Related papers: Resonant helical deformations in nonhomogeneous Ki…
Cyclization of DNA with sticky ends is commonly used to construct DNA minicircles and to measure DNA bendability. The cyclization probability of short DNA (< 150 bp) has a strong length dependence, but how it depends on the rotational…
We study composite assemblages of dielectrics and metamaterials with respectively positive and negative material parameters. In the continuum case, for a scalar equation, such media may exhibit so-called plasmonic resonances for certain…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
Direct time-resolved spectral fitting has been performed on continuous RXTE monitoring of seven Seyfert 1 galaxies in order to study their broadband spectral variability and Fe K alpha variability characteristics on time scales of days to…
In the present paper we study the impact of dispersion and nonlinearity on DNA dynamics. We rely on the helicoidal Peyrard-Bishop model and use the fact that nonlinear DNA dynamics represents an interplay between nonlinearity and…
We report the observation of nonlinearity-induced broadening of resonances in dynamically modulated directional couplers. When the refractive index of the guiding channels in the coupler is harmonically modulated along the propagation…
Instability of the excitation spectrum of an ordered noncollinear Heisenberg antiferromagnet (AF) with respect to spontaneous two-magnon decays is investigated. We use a spin-1/2 AF on a triangular lattice as an example and examine the…
We study the resonances of the quantum kicked rotor subjected to an excitation that follows a deterministic time-dependent prescription. For the primary resonances we find an analytical relation between the long-time behavior of the…
We consider a thin droplet that spreads over a flat, horizontal and chemically heterogeneous surface. The droplet is subjected to changes in its volume though a prescribed, arbitrary spatiotemporal function, which varies slowly and vanishes…
The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of…
Influences of defects generating random fields on modulated phases in materials with the order-disorder type of phase transition are studied. It is shown that under appropriate conditions third harmonics of the ground state modulation may…
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…
DNAs charge transfer and self-assembly characteristics have made it a hallmark of molecular electronics for the past two decades. A fast and efficient charge transfer mechanism with programmable properties using DNA nanostructures is…
We derive a time-domain mean-field equation to model the full temporal and spectral dynamics of light in singly resonant cavity-enhanced second-harmonic generation systems. We show that the temporal walk-off between the fundamental and the…
The frequency dependence of the interlayer conductivity of a layered Fermi liquid in a magnetic field which is tilted away from the normal to the layers is considered. For both quasi-one- and quasi-two-dimensional systems resonances occur…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
We explore the effects of mesh skewness on the accuracy of standard Hybrid High-Order (HHO) schemes for anisotropic diffusion equations. After defining a notion of regular skewed mesh sequences, which allows, e.g., for elements that become…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
Inelastic neutron scattering measurements are reported that show a new longitudinal mode in the antiferromagnetically ordered phase of the spin-1/2 quasi-one-dimensional antiferromagnet KCuF3. This mode signals the cross-over from…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…