59 citations · 301 across the 11 of their papers we have counts for
11 papers
Statistical Mechanics of Multiplectoneme Phases in DNA
Midas Segers, Enrico Skoruppa, Helmut Schiessel +1
A stretched DNA molecule which is also under- or overwound, undergoes a buckling transition forming intertwined looped domains called plectonemes. Here we develop a simple theory t…
Systematic Coarse-Graining of Sequence-Dependent Structure and Elasticity of Double-Stranded DNA
Enrico Skoruppa, Helmut Schiessel
Coarse-grained models have played an important role in the study of the behavior of DNA at length scales beyond a few hundred base pairs. Traditionally, these models have relied on…
Equilibrium Fluctuations of DNA Plectonemes
Enrico Skoruppa, Enrico Carlon
Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e. over- or under-wounded. They are ubiquitous in cellular DNA and their physi…
Comment on "Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs"
Midas Segers, Enrico Skoruppa, Jan A. Stevens +3
While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length…
Length scale dependent elasticity in DNA from coarse-grained and all-atom models
Enrico Skoruppa, Aderik Voorspoels, Jocelyne Vreede +1
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-ato…
Computing the elastic mechanical properties of rod-like DNA nanostructures
Hemani Chhabra, Garima Mishra, Yijing Cao +4
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations i…
Twist-bend coupling, twist waves and the shape of DNA loops
S. K. Nomidis, M. Caraglio, M. Laleman +3
By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately base pairs (bp). We show that in these loops t…
Overtwisting induces polygonal shapes in bent DNA
Michele Caraglio, Enrico Skoruppa, Enrico Carlon
By combining analytical results and simulations of various coarse-grained models we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an…
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…
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…
DNA elasticity from coarse-grained simulations: the effect of groove asymmetry
Enrico Skoruppa, Michiel Laleman, Stefanos Nomidis +1
It is well-established that many physical properties of DNA at sufficiently long length scales can be understood by means of simple polymer models. One of the most widely used elas…