177 citations · 367 across the 6 of their papers we have counts for
7 papers
Twist-bend coupling and the statistical mechanics of the twistable worm-like chain model of DNA: perturbation theory and beyond
Stefanos K. Nomidis, Enrico Skoruppa, Enrico Carlon +1
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupl…
Receptor-ligand rebinding kinetics in confinement
Aykut Erbas, Monica Olvera de la Cruz, John F. Marko
Rebinding kinetics of molecular ligands plays a critical role in biomachinery, from regulatory networks to protein transcription, and is also a key factor for designing drugs and h…
Bend-Induced Twist Waves and the Structure of Nucleosomal DNA
Enrico Skoruppa, Stefanos K. Nomidis, John F. Marko +1
Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we investigate its effect on bent DNA. We provide an analytical solution of the m…
Effects of electrostatic interactions on ligand dissociation kinetics
Aykut Erbas, Monica Olvera de la Cruz, John F. Marko
We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics (MD) simulat…
Supercoiling DNA locates mismatches
Andrew Dittmore, Sumitabha Brahmachari, Yasuhara Takagi +2
We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several…
Unzipping Dynamics of Long DNAs
S. Cocco, R. Monasson, J. F. Marko
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends ar…
Force and kinetic barriers in unzipping of DNA
S. Cocco, R. Monasson, J. Marko
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the d…