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.

Measurement and memory in the periodically driven complex Ginzburg-Landau equation.

In the present work we illustrate that classical but nonlinear systems may possess features reminiscent of quantum ones, such as memory, upon suitable external perturbation. As our prototypical example, we use the two-dimensional complex Ginzburg-Landau equation in its vortex glass regime. We impose an external drive as a perturbation mimicking a quantum measurement protocol, with a given "measurement rate" (the rate of repetition of the drive) and "mixing rate" (characterized by the intensity of the drive). Using a variety of measures, we find that the system may or may not retain its coherence, statistically retrieving its original glass state, depending on the strength and periodicity of the perturbing field. The corresponding parametric regimes and the associated energy cascade mechanisms involving the dynamics of vortex waveforms and domain boundaries are discussed.

Bubble lifetimes in DNA gene promoters and their mutations affecting transcription.

Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity in the framework of the Peyrard-Bishop-Dauxois model. Extensive microcanonical simulations are used with energies corresponding to physiological temperature. The bubble lifetime profiles along the DNA sequences demonstrate a significant reduction of the average lifetime at the mutation sites when the mutated promoter decreases transcription, while a corresponding enhancement of the bubble lifetime is observed in the case of mutations leading to increased transcription. The relative difference in bubble lifetimes between the mutated and wild type promoters at the position of mutation varies from 20% to more than 30% as the bubble length decreases.

Distributions of bubble lifetimes and bubble lengths in DNA.

We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version (ePBD) having a sequence-dependent stacking interaction, emphasizing the effect of the sequences' guanine-cytosine (GC)/adenine-thymine (AT) content on these distributions. For both models we find that base pair-dependent (GC vs AT) thresholds for considering complementary nucleotides to be separated are able to reproduce the observed dependence of the melting temperature on the GC content of the DNA sequence. Using these thresholds for base pair openings, we obtain bubble lifetime distributions for bubbles of lengths up to ten base pairs as the GC content of the sequences is varied, which are accurately fitted with stretched exponential functions. We find that for both models the average bubble lifetime decreases with increasing either the bubble length or the GC content. In addition, the obtained bubble length distributions are also fitted by appropriate stretched exponential functions and our results show that short bubbles have similar likelihoods for any GC content, but longer ones are substantially more likely to occur in AT-rich sequences. We also show that the ePBD model permits more, longer-lived, bubbles than the PBD system.

Speed-of-light pulses in the massless nonlinear Dirac equation with a potential.

We consider the massless nonlinear Dirac (NLD) equation in 1+1 dimension with scalar-scalar self-interaction g^{2}/2(Ψ[over ¯]Ψ)^{2} in the presence of three external electromagnetic real potentials V(x), a potential barrier, a constant potential, and a potential well. By solving numerically the NLD equation, we find different scenarios depending on initial conditions, namely, propagation of the initial pulse along one direction, splitting of the initial pulse into two pulses traveling in opposite directions, and focusing of two initial pulses followed by a splitting. For all considered cases, the final waves travel with the speed of light and are solutions of the massless linear Dirac equation. During these processes the charge and the energy are conserved, whereas the momentum is conserved when the solutions possess specific symmetries. For the case of the constant potential, we derive exact analytical solutions of the massless NLD equation that are also solutions of the massless linearized Dirac equation. Decay or growth of the initial pulse is also predicted from the evolution of the charge for the case of a non-zero imaginary part of the potential.

Variational approach to studying solitary waves in the nonlinear Schrödinger equation with complex potentials.

We discuss the behavior of solitary wave solutions of the nonlinear Schrödinger equation (NLSE) as they interact with complex potentials, using a four-parameter variational approximation based on a dissipation functional formulation of the dynamics. We concentrate on spatially periodic potentials with the periods of the real and imaginary part being either the same or different. Our results for the time evolution of the collective coordinates of our variational ansatz are in good agreement with direct numerical simulation of the NLSE. We compare our method with a collective coordinate approach of Kominis and give examples where the two methods give qualitatively different answers. In our variational approach, we are able to give analytic results for the small oscillation frequency of the solitary wave oscillating parameters which agree with the numerical solution of the collective coordinate equations. We also verify that instabilities set in when the slope dp(t)/dv(t) becomes negative when plotted parametrically as a function of time, where p(t) is the momentum of the solitary wave and v(t) the velocity.

