Video microscopy (VM) experiments and Brownian dynamics (BD) simulations were used to measure and model superparamagnetic colloidal particles in rotating magnetic fields for interaction energies on the order of the thermal energy, $\mathit{kT}$. Results from experiments and simulations were compared for isolated particle rotation, particle rotation within doublets, doublet rotation, and separation within doublets vs field rotation frequency. Agreement between VM and BD results was obtained at all frequencies and amplitudes only by including exact two-body hydrodynamic interactions and relevant relaxation times of magnetic dipoles. Frequency-dependent particle forces and torques cause doublets to rotate at low frequencies via dipolar interactions and at high frequencies via hydrodynamic translation-rotation coupling. By matching measurements and simulations for a range of conditions, our findings unambiguously demonstrate the quantitative forms of dipolar and hydrodynamic interactions necessary to capture nonequilibrium, steady-state dynamics of Brownian colloids in magnetic fields.

In the so-called quasiplanar texture of a nematic layer confined between parallel plates with homeotropic anchoring conditions, the director field rotates by $\pi$ between limit surfaces so that field lines have the shape of a dowsing Y-shaped wooden tool. The orientation of the director field at midheight of the layer is arbitrary for symmetry reasons and is thus very sensitive to perturbations. We point out that contrary to accepted ideas the quasiplanar texture can be preserved infinitely in spite of its metastability with respect to the homogeneous homeotropic texture. We propose to call such a long-lived version of the quasiplanar texture the dowser texture. We demonstrate both experimentally and theoretically that in samples of variable thickness, the director field is sensitive to the gradient of the sample thickness through a linear coupling term. As a result, it has a tendency to follow the direction of the thickness gradient. Because of its sensitivity to perturbations we propose to call the midplane director field the dowser field and its tendency to follow the thickness gradient cuneitropism. Under effect of the gradient field, the dowser field obeys the sine-Gordon equation and exhibits domain walls that correspond to the well-known solitonic solutions of the sine-Gordon model.

By the chemical cross-linking of rigid molecules, liquid crystal polymer (LCP) has been envisaged as a novel heterogeneous material due to the fact that various optical and geometric states of the liquid crystalline (LC) phases are projected onto the polymeric constituents. The phase behavior, which refers to the macroscopic shape change of LCP under thermotropic phase change, is a compelling example of such optical-mechanical coupling. In this study, the photomechanical behavior, which broadly refers to the thermal- or light-induced actuation of smectic solids, is investigated using three-dimensional nonlinear finite element analysis (FEA). First, the various phases of LC are considered as well as their relation to polymeric conformation defined by the strain energy of the smectic polymer; a comprehensive constitutive equation that bridges the strong, optomechanical coupling is then derived. Such photomechanical coupling is incorporated in the FEA considering geometric nonlinearity, which is vital to understanding the large-scale light-induced bending behavior of the smectic solid.To demonstrate the simulation capability of the present model, numerous examples of photomechanical deformations are investigated parametrically, either by changing the operating conditions such as stimuli (postsynthesis) or the intrinsic properties (presynthesis). When compared to nematic solids, distinguished behaviors due to smectic substances are found herein and discussed through experiments. The quasisoftness that bidirectionally couples microscopic variables to mechanical behavior is also explained, while considering the effect of nonlinearity. In addition to providing a comprehensive measure that could deepen the knowledge of photomechanical coupling, the use of the proposed finite element framework offers an insight into the design of light-responsive actuating systems made of smectic solids.

In terms of Darboux transformation we investigate the dynamic process of spin wave passing through a magnetic soliton. It causes nonlinear excitations, such as Akhmediev breathers solution and Kuznetsov-Ma soliton. The former case demonstrates a spatial periodic process of a magnetic soliton forming the petal with four pieces. The spatial separation of adjacent magnetic petals increases rapidly, while one valley splits into two and the amplitude of valley increases gradually with the increasing amplitude of spin wave. The other case shows a localized process of the spin-wave background. In the limit case, we get rogue waves and clarify its formation mechanism.

We study symmetric and asymmetric optical multipeak solitons on a continuous wave background in the femtosecond regime of a single-mode fiber. Key characteristics of such multipeak solitons, such as the formation mechanism, propagation stability, and shape-changing collisions, are revealed in detail. Our results show that this multipeak (symmetric or asymmetric) mode could be regarded as a single pulse formed by a nonlinear superposition of a periodic wave and a single-peak (W-shaped or antidark) soliton. In particular, a phase diagram for different types of nonlinear excitations on a continuous wave background, including the unusual multipeak soliton, the W-shaped soliton, the antidark soliton, the periodic wave, and the known breather rogue wave, is established based on the explicit link between exact solution and modulation instability analysis. Numerical simulations are performed to confirm the propagation stability of the multipeak solitons with symmetric and asymmetric structures. Further, we unveil a remarkable shape-changing feature of asymmetric multipeak solitons. It is interesting that these shape-changing interactions occur not only in the intraspecific collision (soliton mutual collision) but also in the interspecific interaction (soliton-breather interaction). Our results demonstrate that each multipeak soliton exhibits the coexistence of shape change and conservation of the localized energy of a light pulse against the continuous wave background.

