Related papers: Conformation of Circular DNA in 2 Dimensions
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 in these trajectories we obtain estimates of the bend and…
Molecular chirality, a form of stereochemistry most often describing relative spatial arrangements of bonded neighbors around tetrahedral carbon centers, influences the set of 3D conformers accessible to the molecule without changing its 2D…
We employ a molecular dynamics (MD) study to explore pattern selection in binary fluid mixtures ($AB$) undergoing surface-directed spinodal decomposition on a chemically patterned amorphous substrate. We chose a checkerboard pattern with…
Motivated by recent experiments on DNA torsion-force-extension characteristics we consider the writhing geometry of open stiff molecules. We exhibit a cyclic motion which allows arbitrarily large twisting of the end of a molecule via an…
We numerically study the wetting (adsorption) transition of a polymer chain on a disordered substrate in 1+1 dimension.Following the Poland-Scheraga model of DNA denaturation, we use a Fixman-Freire scheme for the entropy of loops. This…
The authors measure the persistence and contour lengths of DNA-psoralen complexes, as a function of psoralen concentration, for intercalated and crosslinked complexes. In both cases, the persistence length monotonically increases until a…
DNA molecules spin-coated on amorphous quartz substrates are shown to form stable films. Electron density profiles (EDPs) along the film depth show that film prepared from aqueous solution of DNA exhibits layering of the molecules in three…
Two-dimensional (2D) mechanical models of confluent tissues have related the mechanical state of a monolayer of cells to the average perimeter length of the cell cross sections, predicting floppiness or rigidity of the material. For the…
The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The…
Loop extrusion convincingly describes how certain Structural Maintenance of Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most of the existing computational models cannot reconcile recent in vitro observations…
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…
For an understanding of DNA elasticity at high mechanical loads (F > 30 pN), its helical nature needs to be taken into account, in the form of coupling between the twist and stretch degrees of freedom. The prevailing model for DNA…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
The present paper is devoted to the study of the combinatorics of 216 maximal $C^3$ circular codes --- a particular type of structure arising in the analysis of genomic sequences. Their circularity property is believed to be intimately…
We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
The amount and type of self-entanglement of DNA filaments is significantly affected by spatial confinement, which is ubiquitous in biological systems. Motivated by recent advancements in single DNA molecule experiments based on nanofluidic…
Self-avoiding polymers in two-dimensional ($d=2$) melts are known to adopt compact configurations of typical size $R(N) \sim N^{1/d}$ with $N$ being the chain length. Using molecular dynamics simulations we show that the irregular shapes of…