Bundles of actin filaments and molecular motors of the myosin family are a common subcellular organizational motif. Typically, such bundles are under contractile stress resulting from interactions between the filaments and the motors. This holds in particular for contractile rings that appear in the late stages of cell division in animal cells and that cleave the mother into two daughter cells. It was recently shown that myosin organizes into regularly spaced clusters along rings in mammalian cells, whereas myosin clusters in fission yeast travel along the perimeter of actomyosin rings [Wollrab et al., Nat. Commun. 7, 11860 (2016)]. A mechanism based on the association of the structurally polar actin filaments into bipolar structures was shown to provide a common explanation for both observations. Here, we analyze the dynamics of this mechanism in detail. We find a rich phase diagram depending on the actomyosin interaction strength and the stability of the bipolar structures. The system can notably organize into traveling waves. Furthermore, we identify the nature of the bifurcations connecting the various patterns as parameters are changed. Finally, we report experimental patterns observed in cytokinetic rings in fission yeast and link them to solutions of our dynamic equations. Our analysis highlights the possible role played by local polarity sorting of actin filaments for the dynamics and functionality of actomyosin networks.

We consider the model of asexual evolution with migration, which was proposed by Waclaw et al. [Phys. Rev. Lett. 105, 268101 (2010)]. This model setting is based on the standard mutation scheme from the quasispecies theory but with replicators moving from one habitat to another. The primary goal is to solve exactly the infinite population-genome length version of the model for the independent random distribution of fitnesses considered in the original paper. Moreover, we propose the analytical solution for the single peak and the symmetric fitness landscape. Our analytical solution is exact at the limit of large $N$. We found two phases—the correlated phase with the identical distributions of mutations in both habitats and the uncorrelated phase where the second habitat is choosing another peak of distribution in sequence space compared to the peak in the first habitat.

Using density functionals from fundamental measure theory, phase diagrams and crystal-fluid surface tensions in additive and nonadditive (Asakura-Oosawa model) two-dimensional binary hard-disk mixtures are determined for the whole range of size ratios $q=\text{small}\text{diameter/large}\text{diameter}$, assuming random disorder (lattice points or interstitial occupied by large or small disks at random) in the crystal phase. The fluid-crystal transitions are first order due to the assumption of a periodic unit cell in the density-functional calculations. Qualitatively, the shape of the phase diagrams is similar to the case of three-dimensional hard-sphere mixtures. For the nonadditive case, a broadening of the fluid-crystal coexistence region is found for small $q$, whereas for large $q$ a vapor-fluid transition intervenes. In the additive case, we find a sequence of spindle-type, azeotropic, and eutectic phase diagrams upon lowering $q$ from 1 to 0.6. The transition from azeotropic to eutectic is different from the three-dimensional case. Surface tensions in general become smaller (up to a factor 2) upon addition of a second species and they are rather small. The minimization of the functionals proceeds without restrictions and optimized graphics card routines are used.

Electric field driven Frèedericksz transition in chiral nematic (cholesteric) planar liquid crystal cell is studied in the presence of flexoelectric effect. An inhomogeneity of electric field and finiteness of anchoring energy are considered. The extra contribution to the electric field induced by flexoelectricity is taken into account as well as the common contribution arising from the applied voltage $U$. Equilibrium director distribution is obtained in dependence on voltage and flexoelectric coefficients by numerical minimization of the free energy. The threshold voltage was found to decrease with the increase of the flexoelectric coefficients within the range of high flexoelectric coefficients. Thus flexoelectricity promotes the transition. The orientational structure becomes asymmetric about the center of the cell due to flexoelectricity, even in the case of symmetric boundary conditions. The equilibrium structure was also shown to be different for $U>0$ and $U<0$. It was found, that for sufficiently high flexoelectric coefficients the director distribution can be described by a simple function. In this case the planar helicoidal structure transfers into a hybrid-aligned one as the voltage increases. This transformation may form the basis for new flexoelectricity-based switching devices. The nonmonotonic behavior of threshold voltage can be observed in the case of small flexoelectric coefficients. An analytical form of the stability conditions was obtained for the planar helicoidal configuration. We have shown that the Frèedericksz transition can be either continuous or discontinuous depending on the material constants and thickness of the liquid crystal cell.

We investigate experimentally the possible buckling of a thin rod when penetrating downwards into a granular packing. When its bottom end reaches a specific depth, the rod may start buckling provided that the embrace is not enough to stop that phenomenon. The critical rod depth $z_c$ at buckling is observed to scale with the rod length $L$ either as $1/L$ or $1/L^2$. These two scalings are shown to arise from the two resistant force terms that come into play during the rod penetration: a pressure force at the bottom of the rod that increases linearly with depth and a frictional force on the rod side that increases quadratically with depth. At the buckling point, the destabilizing force corresponds to the expected value given from conventional Euler's critical load for a rod bottom end considered as fixed in the granular clutch. Finally, we draw a buckling-nonbuckling phase diagram in a parameter space given by the rod aspect ratio and a rod-to-grain stress ratio.

