proteins. Philosophical Transactions of the Royal Society B:
Biological Sciences. [IF=1.629, Cited=6, 29735736].
Li X, Huebner RJ, Williams MLK, ..., Thirumalai D (2024) Emergence of cellular nematic order is a conserved feature of
gastrulation in animal embryos. None. [IF=None, Cited=0, 39071444].
Cho HW, Mugnai ML, Kirkpatrick TR, Thirumalai D (2020) Fragile-to-strong crossover, growing length scales, and dynamic
heterogeneity in Wigner glasses. Physical Review E. [IF=0.912, Cited=1, 32290023].
Samanta HS, Thirumalai D (2019) Origin of superdiffusive behavior in a class of nonequilibrium systems. Physical Review
E. [IF=0.912, Cited=0, 30999548].
Hyeon C, Hinczewski M, Thirumalai D (2014) Evidence of disorder in biological molecules from single molecule pulling
experiments. Physical Review Letters. [IF=2.288, Cited=12, 24745458].
Kang H, Pincus PA, Hyeon C, Thirumalai D (2015) Effects of macromolecular crowding on the collapse of biopolymers.
Physical Review Letters. [IF=2.288, Cited=41, 25723249].
Kang H, Yoon YG, Thirumalai D, Hyeon C (2015) Confinement-Induced Glassy Dynamics in a Model for Chromosome
Organization. Physical Review Letters. [IF=2.288, Cited=32, 26588418].
Vu HT, Chakrabarti S, Hinczewski M, Thirumalai D (2016) Discrete Step Sizes of Molecular Motors Lead to Bimodal Non-
Gaussian Velocity Distributions under Force. Physical Review Letters. [IF=2.288, Cited=7, 27564000].
Cho HW, Shi G, Kirkpatrick TR, Thirumalai D (2021) Random First Order Transition Theory for Glassy Dynamics in a Single
Condensed Polymer. Physical Review Letters. [IF=2.288, Cited=1, 33861095].
Vu HT, Zhang Z, Tehver R, Thirumalai D (2022) Plus and minus ends of microtubules respond asymmetrically to kinesin
binding by a long-range directionally driven allosteric mechanism. Science advances. [IF=2.861, Cited=2, 35417226].
Henning-Knechtel A, Thirumalai D, Kirmizialtin S (2022) Differences in ion-RNA binding modes due to charge density
variations explain the stability of RNA in monovalent salts. Science advances. [IF=2.861, Cited=6, 35857829].
Wolynes PG, Onuchic JN, Thirumalai D (1995) Response. Science. [IF=7.729, Cited=2, 17774212].
Thirumalai D, O'Brien EP, Morrison G, Hyeon C (2010) Theoretical perspectives on protein folding. Annual Review of
Biophysics. [IF=3.276, Cited=105, 20192765].
Straub JE, Thirumalai D (2011) Toward a molecular theory of early and late events in monomer to amyloid fibril
formation. Annual Review of Physical Chemistry. [IF=3.733, Cited=120, 21219143].
Thirumalai D, Lorimer GH (2001) Chaperonin-mediated protein folding. None. [IF=None, Cited=243, 11340060].
Thirumalai D, Lee N, Woodson SA, Klimov D (2001) Early events in RNA folding. Annual Review of Physical Chemistry.
[IF=3.733, Cited=121, 11326079].
Guan X, Tan C, Li W, ..., Thirumalai D (2022) Role of water-bridged interactions in metal ion coupled protein allostery.
PLoS Computational Biology. [IF=1.278, Cited=1, 35653400].
Thirumalai D, Klimov DK (2007) Intermediates and transition states in protein folding. Methods in Molecular Biology.
[IF=0.413, Cited=8, 16957328].
Stan G, Lorimer GH, Thirumalai D (2022) Friends in need: How chaperonins recognize and remodel proteins that require
folding assistance. Frontiers in Molecular Biosciences. [IF=0.92, Cited=4, 36479385].
Hathcock D, Tehver R, Hinczewski M, Thirumalai D (2020) Myosin V executes steps of variable length via structurally
constrained diffusion. eLife. [IF=1.743, Cited=2, 31939739].
Huebner RJ, Malmi-Kakkada AN, Sarıkaya S, ..., Wallingford JB (2021) Mechanical heterogeneity along single cell-cell
junctions is driven by lateral clustering of cadherins during vertebrate axis elongation. eLife. [IF=1.743, Cited=21, 34032216].
