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D. Thirumalai

Identifiers

  • name variant D. Thirumalai 0.60 · backfill

Papers (125)

  1. Loop Extrusion Reversal by Condensin Motor is Mediated by Catch Bonds cond-mat.soft · 2026 · author #4
  2. Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent q-bio.BM · 2019 · author #3
  3. Share, but unequally: A plausible mechanism for emergence and maintenance of intratumor heterogeneity q-bio.PE · 2018 · author #2
  4. On the origin of super-diffusive behavior in a class of non-equilibrium systems cond-mat.stat-mech · 2018 · author #2
  5. Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover q-bio.BM · 2018 · author #3
  6. Charge fluctuation effects on the shape of flexible polyampholytes with applications to Intrinsically disordered proteins cond-mat.stat-mech · 2018 · author #3
  7. Forced-rupture of Cell-Adhesion Complexes Reveals abrupt switch between two Brittle States q-bio.BM · 2017 · author #2
  8. Signaling Networks and Dynamics of Allosteric Transitions in Bacterial Chaperonin GroEL: Implications for Iterative Annealing of Misfolded Proteins q-bio.BM · 2017 · author #1
  9. Giant Casimir non-equilibrium forces drive coil to globule transition in polymers cond-mat.stat-mech · 2017 · author #4
  10. Cell growth rate dictates the onset of glass to fluid-like transition and long time super-diffusion in an evolving cell colony q-bio.CB · 2017 · author #5
  11. Optimal information transfer in enzymatic networks: A field theoretic formulation cond-mat.stat-mech · 2017 · author #3
  12. Ripping RNA by Force using Gaussian Network Models physics.bio-ph · 2016 · author #2
  13. Protein Collapse is Encoded in the Folded State Architecture q-bio.BM · 2016 · author #6
  14. Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension q-bio.BM · 2016 · author #3
  15. Discrete step sizes of molecular motors lead to bimodal non-Gaussian velocity distributions under force cond-mat.stat-mech · 2016 · author #4
  16. Noise control in gene regulatory networks with negative feedback q-bio.MN · 2016 · author #2
  17. Folding PDZ2 domain using the Molecular Transfer Model q-bio.BM · 2016 · author #3
  18. Phenomenological and microscopic theories for catch bonds q-bio.BM · 2016 · author #3
  19. Force-dependent switch in protein unfolding pathways and transition state movements cond-mat.soft · 2015 · author #5
  20. On the importance of hydrodynamic interactions in the stepping kinetics of kinesin physics.bio-ph · 2015 · author #3
  21. Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model q-bio.BM · 2015 · author #2
  22. Confinement-induced glassy dynamics in a model for chromosome organization cond-mat.soft · 2015 · author #3
  23. Unexpected swelling of stiff DNA in a polydisperse crowded environment cond-mat.soft · 2015 · author #4
  24. Extracting folding landscape characteristics of biomolecules using mechanical forces q-bio.BM · 2015 · author #3
  25. Random First Order Theory concepts in Biology and Condensed Matter physics cond-mat.dis-nn · 2014 · author #2
  26. Entropy and enthalpy of interaction between amino acid side chains in nanopores physics.chem-ph · 2014 · author #2
  27. Using Simulations and kinetic network models to reveal the dynamics and functions of Riboswitches q-bio.BM · 2014 · author #4
  28. Effects of macromolecular crowding on the collapse of biopolymers cond-mat.soft · 2014 · author #4
  29. Membrane-protein interactions hold the key to understanding amyloid formation cond-mat.soft · 2014 · author #2
  30. Universal relations in the self-assembly of proteins and RNA q-bio.BM · 2014 · author #1
  31. Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes q-bio.BM · 2014 · author #3
  32. Cellular signaling networks function as generalized Wiener-Kolmogorov filters to suppress noise q-bio.MN · 2014 · author #2
  33. Dynamical Transition and Heterogeneous Hydration Dynamics in RNA q-bio.BM · 2014 · author #4
  34. Evidence of disorder in biological molecules from single molecule pulling experiments physics.bio-ph · 2014 · author #3
  35. Development and applications of Coarse Grained models for RNA q-bio.BM · 2014 · author #3
  36. Sequence-dependent folding landscapes of adenine riboswitch aptamers q-bio.BM · 2013 · author #3
  37. Design principles governing the motility of myosin V q-bio.BM · 2013 · author #3
  38. Urea-induced denaturation of PreQ1-riboswitch q-bio.BM · 2013 · author #2
  39. Force-Induced Unzipping Transitions in an Athermal Crowded Environment q-bio.BM · 2013 · author #2
  40. Generalized Iterative Annealing Model for the action of RNA chaperones q-bio.BM · 2013 · author #2
