138 citations · 306 across the 10 of their papers we have counts for
10 papers
Structural transitions and energy landscape for Cowpea Chlorotic Mottle Virus capsid mechanics from nanomanipulation in vitro and in silico
Olga Kononova, Joost Snijder, Melanie Brasch +6
Physical properties of capsids of plant and animal viruses are important factors in capsid self-assembly, survival of viruses in the extracellular environment, and their cell infec…
Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico
Olga Kononova, Yaroslav Kholodov, Kelly E. Theisen +5
Microtubules, the primary components of the chromosome segregation machinery, are stabilized by longitudinal and lateral non-covalent bonds between the tubulin subunits. However, t…
Langevin dynamics simulations of biomolecules on graphics processors
A. Zhmurov, R. I. Dima, Y. Kholodov +1
Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules,…
Allosteric communication in Dihydrofolate Reductase: Signaling network and pathways for closed to occluded transition and back
Jie Chen, Ruxandra I. Dima, D. Thirumalai
E. Coli. dihydrofolate reductase (DHFR) undergoes conformational transitions between the closed (CS) and occluded (OS) states which, respectively, describe whether the active site…
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…