Das R, Sinha S, Li X, ..., Thirumalai D (2024) Free volume theory explains the unusual behavior of viscosity in a non-
confluent tissue during morphogenesis. eLife. [IF=1.743, Cited=0, 38241331].
Jeong D, Shi G, Li X, Thirumalai D (2024) Structural basis for the preservation of a subset of topologically associating
domains in interphase chromosomes upon cohesin depletion. eLife. [IF=1.743, Cited=0, 38502563].
Li X, Huebner RJ, Williams MLK, ..., Thirumalai D (2024) Emergence of cellular nematic order is a conserved feature of
gastrulation in animal embryos. None. [IF=None, Cited=0, 39070041].

Publication with MISSING institution:

Klimov DK, Thirumalai D (1996) Factors governing the foldability of proteins. Proteins: Structure, Function and
Bioinformatics. [IF=0.897, Cited=67, 8990496].
Honeycutt JD, Thirumalai D (1992) The nature of folded states of globular proteins. Biopolymers. [IF=0.522, Cited=161, 1643270].
Klimov DK, Thirumalai D (2002) Is there a unique melting temperature for two-state proteins? Journal of Computational
Chemistry. [IF=1.045, Cited=14, 11913382].
Camacho CJ, Thirumalai D (1996) Denaturants can accelerate folding rates in a class of globular proteins. Protein
Science. [IF=1.97, Cited=15, 8880906].
Klimov DK, Thirumalai D (2001) Multiple protein folding nuclei and the transition state ensemble in two-state proteins.
Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=51, 11340662].
Buchete NV, Straub JE, Thirumalai D (2008) Dissecting contact potentials for proteins: relative contributions of
individual amino acids. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=8, 17640067].
Liu Z, Chen J, Thirumalai D (2009) On the accuracy of inferring energetic coupling between distant sites in protein
families from evolutionary imprints: illustrations using lattice model. Proteins: Structure, Function and
Bioinformatics. [IF=0.897, Cited=18, 19639636].
Straub JE, Thirumalai D (1993) Theoretical probes of conformational fluctuations in S-peptide and RNase A/3'-UMP enzyme
product complex. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=8, 8460107].
Camacho CJ, Thirumalai D (1995) Modeling the role of disulfide bonds in protein folding: entropic barriers and pathways.
Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=44, 7675784].
Guo Z, Thirumalai D (1996) Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein.
Journal of Molecular Biology. [IF=1.281, Cited=97, 8913310].
Mohanty D, Elber R, Thirumalai D, ..., Roux B (1997) Kinetics of peptide folding: computer simulations of SYPFDV and
peptide variants in water. Journal of Molecular Biology. [IF=1.281, Cited=43, 9325101].
Pan J, Thirumalai D, Woodson SA (1997) Folding of RNA involves parallel pathways. Journal of Molecular Biology.
[IF=1.281, Cited=114, 9367740].
Klimov DK, Thirumalai D (1998) Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse
mechanism. Journal of Molecular Biology. [IF=1.281, Cited=54, 9735420].
Betancourt MR, Thirumalai D (1999) Exploring the kinetic requirements for enhancement of protein folding rates in the
GroEL cavity. Journal of Molecular Biology. [IF=1.281, Cited=86, 10092464].
Heilman-Miller SL, Thirumalai D, Woodson SA (2001) Role of counterion condensation in folding of the Tetrahymena
ribozyme. I. Equilibrium stabilization by cations. Journal of Molecular Biology. [IF=1.281, Cited=105, 11237624].
Heilman-Miller SL, Pan J, Thirumalai D, Woodson SA (2001) Role of counterion condensation in folding of the Tetrahymena
ribozyme. II. Counterion-dependence of folding kinetics. Journal of Molecular Biology. [IF=1.281, Cited=75, 11491301].
Klimov DK, Thirumalai D (2002) Stiffness of the distal loop restricts the structural heterogeneity of the transition
state ensemble in SH3 domains. Journal of Molecular Biology. [IF=1.281, Cited=40, 11955020].
Dima RI, Thirumalai D (2002) Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and
sequence alignments. Biophysical Journal. [IF=0.842, Cited=48, 12202354].
Lee NK, Thirumalai D (2004) Pulling-speed-dependent force-extension profiles for semiflexible chains. Biophysical
Journal. [IF=0.842, Cited=17, 15111385].
