Related papers: Topological interactions in DNA catenanes
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
At low temperatures the interactions between like-oriented steps on a surface are believed to be dominated by elastic repulsions. This belief is based on the results of the classical continuum field theories of elasticity. Electrostatic…
Topological defects are ubiquitous from solid state physics to cosmology, where they drive phase transitions by proliferating as domain walls, monopoles or vortices. As quantum excitations, they often display fractional charge and anyonic…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
We point out an analogy between diffractive electron-nucleus scattering events, and realizations of one-dimensional branching random walks selected according to the height of the genealogical tree of the particles near their boundaries.…
We derive an exact representation of the topological effect on the dynamics of sequence processing neural networks within signal-to-noise analysis. A new network structure parameter, loopiness coefficient, is introduced to quantitatively…
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently…
Network science has become an essential interdisciplinary tool for understanding complex biological systems. However, because these systems undergo continuous, often stimulus-driven changes in both structure and function, traditional static…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
In this article, we present a method to reconstruct the topology of a partially observed radial network of linear dynamical systems with bi-directional interactions. Our approach exploits the structure of the inverse power spectral density…
In graphene moir\'e superlattices, electronic interactions between layers are mostly hidden as band structures get crowded because of folding, making their interpretation cumbersome. Here, the evolution of the electronic band structure as a…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
The conformation of circular DNA molecules of various lengths adsorbed in a 2D conformation on a mica surface is studied. The results confirm the conjecture that the critical exponent $\nu$ is topologically invariant and equal to the SAW…
Interacting disordered zigzag graphene nanoribbons have fractional charges, are quasi-one-dimensional, and display an exponentially small gap. Our numerical computations showed that the topological entanglement entropy of these systems has…
The organization of live cells to tissues is associated with the mechanical interaction between cells, which is mediated through their elastic environment. We model cells as spherical active force dipoles surrounded by an infinite elastic…
We present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible…
Networks of elastic fibers are ubiquitous in biological systems and often provide mechanical stability to cells and tissues. Fiber reinforced materials are also common in technology. An important characteristic of such materials is their…
We report the counter-intuitive instability of charged elastic rings, and the persistence of sinusoidal deformations in the lowest-energy configurations by the combination of high-precision numerical simulations and analytical perturbation…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
We present a computer simulation study of glassy and crystalline states using the standard Lennard-Jones interaction potential that is truncated at a finite cut-off distance, as is typical of many computer simulations. We demonstrate that…