Dynamical playground of a higher-order cubic Ginzburg-Landau equation: From orbital connections and limit cycles to invariant tori and the onset of chaos.

The dynamical behavior of a higher-order cubic Ginzburg-Landau equation is found to include a wide range of scenarios due to the interplay of higher-order physically relevant terms. We find that the competition between the third-order dispersion and stimulated Raman scattering effects gives rise to rich dynamics: this extends from Poincaré-Bendixson-type scenarios, in the sense that bounded solutions may converge either to distinct equilibria via orbital connections or to space-time periodic solutions, to the emergence of almost periodic and chaotic behavior. One of our main results is that third-order dispersion has a dominant role in the development of such complex dynamics, since it can be chiefly responsible (even in the absence of other higher-order effects) for the existence of periodic, quasiperiodic, and chaotic spatiotemporal structures. Suitable low-dimensional phase-space diagnostics are devised and used to illustrate the different possibilities and identify their respective parametric intervals over multiple parameters of the model.

Soliton dynamics in optical fibers using the generalized traveling-wave method.

The generalized traveling wave method (GTWM) is applied to the nonlinear Schrödinger (NLS) equation with general perturbations in order to obtain the equations of motion for an ansatz with six collective coordinates, namely the soliton position, the amplitude, the inverse of the soliton width, the velocity, the chirp, and the phase. The advantage of the new ansatz is that it yields three pairs of canonically conjugated coordinates and momenta that all are well-behaved. The new ansatz is applied to model the dynamics of a soliton in a dispersion-shifted optical fiber described by the generalized NLS, including dissipation, higher-order dispersion, Raman scattering, and self-steepening perturbations. It is shown that the GTWM is equivalent to the modified method of moments, which considers the time variation of the norm, the first and the second moment of the norm, the momentum, the first moment of the momentum, and the energy for the perturbed NLS equation.

Solitons and vortices in two-dimensional discrete nonlinear Schrödinger systems with spatially modulated nonlinearity.

We consider a two-dimensional (2D) generalization of a recently proposed model [Gligoric et al., Phys. Rev. E 88, 032905 (2013)], which gives rise to bright discrete solitons supported by the defocusing nonlinearity whose local strength grows from the center to the periphery. We explore the 2D model starting from the anticontinuum (AC) limit of vanishing coupling. In this limit, we can construct a wide variety of solutions including not only single-site excitations, but also dipole and quadrupole ones. Additionally, two separate families of solutions are explored: the usual "extended" unstaggered bright solitons, in which all sites are excited in the AC limit, with the same sign across the lattice (they represent the most robust states supported by the lattice, their 1D counterparts being those considered as 1D bright solitons in the above-mentioned work), and the vortex cross, which is specific to the 2D setting. For all the existing states, we explore their stability (also analytically, when possible). Typical scenarios of instability development are exhibited through direct simulations.

Allostery through protein-induced DNA bubbles.

Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resulting melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.

Soliton stability criterion for generalized nonlinear Schrödinger equations.

A stability criterion for solitons of the driven nonlinear Schrödinger equation (NLSE) has been conjectured. The criterion states that p'(v)<0 is a sufficient condition for instability, while p'(v)>0 is a necessary condition for stability; here, v is the soliton velocity and p=P/N, where P and N are the soliton momentum and norm, respectively. To date, the curve p(v) was calculated approximately by a collective coordinate theory, and the criterion was confirmed by simulations. The goal of this paper is to calculate p(v) exactly for several classes and cases of the generalized NLSE: a soliton moving in a real potential, in particular a time-dependent ramp potential, and a time-dependent confining quadratic potential, where the nonlinearity in the NLSE also has a time-dependent coefficient. Moreover, we investigate a logarithmic and a cubic NLSE with a time-independent quadratic potential well. In the latter case, there is a bisoliton solution that consists of two solitons with asymmetric shapes, forming a bound state in which the shapes and the separation distance oscillate. Finally, we consider a cubic NLSE with parametric driving. In all cases, the p(v) curve is calculated either analytically or numerically, and the stability criterion is confirmed.