Electron-positron plasmas may be present in laboratory experiments and certain astrophysical environments. Due to the inertia symmetry there have been some debates about whether the nonlinear electrostatic solitons generated easily in electron-proton plasmas may develop in electron-positron plasmas. In this study we show the formation of electrostatic solitons and electromagnetic Alfvén waves in extensive magnetized electron-positron plasma system generated by streaming instabilities based on electromagnetic particle simulations along with fluid theory analyses. In particular, the four-component beam-plasma system may lead to the formation of interlacing electron and positron solitons in the early evolution stage (say, $t<20{\omega }_p^{-1}$, where ${\omega }_p^{}$ is the plasma frequency) and large-amplitude Alfvén waves in the later phase (say, $t>150{\omega }_p^{-1}$). The magnetic-field perturbations are generated by the beam and firehose-type instabilities associated with temperature anisotropy of ${\mathrm{T}}_{\parallel }>{\mathrm{T}}_{\perp }$ resulting from the parallel plasma heating by the electrostatic instability. It is shown that the growth rates and the dominant wavelengths of both electrostatic and electromagnetic instabilities are consistent with the fluid theory. The coexistence of electrostatic solitons and electromagnetic Alfvén waves with significant magnetic field fluctuations in the same system is a unique feature of electron-positron plasmas and the unified theory behind the formation mechanisms is well addressed in the paper.

We develop a lattice Boltzmann (LB) model for immiscible two-phase flow simulations with central moments (CMs). This successfully combines a three-dimensional nonorthogonal CM-based LB scheme [De Rosis, Phys. Rev. E 95, 013310 (2017)] with our previous color-gradient LB model [Saito, Abe, and Koyama, Phys. Rev. E 96, 013317 (2017)]. Hydrodynamic melt-jet breakup simulations show that the proposed model is significantly more stable, even for flow with extremely high Reynolds numbers, up to $O\left({10}^6\right)$. This enables us to investigate the phenomena expected under actual reactor conditions.

From the gambling logs of an online lottery game we extract the probability distribution of various quantities (e.g., bet value, total pool size, waiting time between successive gambles) as well as related correlation coefficients. We view the net change of income of each player as a random walk. The mean-squared displacement of these net income random walks exhibits a transition between a superdiffusive and a normal diffusive regime. We discuss different random-walk models with truncated power-law step lengths distributions that allow us to reproduce some of the properties extracted from the gambling logs. Analyzing the mean-squared displacement and the first-passage time distribution for these models allows us to identify the key features needed for observing this crossover from superdiffusion to normal diffusion.

We consider the triangular kagome XXZ-Ising model (TKL XXZ-Ising model) formed by inserting small triangles (“a-trimers”) with XXZ spin-1 inside the triangles of the kagome lattice (“b-trimers”). It is a mixed spin system and can be solved exactly by transforming into the kagome lattice with the general transformation method for decorated spin systems. In the absence of an external field, we integrate out the quantum spins of the a-trimers and map the TKL model to the kagome Ising model exactly. We obtain the full phase diagram and their zero-temperature entropies (e.g., $s_{\max }=5.48895$ per unit cell is given for the phase with the maximum entropy). When an external field is applied, 20 phases are found due to the quantum fluctuations of a-trimers. Moreover, the high spins in the a-trimers can lead to a stable quantized growth of the magnetization process in the Heisenberg limit.

Due to time delays in signal transmission and processing, phase lags are inevitable in realistic complex oscillator networks. Conventional wisdom is that phase lags are detrimental to network synchronization. Here we show that judiciously chosen phase lag modulations can result in significantly enhanced network synchronization. We justify our strategy of phase modulation, demonstrate its power in facilitating and enhancing network synchronization with synthetic and empirical network models, and provide an analytic understanding of the underlying mechanism. Our work provides an alternative approach to synchronization optimization in complex networks, with insights into control of complex nonlinear networks.

Correlation matrices are a major type of multivariate data. To examine properties of a given correlation matrix, a common practice is to compare the same quantity between the original correlation matrix and reference correlation matrices, such as those derived from random matrix theory, that partially preserve properties of the original matrix. We propose a model to generate such reference correlation and covariance matrices for the given matrix. Correlation matrices are often analyzed as networks, which are heterogeneous across nodes in terms of the total connectivity to other nodes for each node. Given this background, the present algorithm generates random networks that preserve the expectation of total connectivity of each node to other nodes, akin to configuration models for conventional networks. Our algorithm is derived from the maximum entropy principle. We will apply the proposed algorithm to measurement of clustering coefficients and community detection, both of which require a null model to assess the statistical significance of the obtained results.