We present simulations of the one-dimensional Oslo rice pile model in which the critical height at each site is randomly reset after each toppling. We use the fact that the stationary state of this sand-pile model is hyperuniform to reach system of sizes $>{10}^7$. Most previous simulations were seriously flawed by important finite-size corrections. We find that all critical exponents have values consistent with simple rationals: $\nu =\frac{4}{3}$ for the correlation length exponent, $D=\frac{9}{4}$ for the fractal dimension of avalanche clusters, and $z=\frac{10}{7}$ for the dynamical exponent. In addition, we relate the hyperuniformity exponent to the correlation length exponent $\nu$. Finally, we discuss the relationship with the quenched Edwards-Wilkinson model, where we find in particular that the local roughness exponent is ${\alpha }_{\mathrm{loc}}=1$.

We propose a conceptually different method for solving nonlinear inverse scattering problems (ISPs) such as are commonly encountered in tomographic ultrasound imaging, seismology, and other applications. The method is inspired by the theory of nonlocality of physical interactions and utilizes the relevant formalism. We formulate the ISP as a problem whose goal is to determine an unknown interaction potential $V$ from external scattering data. Although we seek a local (diagonally dominated) $V$ as the solution to the posed problem, we allow $V$ to be nonlocal at the intermediate stages of iterations. This allows us to utilize the one-to-one correspondence between $V$ and the $T$ matrix of the problem. Here it is important to realize that not every $T$ corresponds to a diagonal $V$ and we, therefore, relax the usual condition of strict diagonality (locality) of $V$. An iterative algorithm is proposed in which we seek $T$ that is (i) compatible with the measured scattering data and (ii) corresponds to an interaction potential $V$ that is as diagonally dominated as possible. We refer to this algorithm as to the data-compatible $T$-matrix completion. This paper is Part I in a two-part series and contains theory only. Numerical examples of image reconstruction in a strongly nonlinear regime are given in Part II [H. W. Levinson and V. A. Markel, Phys. Rev. E 94, 043318 (2016)]. The method described in this paper is particularly well suited for very large data sets that become increasingly available with the use of modern measurement techniques and instrumentation.

This is Part II of the paper series on data-compatible $T$-matrix completion (DCTMC), which is a method for solving nonlinear inverse problems. Part I of the series [H. W. Levinson and V. A. Markel, Phys. Rev. E 94, 043317 (2016)] contains theory and here we present simulations for inverse scattering of scalar waves. The underlying mathematical model is the scalar wave equation and the object function that is reconstructed is the medium susceptibility. The simulations are relevant to ultrasound tomographic imaging and seismic tomography. It is shown that DCTMC is a viable method for solving strongly nonlinear inverse problems with large data sets. It provides not only the overall shape of the object, but the quantitative contrast, which can correspond, for instance, to the variable speed of sound in the imaged medium.

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

We present a pore-scale dissolution model for the simulation of reactive transport in complex porous media such as those encountered in carbon-storage injection processes. We couple a lattice Boltzmann model for flow calculation with a finite-volume method for solving chemical transport equations, and allow the computational grid to change as mineral surfaces are dissolved according to first-order reaction kinetics. We appraise this scheme for use with high Péclet number flows in three-dimensional geometries and show how the popular first-order convection scheme is affected by severe numerical diffusion when grid Péclet numbers exceed unity, and confirm that this can be overcome relatively easily by using a second-order method in conjunction with a flux-limiter function. We then propose a surface rescaling method which uses parabolic elements to counteract errors in surface area exposed by the Cartesian grid and avoid the use of more complex embedded surface methods when surface reaction kinetics are incorporated. Finally, we compute dissolution in an image of a real porous limestone rock sample injected with HCl for different Péclet numbers and obtain dissolution patterns in concordance with theory and experimental observation. A low injection flow rate was shown to lead to erosion of the pore space concentrated at the face of the rock, whereas a high flow rate leads to wormhole formation.

