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By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
I study the buckling transition under compression of a two-dimensional, hexagonal, regular elastic honeycomb. Under isotropic compression, the system buckles to a configuration consisting of a unit cell containing four of the original…
We study geometrically frustrated antiferromagnets with magnetoelastic coupling. Frustration in these systems may be relieved by a structural transition to a low temperature phase with reduced lattice symmetry. We examine the statistical…
Geometric frustration is a fundamental concept in various areas of physics, and its role in self-assembly processes has recently been recognized as a source of intricate self-limited structures. Here we present an analytic theory of the…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy…
We use a recently proposed perturbative numerical renormalization group algorithm to investigate ground-state properties of a frustrated three dimensional Heisenberg model on an anisotropic lattice. We analyze the ground state energy, the…
Densely-packed bundles of biological filaments (filamentous proteins) are common and critical structural elements in range of biological materials. While most bundles form from intrinsically straight filaments, there are notable examples of…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes…
We systematically study phase transformations from one helical structure to another. Motivated in part by recent work that relates the presence of compatible interfaces with properties such as the hysteresis and reversibility of a phase…
The uniform director field obtained for the nematic ground state of the hard-rod model of liquid crystals in two dimensions reflects the high symmetry of the constituents of the liquid; It is a manifestation of the constituents' local…
A model predicting the structure of repulsive, spherically symmetric, monodisperse particles confined between two walls is presented. We study the buckling transition of a single flat layer as the double layer state develops. Experimental…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
Some frustrated magnets and superconducting arrays possess unusual symmetries that cause the free energy or other physics of a $D$-dimensional quantum or classical problem to be that of a different problem in a reduced dimension $d<D$.…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
We investigate the orientational order of transverse polarization vectors of long, stiff polymer molecules and their coupling to bond orientational and positional order in high density mesophases. Homogeneous ordering of transverse…