January 3, 2025, Filed Under: 2009, PublicationsCrowding effects on the mechanical stability and unfolding pathways of ubiquitin. Citation: Pincus, D. L. ; Thirumalai, D. Crowding effects on the mechanical stability and unfolding pathways of ubiquitin. J Phys Chem B 113, 359-68. Download crowding-effects-on-the-mechanical-stability-and-unfolding-pathways-of-ubiquitin.pdf2.18 MB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsAllostery wiring diagrams in the transitions that drive the GroEL reaction cycle. Citation: Tehver, R. ; Chen, J. ; Thirumalai, D. Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle. J Mol Biol 387, 390-406. Download allostery-wiring-diagrams-in-the-transitions-that-drive-the-groel-reaction-cycle.pdf1.2 MB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsCollapse transition in proteins. Citation: Ziv, G. ; Thirumalai, D. ; Haran, G. Collapse transition in proteins. Phys Chem Chem Phys 11, 83-93. Download collapse-transition-in-proteins.pdf989 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsCoupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II. Citation: Zheng, W. ; Thirumalai, D. Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II. Biophys J 96, 2128-37. Download Citation coupling-between-normal-modes-drives-protein-conformational-dynamics-illustrations-using-allosteric-transitions-in-myosin-ii.pdf845 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsHow accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins? Citation: O’Brien, E. P. ; Morrison, G. ; Brooks, B. R. ; Thirumalai, D. How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins?. J Chem Phys 130, 124903. Download how-accurate-are-polymer-models-in-the-analysis-of-forster-resonance-energy-transfer-experiments-on-proteins.pdf736 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsInfluence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation. Citation: Reddy, G. ; Straub, J. E. ; Thirumalai, D. Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation. J Phys Chem B 113, 1162-72. Download 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.pdf2.11 MB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsSemiflexible chains in confined spaces. Citation: Morrison, G. ; Thirumalai, D. Semiflexible chains in confined spaces. Phys Rev E Stat Nonlin Soft Matter Phys 79, 011924. Download semiflexible-chains-in-confined-spaces.pdf828 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsTransmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations. Citation: Miyashita, N. ; Straub, J. E. ; Thirumalai, D. ; Sugita, Y. Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations. J Am Chem Soc 131, 3438-9. Download transmembrane-structures-of-amyloid-precursor-protein-dimer-predicted_by-replica-exchange-molecular-dynamics-simulations.pdf755 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsWater-mediated interactions between hydrophobic and ionic species in cylindrical nanopores. Citation: Vaitheeswaran, S. ; Reddy, G. ; Thirumalai, D. Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores. J Chem Phys 130, 094502. Download water-mediated-interactions-between-hydrophobic-and-ionic-species-in-cylindrical-nanopores.pdf343 KB Last updated on 08/18/2017 PubMed DOI
January 3, 2025, Filed Under: 2009, PublicationsOn the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: illustrations using lattice model. Citation: Liu, Z. ; Chen, J. ; Thirumalai, D. On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: illustrations using lattice model. Proteins 77, 823-31. Download on-the-accuracy-of-inferring-energetic-coupling-between-distant-sites-in-protein-families-from-evolutionary-imprints-illustrations-using-lattice-model.pdf594 KB Last updated on 08/18/2017 PubMed DOI
