Bogdan Costescu

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BACKGROUND Biomolecules or other complex macromolecules undergo conformational transitions upon exposure to an external perturbation such as ligand binding or mechanical force. To follow fluctuations in pairwise forces between atoms or residues during such conformational changes as observed in Molecular Dynamics (MD) simulations, we developed Time-Resolved(More)
Previous Atomic Force Microscopy (AFM) experiments found single layers of defect-free graphene to rupture at unexpectedly high loads in the micronewton range. Using molecular dynamics simulations, we modeled an AFM spherical tip pressing on a circular graphene sheet and studied the stress distribution during the indentation process until rupture. We found(More)
Protein unfolding often does not obey a simple two-state behavior. Previous single molecule force spectroscopy studies demonstrated stretched exponential kinetics of protein unfolding under a constant pulling force, the molecular origin of which remains subject to debate. We here set out to extensively sample the mechanical unfolding of ubiquitin and NuG2(More)
We present a computationally efficient pairwise potential for use in molecular dynamics simulations of large graphene or carbon nanotube systems, in particular, for those under mechanical deformation, and also for mixed systems including biomolecules. Based on the Morse potential, it is only slightly more complex and computationally expensive than a(More)
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