Thermomechanical stability and mechanochemical response of DNA: a minimal mesoscale model.

We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures for denaturation under torque and stretch, phase diagrams for stable DNA, probe/response profiles under mechanical loads, and the density of dsDNA as a function of stretch and twist. We compare our predictions with available single molecule manipulation experiments and find strong agreement. In particular we elucidate the difference between angularly constrained and unconstrained overstretching. We propose that the smoothness of the angularly constrained overstretching transition is a consequence of the molecule being in the vicinity of criticality for a broad range of values of applied tension.

Phonon localization drives polar nanoregions in a relaxor ferroelectric.

Relaxor ferroelectrics exemplify a class of functional materials where interplay between disorder and phase instability results in inhomogeneous nanoregions. Although known for about 30 years, there is no definitive explanation for polar nanoregions (PNRs). Here we show that ferroelectric phonon localization drives PNRs in relaxor ferroelectric PMN-30%PT using neutron scattering. At the frequency of a preexisting resonance mode, nanoregions of standing ferroelectric phonons develop with a coherence length equal to one wavelength and the PNR size. Anderson localization of ferroelectric phonons by resonance modes explains our observations and, with nonlinear slowing, the PNRs and relaxor properties. Phonon localization at additional resonances near the zone edges explains competing antiferroelectric distortions known to occur at the zone edges. Our results indicate the size and shape of PNRs that are not dictated by complex structural details, as commonly assumed, but by phonon resonance wave vectors. This discovery could guide the design of next generation relaxor ferroelectrics.

Attractive inverse square potential, U(1) gauge, and winding transitions.

The inverse square potential arises in a variety of different quantum phenomena, yet notoriously it must be handled with care: it suffers from pathologies rooted in the mathematical foundations of quantum mechanics. We show that its recently studied conformality breaking corresponds to an infinitely smooth winding-unwinding topological transition for the classical statistical mechanics of a one-dimensional system: this describes the tangling or untangling of floppy polymers under a biasing torque. When the ratio between torque and temperature exceeds a critical value the polymer undergoes tangled oscillations, with an extensive winding number. At lower torque or higher temperature the winding number per unit length is zero. Approaching criticality, the correlation length of the order parameter-the extensive winding number-follows a Kosterlitz-Thouless-type law. The model is described by the Wilson line of a (0+1) U(1) gauge theory, and applies to the tangling or untangling of floppy polymers and to the winding or diffusing kinetics in diffusion-convection reactions.

Static and dynamic phases for magnetic vortex matter with attractive and repulsive interactions.

Exotic vortex states with long range attraction and short range repulsion have recently been proposed to arise in certain superconducting hybrid structures such as type-I/type-II layered systems as well as multi-band superconductors. In previous work it has been shown that such systems can form clump or phase separated states, but little is known about how they behave in the presence of pinning and under an applied drive. Using large scale simulations we examine the static and dynamic properties of such vortex states interacting with random and periodic pinning. In the absence of pinning this system does not form patterns but instead undergoes complete phase separation. When pinning is present there is a transition from inhomogeneous to homogeneous vortex configurations similar to a wetting phenomenon. Under an applied drive, a dynamical dewetting process can occur from a strongly pinned homogeneous state into pattern forming states, such as moving stripes that are aligned with the direction of drive or moving labyrinth or clump phases. We show that a signature of the exotic vortex interactions observable with transport measurements is a robust double peak feature in the differential resistance curves. Our results should be valuable for determining whether such vortex interactions are occurring in these systems and also for addressing the general problem of systems with competing interactions in the presence of random and periodic pinning.

RKKY interaction and intrinsic frustration in non-Fermi-liquid metals.