Pincus DL, Cho SS, Hyeon C, Thirumalai D (2008) Minimal models for proteins and RNA from folding to function. None.
[IF=None, Cited=17, 19121703].
Veitshans T, Klimov D, Thirumalai D (1997) Protein folding kinetics: timescales, pathways and energy landscapes in terms
of sequence-dependent properties. None. [IF=None, Cited=191, 9080195].
Guo Z, Thirumalai D (1997) The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the
folding nucleus. None. [IF=None, Cited=36, 9427012].
Denning EJ, Thirumalai D, MacKerell AD (2013) Protonation of trimethylamine N-oxide (TMAO) is required for stabilization
of RNA tertiary structure. Biophysical Chemistry. [IF=0.78, Cited=12, 24012912].
Roh JH, Briber RM, Damjanovic A, ..., Sokolov AP (2009) Dynamics of tRNA at different levels of hydration. Biophysical
Journal. [IF=0.842, Cited=31, 19348758].
Zheng W, Thirumalai D (2009) Coupling between normal modes drives protein conformational dynamics: illustrations using
allosteric transitions in myosin II. Biophysical Journal. [IF=0.842, Cited=33, 19289039].
Rivera E, Straub J, Thirumalai D (2009) Sequence and crowding effects in the aggregation of a 10-residue fragment
derived from islet amyloid polypeptide. Biophysical Journal. [IF=0.842, Cited=23, 19486677].
Hyeon C, Thirumalai D (2012) Chain length determines the folding rates of RNA. Biophysical Journal. [IF=0.842,
Cited=26, 22325296].
Lin JC, Thirumalai D (2012) Gene regulation by riboswitches with and without negative feedback loop. Biophysical
Journal. [IF=0.842, Cited=7, 23283231].
Koculi E, Lee NK, Thirumalai D, Woodson SA (2004) Folding of the Tetrahymena ribozyme by polyamines: importance of
counterion valence and size. Journal of Molecular Biology. [IF=1.281, Cited=42, 15312760].
Tarus B, Straub JE, Thirumalai D (2004) Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing
the propensity for peptide dimerization. Journal of Molecular Biology. [IF=1.281, Cited=59, 15644211].
Dima RI, Hyeon C, Thirumalai D (2005) Extracting stacking interaction parameters for RNA from the data set of native
structures. Journal of Molecular Biology. [IF=1.281, Cited=36, 15733917].
Stan G, Brooks BR, Thirumalai D (2005) Probing the "annealing" mechanism of GroEL minichaperone using molecular dynamics
simulations. Journal of Molecular Biology. [IF=1.281, Cited=16, 15967467].
Chauhan S, Caliskan G, Briber RM, ..., Woodson SA (2005) RNA tertiary interactions mediate native collapse of a
bacterial group I ribozyme. Journal of Molecular Biology. [IF=1.281, Cited=50, 16214167].
Klimov DK, Thirumalai D (2005) Symmetric connectivity of secondary structure elements enhances the diversity of folding
pathways. Journal of Molecular Biology. [IF=1.281, Cited=37, 16219323].
Cheung MS, Thirumalai D (2006) Nanopore-protein interactions dramatically alter stability and yield of the native state
in restricted spaces. Journal of Molecular Biology. [IF=1.281, Cited=38, 16427652].
Koculi E, Thirumalai D, Woodson SA (2006) Counterion charge density determines the position and plasticity of RNA
folding transition states. Journal of Molecular Biology. [IF=1.281, Cited=30, 16626736].
Chen J, Dima RI, Thirumalai D (2007) Allosteric communication in dihydrofolate reductase: signaling network and pathways
for closed to occluded transition and back. Journal of Molecular Biology. [IF=1.281, Cited=41, 17916364].
Tehver R, Thirumalai D (2008) Kinetic model for the coupling between allosteric transitions in GroEL and substrate
protein folding and aggregation. Journal of Molecular Biology. [IF=1.281, Cited=20, 18313071].
Tarus B, Straub JE, Thirumalai D (2008) 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. [IF=1.281, Cited=35, 18479708].
Tehver R, Chen J, Thirumalai D (2008) Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle.
Journal of Molecular Biology. [IF=1.281, Cited=40, 19121324].