  41. Entropic stabilization of the folded states of RNA due to macromolecular crowding q-bio.BM · 2013 · author #2
  42. A Coarse-Grained Model for Predicting RNA Folding Thermodynamics q-bio.BM · 2013 · author #2
  43. From mechanical folding trajectories to intrinsic energy landscapes of biopolymers q-bio.BM · 2013 · author #4
  44. Manifestation of Random First Order Transition theory in Wigner glasses cond-mat.stat-mech · 2012 · author #3
  45. RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity q-bio.BM · 2012 · author #3
  46. Exact solution of the Zwanzig-Lauritzen model of Polymer Crystallization under Tension cond-mat.stat-mech · 2012 · author #2
  47. Hidden Complexity in the Isomerization Dynamics of Holliday Junctions cond-mat.soft · 2012 · author #5
  48. Gene Regulation by Riboswitches with and without Negative Feedback Loop q-bio.MN · 2012 · author #2
  49. On the origin of the unusual behavior in the stretching of single-stranded DNA cond-mat.soft · 2012 · author #2
  50. Multiple barriers in forced rupture of protein complexes physics.bio-ph · 2012 · author #2
  51. Chain Length Determines the Folding Rates of RNA cond-mat.soft · 2012 · author #2
  52. Entropic Stabilization of Proteins by TMAO q-bio.BM · 2011 · author #4
  53. Capturing the essence of folding and functions of biomolecules using Coarse-Grained Models cond-mat.soft · 2011 · author #2
  54. Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA q-bio.BM · 2011 · author #2
  55. Role of water in Protein Aggregation and Amyloid Polymorphism cond-mat.soft · 2011 · author #1
  56. Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins cond-mat.soft · 2011 · author #3
  57. Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide cond-mat.soft · 2011 · author #4
  58. Polyelectrolyte and polyampholyte effects in synthetic and biological macromolecules cond-mat.soft · 2011 · author #3
  59. Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments cond-mat.soft · 2011 · author #4
  60. Factors governing fibrillogenesis of polypeptide chains cond-mat.soft · 2010 · author #6
  61. Theoretical Perspectives on Protein Folding cond-mat.soft · 2010 · author #1
  62. Determination of factors governing fibrillogenesis of polypeptide chains using lattice models q-bio.BM · 2010 · author #5
  63. Random First Order Phase Transition Theory of the Structural Glass Transition cond-mat.soft · 2009 · author #2
  64. Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases q-bio.BM · 2009 · author #3
  65. Refolding dynamics of stretched biopolymers upon force quench physics.bio-ph · 2009 · author #4
  66. Theory of biopolymer stretching at high forces cond-mat.stat-mech · 2009 · author #2
  67. How accurate are polymer models in the analysis of Forster resonance energy transfer experiments on proteins? q-bio.BM · 2009 · author #4
  68. Crowding effects on the structural transitions in a flexible helical homopolymer cond-mat.soft · 2009 · author #3
  69. Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores cond-mat.soft · 2009 · author #3
  70. Probing the Mechanisms of Fibril Formation Using Lattice Models q-bio.BM · 2008 · author #4
  71. Crowding effects on the mechanical stability and unfolding pathways of Ubiquitin q-bio.BM · 2008 · author #2
  72. Compression and stretching of a self-avoiding chain in cylindrical nanopores cond-mat.soft · 2008 · author #2
  73. Minimal models for proteins and RNA: From folding to function q-bio.BM · 2008 · author #4
  74. Semiflexible Chains in Confined Spaces cond-mat.soft · 2008 · author #2
  75. Force Dependent Hopping Rates of RNA Hairpins can be Estimated from Accurate Measurement of the Folding Landscapes cond-mat.soft · 2008 · author #3
  76. The role of internal chain dynamics on the rupture kinetics of adhesive contacts cond-mat.soft · 2008 · author #3
  77. Allosteric communication in Dihydrofolate Reductase: Signaling network and pathways for closed to occluded transition and back q-bio.BM · 2007 · author #3
  78. Kinetics of Loop Formation in Polymer Chains cond-mat.soft · 2007 · author #4
  79. Stretching Homopolymers cond-mat.soft · 2007 · author #5
  80. Effect of finite size on cooperativity and rates of protein folding q-bio.BM · 2006 · author #5
  81. Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments cond-mat.soft · 2006 · author #2
  82. Dynamics of allosteric transitions in GroEL q-bio.BM · 2006 · author #3
  83. Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins q-bio.BM · 2006 · author #3
  84. Size, shape, and flexibility of RNA structures q-bio.BM · 2006 · author #3
