January 3, 2025, Filed Under: 2009, PublicationsAllosteric transitions in biological nanomachines are described by robust normal modes of elastic networks. Citation: Zheng, W. ; Brooks, B. R. ; Thirumalai, D. Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks. Curr Protein Pept Sci 10, 128-32. Download Citation PubMed
January 3, 2025, Filed Under: 2009, PublicationsAssembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures. Citation: Cho, S. S. ; Pincus, D. L. ; Thirumalai, D. Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures. Proc Natl Acad Sci U S A 106, 17349-54. Download assembly-mechanisms-of-rna-pseudoknots-are-determined-by-the-stabilities-of-constituent-secondary-structures.pdf2.38 MB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsCrowding effects on the structural transitions in a flexible helical homopolymer. Citation: Kudlay, A. ; Cheung, M. S. ; Thirumalai, D. Crowding effects on the structural transitions in a flexible helical homopolymer. Phys Rev Lett 102, 118101. Download crowding-effects-on-the-structural-transitions-in-a-flexible-helical-homopolymer.pdf442 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsDynamics of locking of peptides onto growing amyloid fibrils. Citation: Reddy, G. ; Straub, J. E. ; Thirumalai, D. Dynamics of locking of peptides onto growing amyloid fibrils. Proc Natl Acad Sci U S A 106, 11948-53. Download dynamics-of-locking-of-peptides-onto-growing-amyloid-fibrils.pdf1.43 MB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsDynamics of tRNA at different levels of hydration. Citation: Roh, J. H. ; Briber, R. M. ; Damjanovic, A. ; Thirumalai, D. ; Woodson, S. A. ; Sokolov, A. P. Dynamics of tRNA at different levels of hydration. Biophys J 96, 2755-62. Download dynamics-of-trna-at-different-levels-of-hydration.pdf649 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsMetal ion dependence of cooperative collapse transitions in RNA. Citation: Moghaddam, S. ; Caliskan, G. ; Chauhan, S. ; Hyeon, C. ; Briber, R. M. ; Thirumalai, D. ; Woodson, S. A. Metal ion dependence of cooperative collapse transitions in RNA. J Mol Biol 393, 753-64. Download metal-ion-dependence-of-cooperative-collapse-transitions-in-rna.pdf796 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsSequence and crowding effects in the aggregation of a 10-residue fragment derived from islet amyloid polypeptide. Citation: Rivera, E. ; Straub, J. ; Thirumalai, D. Sequence and crowding effects in the aggregation of a 10-residue fragment derived from islet amyloid polypeptide. Biophys J 96, 4552-60. Download sequence-and-crowding-effects-in-the-aggregation-of-a-10-residue-fragment-derived-from-islet-amyloid-polypeptide.pdf917 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsRefolding dynamics of stretched biopolymers upon force quench. Citation: Hyeon, C. ; Morrison, G. ; Pincus, D. L. ; Thirumalai, D. Refolding dynamics of stretched biopolymers upon force quench. Proc Natl Acad Sci U S A 106, 20288-93. Download refolding-dynamics-of-stretched-biopolymers-upon-force-quench.pdf2.24 MB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsStructures 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. Citation: Miyashita, N. ; Straub, J. E. ; Thirumalai, D. Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase. J Am Chem Soc 131, 17843-52. Download Citation PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsThermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils. Citation: O’Brien, E. P. ; Okamoto, Y. ; Straub, J. E. ; Brooks, B. R. ; Thirumalai, D. Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils. J Phys Chem B 113, 14421-30. Download thermodynamic-perspective-on-the-docklock-growth-mechanism-of-amyloid-fibrils.pdf3.27 MB Last updated on 08/18/2017 PubMed DOI