Protein fibrils are currently of great academic and practical interest because of their involvement in scores of severe human diseases and their promising use in various high-technology devices. The Oosawa-Kasai (OK) model of protein self-assembly into fibrils has been widely used to gain mechanistic insight into the process of fibril formation and growth. Here this model is employed to obtain exact and mathematically simple expressions for the probability $P_n$ of an individual fibril of $n$ protein monomers to grow to a macroscopically large size and for the mean time ${\tau }_n$ that such a fibril needs for its formation. These expressions quantify the increase of $P_n$ and the decrease of ${\tau }_n$ with increasing the concentration of monomeric protein in the solution. When used for analysis of experimental $P_n$ and ${\tau }_n$ data, they make it possible to determine the parameters characterizing fibril nucleation and growth in the framework of the OK model. Finally, an expression is found for the mean time of the first appearance of an $n$-sized fibril in the protein solution. The results obtained are applicable to the formation of other aggregates corresponding to the OK fibrils, such as the one-dimensional Kossel-Stranski crystals and Ising ferromagnets.

When a material surface is functionalized so as to acquire some type of order, functionalization of which soft condensed matter systems have recently provided many interesting examples, the modeler faces an alternative. Either the order is described on the curved, physical surface where it belongs, or it is described on a flat surface that is unrolled as preimage of the physical surface under a suitable height function. This paper applies a general method that pursues the latter avenue by lifting whatever order tensor is deemed appropriate from a flat to a curved surface. We specialize this method to nematic shells, for which it also provides a simple but perhaps convincing interpretation of the outcomes of some molecular dynamics experiments on ellipsoidal shells.

This paper considers the non-Hermitian Zakharov-Shabat scattering problem which forms the basis for defining the $\mathrm{SU}\left(2\right)$-nonlinear Fourier transform (NFT). The theoretical underpinnings of this generalization of the conventional Fourier transform is quite well established in the Ablowitz-Kaup-Newell-Segur formalism; however, efficient numerical algorithms that could be employed in practical applications are still unavailable. In this paper, we present two fast inverse NFT algorithms with $O(KN+N{log}^{2}N)$ complexity and a convergence rate of $O\left(N^{-2}\right)$, where $N$ is the number of samples of the signal and $K$ is the number of eigenvalues. These algorithms are realized using a new fast layer-peeling (LP) scheme $\left[O\left(N{log}^{2}N\right)\right]$ together with a new fast Darboux transformation (FDT) algorithm $\left[O(KN+N{log}^{2}N)\right]$ previously developed by V. Vaibhav [Phys. Rev. E 96, 063302 (2017)]. The proposed fast inverse NFT algorithm proceeds in two steps: The first step involves computing the radiative part of the potential using the fast LP scheme for which the input is synthesized under the assumption that the radiative potential is nonlinearly bandlimited, i.e., the continuous spectrum has a compact support. The second step involves addition of bound states using the FDT algorithm. Finally, the performance of these algorithms is demonstrated through exhaustive numerical tests.

We show by extensive molecular dynamics simulations that accurate predictions of liquid-vapor coexistence in molten alkali halides can be achieved in terms of a rigid ion potential description in which temperature-dependent ionic diameters are employed. The new ionic sizes result from the fitting of the experimental isothermal compressibilities, a condition whose physical implications and consequences are illustrated. The same diameters also allow us to formulate confident predictions for the compressibilities of salts in cases where the experimental data are lacking. The extension of the present approach to molten alkali-halide mixtures and to other classes of molten salts is discussed.

We consider closed quantum systems (into which baths may be integrated) that are driven, i.e., subject to time-dependent Hamiltonians. Our point of departure is the assumption that if systems start in non-Gibbsian states at some initial energies, the resulting probability distributions of work may be largely independent of the specific initial energies. It is demonstrated that this assumption has some far-reaching consequences, e.g., it implies the validity of the Jarzynski relation for a large class of non-Gibbsian initial states. By performing numerical analysis on integrable and nonintegrable spin systems, we find the above assumption fulfilled for all examples considered. Through an analysis based on Fermi's golden rule, we partially relate these findings to the applicability of the eigenstate thermalization ansatz to the respective driving operators.

We consider the two- (2D) and three-dimensional (3D) Ising models on a square lattice at the critical temperature $T_c$, under Monte Carlo spin flip dynamics. The bulk magnetization and the magnetization of a tagged line in the 2D Ising model, and the bulk magnetization and the magnetization of a tagged plane in the 3D Ising model, exhibit anomalous diffusion. Specifically, their mean-square displacements increase as power laws in time, collectively denoted as $\sim t^c$, where $c$ is the anomalous exponent. We argue that the anomalous diffusion in all these quantities for the Ising model stems from time-dependent restoring forces, decaying as power laws in time—also with exponent $c$ —in striking similarity to anomalous diffusion in polymeric systems. Prompted by our previous work that has established a memory-kernel based generalized Langevin equation (GLE) formulation for polymeric systems, we show that a closely analogous GLE formulation holds for the Ising model as well. We obtain the memory kernels from spin-spin correlation functions, and the formulation allows us to consistently explain anomalous diffusion as well as anomalous response of the Ising model to an externally applied magnetic field in a consistent manner.