Moghaddam S, Caliskan G, Chauhan S, ..., Woodson SA (2009) Metal ion dependence of cooperative collapse transitions in
RNA. Journal of Molecular Biology. [IF=1.281, Cited=40, 19712681].
Buchete NV, Straub JE, Thirumalai D (2004) Continuous anisotropic representation of coarse-grained potentials for
proteins by spherical harmonics synthesis. Journal of Molecular Graphics and Modelling. [IF=0.677, Cited=11, 15099839].
Buchete NV, Straub JE, Thirumalai D (2004) Development of novel statistical potentials for protein fold recognition.
Current Opinion in Structural Biology. [IF=1.4, Cited=72, 15093838].
Zheng W, Brooks BR, Doniach S, Thirumalai D (2005) Network of dynamically important residues in the open/closed
transition in polymerases is strongly conserved. Structure. [IF=1.155, Cited=83, 15837195].
Hyeon C, Dima RI, Thirumalai D (2006) Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and
proteins. Structure. [IF=1.155, Cited=78, 17098189].
Tehver R, Thirumalai D (2010) Rigor to post-rigor transition in myosin V: link between the dynamics and the supporting
architecture. Structure. [IF=1.155, Cited=39, 20399184].
Zhang Z, Thirumalai D (2012) Dissecting the kinematics of the kinesin step. Structure. [IF=1.155, Cited=42, 22483110].
Stan G, Thirumalai D, Lorimer GH, Brooks BR (2003) Annealing function of GroEL: structural and bioinformatic analysis.
Biophysical Chemistry. [IF=0.78, Cited=28, 12646383].
Klimov DK, Thirumalai D (2003) Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets.
Structure. [IF=1.155, Cited=198, 12623017].
Klimov DK, Thirumalai D (1998) Cooperativity in protein folding: from lattice models with sidechains to real proteins.
None. [IF=None, Cited=68, 9565757].
Klimov DK, Betancourt MR, Thirumalai D (1998) Virtual atom representation of hydrogen bonds in minimal off-lattice
models of alpha helices: effect on stability, cooperativity and kinetics. None. [IF=None, Cited=27, 9889160].
Liu Z, Reddy G, Thirumalai D (2012) Theory of the molecular transfer model for proteins with applications to the folding
of the src-SH3 domain. Journal of Physical Chemistry B. [IF=0.893, Cited=11, 22497652].
O'Brien EP, Straub JE, Brooks BR, Thirumalai D (2011) Influence of Nanoparticle Size and Shape on Oligomer Formation of
an Amyloidogenic Peptide. Journal of Physical Chemistry Letters. [IF=1.158, Cited=19, 21691423].
Thirumalai D, Reddy G (2011) Protein thermodynamics: Are native proteins metastable? Nature Chemistry. [IF=3.667,
Cited=10, 22109266].
Hyeon C, Lee J, Yoon J, ..., Thirumalai D (2012) Hidden complexity in the isomerization dynamics of Holliday junctions.
Nature Chemistry. [IF=3.667, Cited=50, 23089865].
Hyeon C, Thirumalai D (2011) Capturing the essence of folding and functions of biomolecules using coarse-grained models.
Nature Communications. [IF=3.268, Cited=89, 21952221].
Han CC, Balakumar R, Thirumalai D, Chung MT (2006) The different electronic natures displayed by the alkylthio groups in
simple and higher conjugated aniline systems. Organic and Biomolecular Chemistry. [IF=0.77, Cited=2, 17036147].
Ziv G, Thirumalai D, Haran G (2008) Collapse transition in proteins. Physical Chemistry Chemical Physics. [IF=0.906,
Cited=81, 19081910].
Lin JC, Hyeon C, Thirumalai D (2013) Sequence-dependent folding landscapes of adenine riboswitch aptamers. Physical
Chemistry Chemical Physics. [IF=0.906, Cited=11, 24366448].
Koculi E, Cho SS, Desai R, ..., Woodson SA (2012) Folding path of P5abc RNA involves direct coupling of secondary and
tertiary structures. Nucleic Acids Research. [IF=4.663, Cited=23, 22641849].
Tian S, Nguyen H, Ye Z, ..., Trcek T (2024) The Folding of Germ Granule mRNAs Controls Intermolecular Base Pairing in
Germ Granules and Maintains Normal Fly Development. None. [IF=None, Cited=0, 38853845].
Morrison G, Thirumalai D (2009) Semiflexible chains in confined spaces. None. [IF=None, Cited=19, 19257086].