  85. Mechanical unfolding of RNA: From hairpins to structures with internal multiloops q-bio.BM · 2006 · author #2
  86. Hydrophobic and Ionic Interactions in Nano-sized Water Droplets physics.chem-ph · 2006 · author #2
  87. Scenarios for protein aggregation: Molecular Dynamics simulations and Bioinformatic Analysis q-bio.BM · 2006 · author #4
  88. Forced-unfolding and force-quench refolding of RNA hairpins q-bio.BM · 2006 · author #2
  89. Kinetics of Interior Loop Formation in Semiflexible Chains cond-mat.soft · 2006 · author #2
  90. Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy (FCS): Theory and applications cond-mat.soft · 2006 · author #3
  91. Persistence Length Changes Dramatically as RNA Folds q-bio.BM · 2005 · author #6
  92. Influence of surface interactions on folding and forced unbinding of semiflexible chains cond-mat.soft · 2005 · author #2
  93. Probing protein-protein interactions by dynamic force correlated spectroscopy (FCS) cond-mat.soft · 2005 · author #2
  94. The shape of a flexible polymer in a cylindrical pore cond-mat.soft · 2005 · author #2
  95. Mechanical unfolding of RNA hairpins q-bio.BM · 2005 · author #2
  96. Finite size effects on calorimetric cooperativity of two-state proteins q-bio.BM · 2004 · author #3
  97. Finite size effects on thermal denaturation of globular proteins q-bio.BM · 2004 · author #3
  98. Proteins associated with diseases show enhanced sequence correlation between charged residues q-bio.BM · 2004 · author #2
  99. Asymmetry in the shapes of folded and denatured states of proteins q-bio.BM · 2003 · author #2
  100. Thermal denaturation and folding rates of single domain proteins: size matters q-bio.BM · 2003 · author #3
  101. Anisotropic coarse-grained statistical potentials improve the ability to identify native-like protein structures physics.chem-ph · 2003 · author #3
  102. Folding in lattice models with side chains cond-mat.soft · 2002 · author #3
  103. Dependence of folding rates on protein length cond-mat.soft · 2002 · author #3
  104. Bending rigidity of stiff polyelectrolyte chains: Single chain and a bundle of multichains cond-mat.soft · 2002 · author #2
  105. Introducing Protein Folding Using Simple Models cond-mat.soft · 2001 · author #1
  106. Dynamics of Collapse of flexible Polyelectrolytes and Polyampholytes cond-mat.soft · 2000 · author #2
  107. Emergence of stable and fast folding protein structures cond-mat.soft · 1999 · author #1
  108. Two Landmarks in Polymer Physics: The Edwards Model and de Gennes Observation cond-mat.soft · 1999 · author #1
  109. Kinetics of condensation of flexible polyelectrolytes in poor solvents: effects of solvent quality, valence and size of counterions cond-mat.soft · 1999 · author #2
  110. Stretching Single Domain Proteins: Phase Diagram and Kinetics of Force-Induced Unfolding cond-mat.soft · 1999 · author #2
  111. Persistence Length of Flexible Polyelectrolyte Chains cond-mat.stat-mech · 1998 · author #2
  112. Stretching DNA: Role of electrostatic interaction cond-mat.soft · 1998 · author #2
  113. Fractal Analysis of Protein Potential Energy Landscapes cond-mat.soft · 1998 · author #2
  114. Linking Rates of Folding in Lattice Models of Proteins with Underlying Thermodynamic Characteristics cond-mat.soft · 1998 · author #2
  115. Cooperativity in Protein Folding: From Lattice Models with Side Chains to Real Proteins cond-mat.soft · 1998 · author #2
  116. Distribution Function of the End-to-End Distance of Semiflexible Polymers cond-mat.stat-mech · 1997 · author #2
  117. Thermodynamic stability of folded proteins against mutations cond-mat.soft · 1997 · author #2
  118. Viscosity Dependence of the Folding Rates of Proteins cond-mat.soft · 1997 · author #2
  119. Statistical Mechanics of Semiflexible Chains: A Meanfield Variational Approach cond-mat.soft · 1997 · author #1
  120. Kinetic Partitioning Mechanism as a Unifying Theme in the Folding of Biomolecules cond-mat.soft · 1997 · author #1
  121. Protein Folding Kinetics: Time Scales, Pathways, and Energy Landscapes in Terms of Sequence Dependent Properties cond-mat.stat-mech · 1996 · author #3
  122. Factors Governing the Foldability of Proteins cond-mat · 1996 · author #2
  123. Semiflexible Chains under Tension cond-mat · 1996 · author #2
  124. Reply to Comment on "Criterion that Determines the Foldability of Proteins" cond-mat · 1996 · author #2
  125. Localization of a Polymer with Internal Constraints cond-mat · 1996 · author #2

Mentions

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Frequent Coauthors