We study the RKKY interaction in non-Fermi-liquid metals. We find that the RKKY interaction mediated by some non-Fermi-liquid metals can be of much longer range than for a Fermi liquid. The oscillatory nature of the RKKY interaction thus becomes more important in such non-Fermi liquids, and gives rise to enhanced frustration when the spins form a lattice. Frustration suppresses the magnetic ordering temperature of the lattice spin system. Furthermore, we find that the spin system with a longer range RKKY interaction can be described by the Brazovskii model, where the ordering wave vector lies on a higher dimensional manifold. Strong fluctuations in such a model lead to a first-order phase transition and/or glassy phase. This may explain some recent experiments where glassy behavior was observed in stoichiometric heavy fermion material close to a ferromagnetic quantum critical point.

Inelastic electron tunneling spectroscopy for topological insulators.

Inelastic electron tunneling spectroscopy is a powerful spectroscopy that allows one to investigate the nature of local excitations and energy transfer in the system of interest. We study inelastic electron tunneling spectroscopy for topological insulators and investigate the role of inelastic scattering on the Dirac node states on the surface of topological insulators. Local inelastic scattering is shown to significantly modify the Dirac node spectrum. In the weak coupling limit, peaks and steps are induced in second derivative d2I/dV2. In the strong coupling limit, the local negative-U centers are formed at impurity sites, and the Dirac cone structure is fully destroyed locally. At intermediate coupling, resonance peaks emerge. We map out the evolution of the resonance peaks from weak to strong coupling, which interpolate nicely between the two limits. There is a sudden qualitative change of behavior at intermediate coupling, indicating the possible existence of a local quantum phase transition. We also find that, even for a simple local phonon mode, the inherent coupling of spin and orbital degrees in topological insulators leads to the spin-polarized texture in inelastic Friedel oscillations induced by the local mode.

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.

Discrete breathers in a nonlinear polarizability model of ferroelectrics.

We present a family of discrete breathers, which exists in a nonlinear polarizability model of ferroelectric materials. The core-shell model is set up in its nondimensionalized Hamiltonian form and its linear spectrum is examined in a range of temperatures. Subsequently, seeking localized solutions in the gap of the linear spectrum, we establish that numerically exact and potentially stable discrete breathers exist for a wide range of frequencies therein. In addition, we present nonlinear normal mode, extended spatial profile solutions from which the breathers bifurcate, as well as other associated phenomena such as the formation of phantom breathers within the model. The full bifurcation picture of the emergence and disappearance of the breathers is complemented by direct numerical simulations of their dynamical instability, when the latter arises. The effect of breathers on properties such as nonlinear dielectric response is discussed.

Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia.

In a previous study, we detected a 6p25-p24 region linked to schizophrenia in families with high composite cognitive deficit (CD) scores, a quantitative trait integrating multiple cognitive measures. Association mapping of a 10 Mb interval identified a 260 kb region with a cluster of single-nucleotide polymorphisms (SNPs) significantly associated with CD scores and memory performance. The region contains two colocalising genes, LYRM4 and FARS2, both encoding mitochondrial proteins. The two tagging SNPs with strongest evidence of association were located around the overlapping putative promoters, with rs2224391 predicted to alter a transcription factor binding site (TFBS). Sequencing the promoter region identified 22 SNPs, many predicted to affect TFBSs, in a tight linkage disequilibrium block. Luciferase reporter assays confirmed promoter activity in the predicted promoter region, and demonstrated marked downregulation of expression in the LYRM4 direction under the haplotype comprising the minor alleles of promoter SNPs, which however is not driven by rs2224391. Experimental evidence from LYRM4 expression in lymphoblasts, gel-shift assays and modelling of DNA breathing dynamics pointed to two adjacent promoter SNPs, rs7752203-rs4141761, as the functional variants affecting expression. Their C-G alleles were associated with higher transcriptional activity and preferential binding of nuclear proteins, whereas the G-A combination had opposite effects and was associated with poor memory and high CD scores. LYRM4 is a eukaryote-specific component of the mitochondrial biogenesis of Fe-S clusters, essential cofactors in multiple processes, including oxidative phosphorylation. LYRM4 downregulation may be one of the mechanisms involved in inefficient oxidative phosphorylation and oxidative stress, increasingly recognised as contributors to schizophrenia pathogenesis.