Kang H, Kirkpatrick TR, Thirumalai D (2013) Manifestation of random first-order transition theory in Wigner glasses.
None. [IF=None, Cited=1, 24229173].
Barsegov V, Morrison G, Thirumalai D (2008) Role of internal chain dynamics on the rupture kinetic of adhesive contacts.
Physical Review Letters. [IF=2.288, Cited=13, 18643632].
Jun S, Thirumalai D, Ha BY (2008) Compression and stretching of a self-avoiding chain in cylindrical nanopores. Physical
Review Letters. [IF=2.288, Cited=40, 18851496].
Kudlay A, Cheung MS, Thirumalai D (2009) Crowding effects on the structural transitions in a flexible helical
homopolymer. Physical Review Letters. [IF=2.288, Cited=17, 19392239].
Li MS, Co NT, Reddy G, ..., Thirumalai D (2010) Factors governing fibrillogenesis of polypeptide chains revealed by
lattice models. Physical Review Letters. [IF=2.288, Cited=49, 21231356].
Morrison G, Hyeon C, Hinczewski M, Thirumalai D (2011) Compaction and tensile forces determine the accuracy of folding
landscape parameters from single molecule pulling experiments. Physical Review Letters. [IF=2.288, Cited=18, 21517423].
Kirkpatrick T, Thirumalai D (1987) Dynamics of the structural glass transition and the p-spin-interaction spin-glass
model. Physical Review Letters. [IF=2.288, Cited=77, 10034647].
Bhattacharjee J, Thirumalai D (1991) Drag reduction in turbulent flows by polymers. Physical Review Letters. [IF=2.288,
Cited=10, 10044519].
Camacho C, Thirumalai D (1993) Minimum energy compact structures of random sequences of heteropolymers. Physical Review
Letters. [IF=2.288, Cited=62, 10054697].
Klimov D, Thirumalai D (1996) Criterion that determines the foldability of proteins. Physical Review Letters. [IF=2.288,
Cited=96, 10061184].
Bryngelson J, Thirumalai D (1996) Internal constraints induce localization in an isolated polymer molecule. Physical
Review Letters. [IF=2.288, Cited=17, 10061483].
Bryngelson J, Thirumalai D (1996) Bryngelson and Thirumalai Reply. Physical Review Letters. [IF=2.288, Cited=0, 10062496].
Thirumalai D, Ashwin V, Bhattacharjee J (1996) Dynamics of Random Hydrophobic-Hydrophilic Copolymers with Implications
for Protein Folding. Physical Review Letters. [IF=2.288, Cited=13, 10062790].
Li MS, Klimov DK, Thirumalai D (2004) Finite size effects on thermal denaturation of globular proteins. Physical Review
Letters. [IF=2.288, Cited=29, 15698029].
Barsegov V, Thirumalai D (2005) Probing protein-protein interactions by dynamic force correlation spectroscopy. Physical
Review Letters. [IF=2.288, Cited=13, 16241846].
Caliskan G, Hyeon C, Perez-Salas U, ..., Thirumalai D (2005) Persistence length changes dramatically as RNA folds.
Physical Review Letters. [IF=2.288, Cited=39, 16486414].
Rosenberg R, Thirumalai D (1986) Structure and dynamics of screened-Coulomb colloidal liquids. None. [IF=None, Cited=8, 9897215].
Mountain R, Thirumalai D (1987) Molecular-dynamics study of glassy and supercooled states of a binary mixture of soft
spheres. None. [IF=None, Cited=19, 9899249].
Rosenberg R, Thirumalai D (1987) Order-disorder transition in colloidal suspensions. None. [IF=None, Cited=13, 9898859].
Bagchi B, Thirumalai D (1988) Freezing of a colloidal liquid subject to shear flow. None. [IF=None, Cited=6, 9899961].
Thirumalai D (1988) Isolated polymer molecule in a random environment. None. [IF=None, Cited=14, 9899464].
Kirkpatrick T, Thirumalai D (1988) Comparison between dynamical theories and metastable states in regular and glassy
mean-field spin models with underlying first-order-like phase transitions. None. [IF=None, Cited=25, 9899574].
Thirumalai D, Mountain R, Kirkpatrick T (1989) Ergodic behavior in supercooled liquids and in glasses. None. [IF=None,
Cited=63, 9901660].
