264 citations · 2.7k across the 64 of their papers we have counts for
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Effect of finite size on cooperativity and rates of protein folding
Maksim Kouza, Mai Suan Li, Edward P. O'Brien +2
We analyze the dependence of cooperativity of the thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, , using lattice mo…
Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments
Changbong Hyeon, D. Thirumalai
Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the ene…
Dynamics of allosteric transitions in GroEL
Changbong Hyeon, George H. Lorimer, D. Thirumalai
The chaperonin GroEL-GroES, a machine which helps some proteins to fold, cycles through a number of allosteric states, the state, with high affinity for substrate proteins (SPs…
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins
Changbong Hyeon, Ruxandra I Dima, D. Thirumalai
Using self-organized polymer models, we predict mechanical unfolding and refolding pathways of ribo-zymes, and the green fluorescent protein. In agreement with experiments, there a…
Size, shape, and flexibility of RNA structures
Changbong Hyeon, Ruxandra I. Dima, D. Thirumalai
Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and D…
Mechanical unfolding of RNA: From hairpins to structures with internal multiloops
Changbong Hyeon, D. Thirumalai
Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape…
Hydrophobic and Ionic Interactions in Nano-sized Water Droplets
S. Vaitheeswaran, D. Thirumalai
We investigate the solvation of methane and methane decorated with charges in spherically confined water droplets. Free energy profiles for a single methane molecule in droplets, r…
Scenarios for protein aggregation: Molecular Dynamics simulations and Bioinformatic Analysis
Ruxandra I. Dima, Bogdan Tarus, John E. Straub +1
The need to understand the assembly kinetics of fibril formation has become urgent because of the realization that soluble oligomers of amyloidogenic peptides may be even more neur…
Forced-unfolding and force-quench refolding of RNA hairpins
Changbong Hyeon, D. Thirumalai
Using coarse-grained model we have explored forced-unfolding of RNA hairpin as a function of and the loading rate (). The simulations and theoretical analysis have been…