The roles that metal ions play in the structure and dynamics of RNA molecules are long-standing problems that have been studied extensively but are still not well understood. Here we show that metal ions have distributions around RNA molecules that strongly depend on the types and concentrations of the metal ions and also the electrostatic surface of the molecule. In particular, the ion distributions may not balance all the local electronegativity of the molecule. These ion distributions do not only greatly affect local structures but also lead to different local dynamics of RNA. We studied the effects of different ion solutions on the structure and dynamics of RNA by taking the $\mathrm{pre}{\mathrm{Q}}_1$ riboswitch aptamer domain as an illustrative example and using molecular dynamics simulations. Since the local structures and dynamics of RNAs are important to their functions, our results also indicate that the selection of proper ion conditions is necessary to model them correctly, in contrast to the use of diverse ion solutions in current molecular dynamics simulations.

We use supersymmetry to calculate exact spectral densities for a class of complex random matrix models having the form $M=S+LXR$, where $X$ is a random noise part $X$, and $S,L,R$ are fixed structure parts. This is a certain version of the “external field” random matrix models. We find twofold integral formulas for arbitrary structural matrices. We investigate some special cases in detail and carry out numerical simulations. The presence or absence of a normality condition on $S$ leads to a qualitatively different behavior of the eigenvalue densities.

We consider pinned diffusion paths that are explored by a particle moving via a conservative force while being in thermal equilibrium with its surroundings. To probe rare transitions, we use the Onsager-Machlup (OM) functional as a path probability distribution function for transition paths that are constrained to start and stop at predesignated points in different energy basins after a fixed time. The OM theory is based on a discrete-time version of Brownian dynamics, and thus it possesses a finite number of time steps. Here we explore the continuous-time limit where the number of time steps, and hence the dimensionality, becomes infinite. In this regime, the OM functional has been commonly regularized by using the Ito-Girsanov change of measure. This regularized form can then be used as a basis of a numerical algorithm to probe transition paths. In doing so, time again is discretized, progressing in fixed increments. When sampling paths, we find that numerical schemes based on this regularized continuous-time limit can fail catastrophically in describing the path of a particle moving in a potential with multiple wells. The origin of this behavior is traced to numerical instabilities in the discrete version of the continuous-time path measure that are not present in the infinite-dimensional limit. These instabilities arise because of the difficulty of satisfying, in finite dimensions, the conditions imposed by Ito's lemma that was an essential ingredient in the derivation of the regularized continuous-time measure. As an important consequence of this analysis, we conclude that the most probable diffusion path is not a physical entity because the thermodynamic action is effectively flat and cannot be minimized.

We consider the survival probability $f\left(t\right)$ of a random walk with a constant hopping rate $w$ on a host lattice of fractal dimension $d$ and spectral dimension $d_s\le 2$, with spatially correlated traps. The traps form a sublattice with fractal dimension $d_a<d$ and are characterized by the absorption rate $w_a$ which may be finite (imperfect traps) or infinite (perfect traps). Initial coordinates are chosen randomly at or within a fixed distance of a trap. For weakly absorbing traps ($w_a\ll w$), we find that $f\left(t\right)$ can be closely approximated by a stretched exponential function over the initial stage of relaxation, with stretching exponent $\alpha =1-(d-d_a)/d_w$, where $d_w$ is the random walk dimension of the host lattice. At the end of this initial stage there occurs a crossover to power-law kinetics $f\left(t\right)\sim t^{-\alpha }$ with the same exponent $\alpha$ as for the stretched exponential regime. For strong absorption $w_a\gtrsim w$, including the limit of perfect traps $w_a\to \infty$, the stretched exponential regime is absent and the decay of $f\left(t\right)$ follows, after a short transient, the aforementioned power law for all times.

Random search processes for targets that are inhomogeneously distributed in a search domain require spatially inhomogeneous search strategies to find the target as fast as possible. Here, we compare systematically the efficiency of homogeneous and inhomogeneous strategies for intermittent search, which alternates stochastically between slow, diffusive motion in which the target can be detected and fast ballistic motion during which targets cannot be detected. We analyze the mean first-passage time of homogeneous and inhomogeneous strategies for three paradigmatic search problems: (1) the narrow escape problem, i.e., the searcher looks for a small area on the boundary of the search domain, (2) reaction kinetics, i.e., the detection of an immobile target in the interior of a search domain, and (3) the reaction-escape problem, i.e., the searcher first needs to find a mobile target before it can escape through a narrow area on the boundary. Using families of inhomogeneous strategies, partially motivated by the organization of the cytoskeleton in cells with a centrosome, we show that they are almost always more efficient than homogeneous strategies.

