Patterns and Stability of Coupled Multi-Stable Nonlinear Oscillators

Nonlinear isolated and coupled oscillators are extensively studied as prototypical nonlinear dynamics models. Much attention has been devoted to oscillator synchronization or the lack thereof. Here, we study the synchronization and stability of coupled driven-damped Helmholtz-Duffing oscillators in bi-stability regimes. We find that despite the fact that the system parameters and the driving force are identical, the stability of the two states to spatially non-uniform perturbations is very different. Moreover, the final stable states, resulting from these spatial perturbations, are not solely dictated by the wavelength of the perturbing mode and take different spatial configurations in terms of the coupled oscillator phases.

Describing nonequilibrium soft matter with mean field game theory

We demonstrate that combining an emerging approach to game theory with self-consistent mean field theory provides realistic treatments of diblock copolymer phase evolution. We especially examine order-order phase transformations upon quenched temperature change involving hexagonal cylinders, lamellae, and the gyroid. Our findings demonstrate that (i) the game theoretical dynamics produce realistic trajectories for the evolution of the local compositions, (ii) the predicted small-angle scattering follows experimentally observed trends, (iii) nucleation and growth is active when the system is quenched far from the critical point, and (iv) epitaxial growth is manifest. To our knowledge, the methodology presented provides the first merger of mean field game theory and statistical mechanics for soft matter systems, giving a new inroad to studying polymer dynamics.

Models for energy and charge transport and storage in biomolecules

Two models for energy and charge transport and storage in biomolecules are considered. A model based on the discrete nonlinear Schrödinger equation with long-range dispersive interactions (LRI's) between base pairs of DNA is offered for the description of nonlinear dynamics of the DNA molecule. We show that LRI's are responsible for the existence of an interval of bistability where two stable stationary states, a narrow, pinned state and a broad, mobile state, coexist at each value of the total energy. The possibility of controlled switching between pinned and mobile states is demonstrated. The mechanism could be important for controlling energy storage and transport in DNA molecules. Another model is offered for the description of nonlinear excitations in proteins and other anharmonic biomolecules. We show that in the highly anharmonic systems a bound state of Davydov and Boussinesq solitons can exist.

Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing

We study the effects of the anharmonic strand-separation dynamics of double-stranded DNA on the infrared spectra of the intramolecular base-pairing hydrogen bonds. Using the extended Peyrard-Bishop-Dauxois model for the DNA breathing dynamics coupled with the Lippincott-Schroeder potential for N-H· · ·N and N-H· · ·O hydrogen bonding, we identify a high-frequency (~96 THz) feature in the infrared spectra. We show that this sharp peak arises as a result of the anharmonic base-pair breathing dynamics of DNA. In addition, we study the effects of friction on the infrared spectra. For higher temperatures (~300 K), where the anharmonicity of DNA dynamics is pronounced, the high-frequency peak is always present irrespective of the friction strength.

Feigenbaum cascade of discrete breathers in a model of DNA

We demonstrate that period-doubled discrete breathers appear from the anticontinuum limit of the driven Peyrard-Bishop-Dauxois model of DNA. These novel breathers result from a stability overlap between subharmonic solutions of the driven Morse oscillator. Subharmonic breathers exist whenever a stability overlap is present within the Feigenbaum cascade to chaos and therefore an entire cascade of such breathers exists. This phenomenon is present in any driven lattice where the on-site potential admits subharmonic solutions. In DNA these breathers may have ramifications for cellular gene expression.

DNA Breathing Dynamics in the Presence of a Terahertz Field

We consider the influence of a terahertz field on the breathing dynamics of double-stranded DNA. We model the spontaneous formation of spatially localized openings of a damped and driven DNA chain, and find that linear instabilities lead to dynamic dimerization, while true local strand separations require a threshold amplitude mechanism. Based on our results we argue that a specific terahertz radiation exposure may significantly affect the natural dynamics of DNA, and thereby influence intricate molecular processes involved in gene expression and DNA replication.

Stress distributions in diblock copolymers

We demonstrate how a generalized self-consistent field theory for polymer melts that includes elastic stress and strain fields can be applied to the study of AB diblock copolymers melts. By obtaining the stress distributions for volume conserving strain loadings where lamellar and hexagonal morphologies are stable, we show that the local stress is reduced at the domain interface but slightly enhanced in the immediate vicinity of the interface. The overall stress profile is the result of the combined effects of chain connectivity across the interface, which yields a positive contribution, and the immiscible nature of the monomers, which leads to a stress reduction because of interfacial tension.

