Related papers: Nonlinear dynamics of damped DNA systems with long…
Recent papers have considered moving breathers (MBs) in DNA models including long range interaction due to the dipole moments of the hydrogen bonds. We have recalculated the value of the charge transfer when hydrogen bonds stretch using…
In previous work, the dynamics of the elastic rod was recast in a Lax pair formulation, with fiducial arc length s and time t as continuous independent variables. However, the solution of these equations cannot apply directly to a system…
In this report, we present a dynamical systems' approach to study the exact nonlinear wave-particle interaction in relativistic regime. We give a particular attention to the effect of wave obliquity on the dynamics of the orbits by studying…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
We simulate the nonlinear dynamic responses in Kirchhoff rod by including the important effects due to inertia and kinematic coupling of tension and torsion. We begin by reviewing a dynamic rod model of a strand (length of cable or DNA) in…
These lectures present the analysis of stability and control of long time behavior of PDE models described by nonlinear evolutions of hyperbolic type. Specific examples of the models under consideration include: (i) nonlinear systems of…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
Hydrodynamic interactions in systems comprised of self-propelled particles, such as swimming microorganisms, and passive tracers have a significant impact on the tracer dynamics compared to the equivalent "dry" sample. However, such…
We introduce a theoretical scheme for the analog quantum simulation of long-range XYZ models using current trapped-ion technology. In order to achieve fully-tunable Heisenberg-type interactions, our proposal requires a state-dependent…
Nonlinear lattice models can support "discrete breather" excitations that stay localized in space for all time. By contrast, the localized Wannier states of linear lattice models are dynamically unstable. Nevertheless, symmetric and…
We explain the origin of the generation of discrete breathers (DBs) in experiments on damped and driven micromechanical cantilever arrays (M.Sato et al. Phys. Rev. Lett. {\bf 90}, 044102, 2003). Using the concept of the nonlinear response…
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…
We report the experimental observation of discrete breathers in a one-dimensional diatomic granular crystal composed of compressed elastic beads that interact via Hertzian contact. We first characterize their effective linear spectrum both…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
Nonequilibrium, quasi-stationary states of a one-dimensional "hard" $\phi^4$ deterministic lattice, initially thermalized to a particular temperature, are investigated when brought into contact with a stochastic thermal bath at lower…
We have performed non-equilibrium dynamics simulations of a binary Lennard-Jones mixture in which an external force is applied on a single tagged particle. For the diffusive properties of this particle parallel to the force superdiffusive…
The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other…
Intrinsic localized modes or discrete breathers are investigated by molecular dynamics simulations in free-standing graphene. Discrete breathers are generated either through thermal quenching of the graphene lattice or by proper…
Nonlinear contact dynamics are widely regarded as intrinsically nonlinear systems whose behaviour depends strongly on geometry and impact conditions. Here we show that any one-dimensional conservative contact system satisfying monotone…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…