We present experimental measurements concerning the response of an excitable micropillar laser with saturable absorber to incoherent as well as coherent perturbations. The excitable response is similar to the behavior of spiking neurons but with much faster time scales. It is accompanied by a subnanosecond nonlinear delay that is measured for different bias pump values. This mechanism provides a natural scheme for encoding the strength of an ultrafast stimulus in the response delay of excitable spikes (temporal coding). Moreover, we demonstrate coherent and incoherent perturbations techniques applied to the micropillar with perturbation thresholds in the range of a few femtojoules. Responses to coherent perturbations assess the cascadability of the system. We discuss the physical origin of the responses to single and double perturbations with the help of numerical simulations of the Yamada model and, in particular, unveil possibilities to control the relative refractory period that we recently evidenced in this system. Experimental measurements are compared to both numerical simulations of the Yamada model and analytic expressions obtained in the framework of singular perturbation techniques. This system is thus a good candidate to perform photonic spike processing tasks in the framework of novel neuroinspired computing systems.

We study the dynamical properties of human communication through different channels, i.e., short messages, phone calls, and emails, adopting techniques from neuronal spike train analysis in order to characterize the temporal fluctuations of successive interevent times. We first measure the so-called local variation (LV) of incoming and outgoing event sequences of users and find that these in- and out-LV values are positively correlated for short messages and uncorrelated for phone calls and emails. Second, we analyze the response-time distribution after receiving a message to focus on the input-output relationship in each of these channels. We find that the time scales and amplitudes of response differ between the three channels. To understand the effects of the response-time distribution on the correlations between the LV values, we develop a point process model whose activity rate is modulated by incoming and outgoing events. Numerical simulations of the model indicate that a quick response to incoming events and a refractory effect after outgoing events are key factors to reproduce the positive LV correlations.

A hybrid asymptotic-numerical method is presented for obtaining an asymptotic estimate for the full probability distribution of capture times of a random walker by multiple small traps located inside a bounded two-dimensional domain with a reflecting boundary. As motivation for this study, we calculate the variance in the capture time of a random walker by a single interior trap and determine this quantity to be comparable in magnitude to the mean. This implies that the mean is not necessarily reflective of typical capture times and that the full density must be determined. To solve the underlying diffusion equation, the method of Laplace transforms is used to obtain an elliptic problem of modified Helmholtz type. In the limit of vanishing trap sizes, each trap is represented as a Dirac point source that permits the solution of the transform equation to be represented as a superposition of Helmholtz Green's functions. Using this solution, we construct asymptotic short-time solutions of the first-passage-time density, which captures peaks associated with rapid capture by the absorbing traps. When numerical evaluation of the Helmholtz Green's function is employed followed by numerical inversion of the Laplace transform, the method reproduces the density for larger times. We demonstrate the accuracy of our solution technique with a comparison to statistics obtained from a time-dependent solution of the diffusion equation and discrete particle simulations. In particular, we demonstrate that the method is capable of capturing the multimodal behavior in the capture time density that arises when the traps are strategically arranged. The hybrid method presented can be applied to scenarios involving both arbitrary domains and trap shapes.

The sporadic nature of gene expression at the single-cell level—long periods of inactivity punctuated by bursts of mRNA or protein production—plays a critical role in diverse cellular processes. To elucidate the cellular role of bursting in gene expression, synthetic biology approaches have been used to design simple genetic circuits with bursty mRNA or protein production. Understanding how such genetic circuits can be designed with the ability to control burst-related parameters requires the development of quantitative stochastic models of gene expression. In this work, we analyze stochastic models for the regulation of gene expression bursts by strongly interacting small RNAs. For the parameter range considered, results based on mean-field approaches are significantly inaccurate and alternative analytical approaches are needed. Using simplifying approximations, we obtain analytical results for the corresponding steady-state distributions that are in agreement with results from stochastic simulations. These results indicate that regulation by small RNAs, in the strong interaction limit, can be used to effectively modulate the frequency of bursting. We explore the consequences of such regulation for simple genetic circuits involving feedback effects and switching between promoter states.

The phase-flip transition has been demonstrated in a host of coupled nonlinear oscillator models, many pertaining directly to understanding neural dynamics. However, there is little evidence that this phenomenon occurs in the brain. Using simultaneous microelectrode recordings in the nonhuman primate cerebral cortex, we demonstrate the presence of phase-flip transitions between oscillatory narrow-band local field potential signals separated by several centimeters. Specifically, we show that sharp transitions between in-phase and antiphase synchronization are accompanied by a jump in synchronization frequency. These findings are significant for two reasons. First, they validate predictions made by model systems. Second, they have potentially far reaching implications for our understanding of the mechanisms underlying corticocortical communication, which are thought to rely on narrow-band oscillatory synchronization with specific relative phase relationships.