Kirkpatrick T, Thirumalai D, Wolynes P (1989) Scaling concepts for the dynamics of viscous liquids near an ideal glassy
state. None. [IF=None, Cited=252, 9902230].
Thirumalai D, Mountain R (1990) Ergodic convergence properties of supercooled liquids and glasses. None. [IF=None,
Cited=24, 9904563].
Shaw M, Thirumalai D (1991) Free polymer in a colloidal solution. None. [IF=None, Cited=18, 9906594].
Mountain R, Thirumalai D (1992) Ergodicity and activated dynamics in supercooled liquids. None. [IF=None, Cited=7, 9907482].
Ha B, Thirumalai D (1992) Conformations of a polyelectrolyte chain. None. [IF=None, Cited=25, 9908546].
Kirkpatrick T, Thirumalai D (1987) p-spin-interaction spin-glass models: Connections with the structural glass problem.
None. [IF=None, Cited=93, 9942177].
Kirkpatrick T, Thirumalai D (1988) Mean-field soft-spin Potts glass model: Statics and dynamics. None. [IF=None,
Cited=16, 9943716].
Thirumalai D, Kirkpatrick T (1988) Mean-field Potts glass model: Initial-condition effects on dynamics and properties of
metastable states. None. [IF=None, Cited=10, 9946882].
Thirumalai D, Mountain R (1993) Activated dynamics, loss of ergodicity, and transport in supercooled liquids. None.
[IF=None, Cited=42, 9960024].
Thirumalai D, Bhattacharjee J (1996) Polymer-induced drag reduction in turbulent flows. None. [IF=None, Cited=2, 9964284].
Subbiah Pandi A, Velmurugan D, Shanmuga Sundara Raj S, ..., Thirumalai D (2001)
10-(4-fluorophenyl)-3,3,6,6,9-pentamethyl-3,4,6,7,9,10-hexahydroacridine-1,8(2h,5h)-dione and
10-(4-fluorophenyl)-3,3,6,6-tetramethyl-9-propyl-3,4,6,7,9,10-hexahydroacridine-1,8(2h,5h)-dione. None. [IF=None,
Cited=0, 11443253].
Stan G, Brooks BR, Lorimer GH, Thirumalai D (2004) Identifying natural substrates for chaperonins using a sequence-based
approach. Protein Science. [IF=1.97, Cited=17, 15576562].
Dima RI, Thirumalai D (2006) Determination of network of residues that regulate allostery in protein families using
sequence analysis. Protein Science. [IF=1.97, Cited=55, 16434743].
Massi F, Klimov D, Thirumalai D, Straub JE (2002) Charge states rather than propensity for beta-structure determine
enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant. Protein Science.
[IF=1.97, Cited=44, 12070316].
Dima RI, Thirumalai D (2002) Exploring protein aggregation and self-propagation using lattice models: phase diagram and
kinetics. Protein Science. [IF=1.97, Cited=87, 11967361].
Betancourt MR, Thirumalai D (1999) Pair potentials for protein folding: choice of reference states and sensitivity of
predicted native states to variations in the interaction schemes. Protein Science. [IF=1.97, Cited=175, 10048329].
Wolynes PG, Onuchic JN, Thirumalai D (1995) Navigating the folding routes. Science. [IF=7.729, Cited=543, 7886447].
Barsegov V, Klimov DK, Thirumalai D (2006) Mapping the energy landscape of biomolecules using single molecule force
correlation spectroscopy: theory and applications. Biophysical Journal. [IF=0.842, Cited=12, 16533852].
Hyeon C, Thirumalai D (2006) Forced-unfolding and force-quench refolding of RNA hairpins. Biophysical Journal.
[IF=0.842, Cited=52, 16473903].
Hyeon C, Thirumalai D (2006) Mechanical unfolding of RNA: from hairpins to structures with internal multiloops.
Biophysical Journal. [IF=0.842, Cited=54, 17028142].
Zheng W, Brooks BR, Thirumalai D (2007) Allosteric transitions in the chaperonin GroEL are captured by a dominant normal
mode that is most robust to sequence variations. Biophysical Journal. [IF=0.842, Cited=73, 17557788].
Zheng W, Brooks BR, Thirumalai D (2009) Allosteric transitions in biological nanomachines are described by robust normal
modes of elastic networks. Current Protein and Peptide Science. [IF=0.718, Cited=35, 19355980].