Related papers: Conformational impact on deformation of DNA TATA-b…
It is known that nuclear deformation plays an important role in inducing the halo structure in neutron-rich nuclei by mixing several angular momentum components. While previous theoretical studies on this problem in the literature assume…
The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA…
A new class of deformation of the matrix model of M-theory is considered. The deformation is analogous to the so-called $\b$-deformation of $D=3+1$, $\mN=4$ Super Yang-Mills theory, which preserves the conformal symmetry. It is shown that…
DNA toroidal bundles form upon condensation of one or multiple DNA filaments. DNA filaments in toroidal bundles are hexagonally packed, and collectively twist around the center line of the toroid. In a previous study, we and our coworkers…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
We study a model for polaron-like charge transport mechanism along DNA molecules with emphasis on the impact of parametrical and structural disorder. Our model Hamiltonian takes into account the coupling of the charge carrier to two…
Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation…
We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi--site breathers in a DNA--shaped double strand. Within a network model of the double helix we take individual motions of the bases within…
Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…
The macroscopic curvature induced in double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount and…
It is suggested that there is an interesting transition in double helices. The transition is between a helix, which has maximal torsion for the constituting helical strands, and a double helix which is nearly optimally packed illustrated by…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
Deformations of cell sheets during morphogenesis are driven by developmental processes such as cell division and cell shape changes. In morphoelastic shell theories of development, these processes appear as variations of the intrinsic…
Nonlinear superlattices exhibit unique features allowing for wave manipulations. Despite the increasing attention received, the underlying physical mechanisms and the evolution process of the band structures and bandgaps in strongly…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…
DNA nanotubes are tubular structures composed of DNA crossover molecules. We present a bottom up approach for construction and characterization of these structures. Various possible topologies of nanotubes are constructed such as 6-helix,…
The water hydration shell has decisive impact on the structural and functional properties of RNA. Changes of RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process which is…
We present an elastic model of B-form DNA as a stack of thin, rigid plates or base pairs that are not permitted to deform. The symmetry of DNA and the constraint of plate rigidity limit the number of bulk elastic constants contributing to a…
Damping of rotational motion in superdeformed Hg and Dy-region nuclei is studied by means of cranked shell model diagonalization. It is shown that a shell oscillation in single-particle alignments affects significantly properties of…
The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The…