Bubble statistics and dynamics in double-stranded DNA

The dynamical properties of double-stranded DNA are studied in the framework of the Peyrard-Bishop-Dauxois model using Langevin dynamics. Our simulations are analyzed in terms of two distribution functions describing localized separations ("bubbles") of the double strand. The result that the bubble distributions are more sharply peaked at the active sites than thermodynamically obtained distributions is ascribed to the fact that the bubble lifetimes affect the distributions. Certain base-pair sequences are found to promote long-lived bubbles, and we argue that this is a result of length scale competition between the nonlinearity and disorder present in the system.

Probing the mechanical unzipping of DNA

A study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique that allows accurate determination of the dependence of the unzipping forces on unzipping speed and temperature. Our findings agree quantitatively with experimental results for homogeneous DNA, and for lamda-phage DNA we reproduce the recently obtained experimental force-temperature phase diagram. Finally, we argue that there may be fundamental differences between in vivo and in vitro DNA unzipping.

Multipeaked polarons in soft potentials

We consider a minimal coupled charge / excitation-lattice model capturing a competition between linear polaronic self-trapping and the self-focusing effects of a soft nonlinear on-site potential. The standard single-humped polaron ceases to exist above a critical value of the coupling strength, closely related to the inflection point in the nonlinear potential. For couplings beyond this critical value, we find that successive multihumped polaronic solutions correspond to the lowest-energy stationary states of the system, which may admit interesting quantum resonance behavior.

Elastic moduli of multiblock copolymers in the lamellar phase

We study the linear elastic response of multiblock copolymer melts in the lamellar phase, where the molecules are composed of tethered symmetric AB diblock copolymers. We use a self-consistent field theory method, and introduce a real space approach to calculate the tensile and shear moduli as a function of block number. The former is found to be in qualitative agreement with experiment. We find that the increase in bridging fraction with block number, that follows the increase in modulus, is not responsible for the increase in modulus. It is demonstrated that the change in modulus is due to an increase in mixing of repulsive A and B monomers. Under extension, this increase originates from a widening of the interface, and more molecules pulled free of the interface. Under compression, only the second of these two processes acts to increase the modulus.

Improved convergence in block copolymer self-consistent field theory by Anderson mixing

A modification to real space polymeric self-consistent field theory algorithms that greatly improves the convergence properties is presented. The method is based on Anderson mixing [D. G. Anderson, J. Assoc. Comput. Mach. 12, 547 (1965)], and each iteration computed takes negligibly longer to perform than with other methods, but the number of iterations required to reach a high accuracy solution is greatly reduced. No a priori knowledge of possible phases is required to apply this method. We apply our approach to a standard diblock copolymer melt, and demonstrate iteration reductions of more than a factor of 5 in some cases.

Hysteresis and metastability in the quenched turbulent dynamics of the complex Ginzburg-Landau equation

We consider the quenched dynamics of the two-dimensional complex Ginzburg-Landau equation in its turbulent regime. We initialize the system in a frustrated state and observe how frustration affects the evolution towards the turbulent state. This process is performed for parameter values where, for random initial conditions, the system evolves into the turbulent state. We observe that the glassiness of the initial condition can inhibit the occurrence of the absolute instability close to the critical point for that instability in parameter space. Sufficiently far from the critical point, the turbulent state will develop, but only after spending considerable time in a transient metastable state of fixed vortex density. The parameter distance from the critical point is found to scale as an exponential of a power of the lifetime of the metastable state, and with a power exponent depending on the "depth" of the original quench. The limiting regimes of shallow and deep quench are identified by their respective values of the exponent, and the distinct mechanisms leading to the relaxation to turbulence in each case are highlighted.

Three-dimensional elastic compatibility and varieties of twins in martensites

We model a cubic-to-tetragonal martensitic transition by a Ginzburg-Landau free energy in the symmetric strain tensor. We show in three dimensions (3D) that solving the St. Venant compatibility relations for strain, treated as independent field equations, generates three anisotropic long-range potentials between the two order parameter components. These potentials encode 3D discrete symmetries, express the energetics of lattice integrity, and determine 3D textures. Simulation predictions include twins with temperature-varying orientation, helical twins, competing metastable states, and compatibility-induced elastic frustration. Our approach also applies to improper ferroelastics.

Twisted localized modes

In a number of recent papers the so-called twisted localized mode of the discrete nonlinear Schrödinger equation has been proposed. Herein, we study the existence and stability properties of such modes. We analyze the persistence of quasiperiodic modes and study the domains of existence and numerical stability of the exact form of such solutions. We identify the bifurcations through which they lose their stability and follow the behavior of the intrinsic localized modes and their eigenmodes even in the unstable regime.