We studied the role of active deformation dynamics in cell nuclei in chromatin positioning. Model chains containing two types of regions, with high (euchromatic) or low (heterochromatic) mobility, were confined in a pulsating container simulating a nucleus showing dynamic deformations. Brownian dynamic simulations show that the positioning of low mobility regions changes from sites near the periphery to the center if the affinity between these regions and the container periphery disappears. The former and latter positionings are similar to the “conventional” and “inverted” chromatin positionings in nuclei of normal differentiated cells and cells lacking Lamin-related proteins. Additionally, nuclear dynamical deformation played essential roles in “inverted” chromatin positioning.

Coherent x-ray diffraction imaging (CXDI) enables us to visualize noncrystalline sample particles with micrometer to submicrometer dimensions. Using x-ray free-electron laser (XFEL) sources, two-dimensional diffraction patterns are collected from fresh samples supplied to the irradiation area in the “diffraction-before-destruction” scheme. A recent significant increase in the intensity of the XFEL pulse is promising and will allow us to visualize the three-dimensional structures of proteins using XFEL-CXDI in the future. For the protocol proposed for molecular structure determination using future XFEL-CXDI [T. Oroguchi and M. Nakasako, Phys. Rev. E 87, 022712 (2013)], we require an algorithm that can classify the data in accordance with the structural polymorphism of proteins arising from their conformational dynamics. However, most of the algorithms proposed primarily require the numbers of conformational classes, and then the results are biased by the numbers. To improve this point, here we examine whether a method based on the manifold concept can classify simulated XFEL-CXDI data with respect to the structural polymorphism of a protein that predominantly adopts two states. After random sampling of the conformations of the two states and in-between states from the trajectories of molecular dynamics simulations, a diffraction pattern is calculated from each conformation. Classification was performed by using our custom-made program suite named enma, in which the diffusion map (DM) method developed based on the manifold concept was implemented. We successfully classify most of the projection electron density maps phase retrieved from diffraction patterns into each of the two states and in-between conformations without the knowledge of the number of conformational classes. We also examined the classification of the projection electron density maps of each of the three states with respect to the Euler angle. The present results suggest that the DM method is imperative for future applications of XFEL-CXDI experiments for proteins, and clarify issues to be taken care of in the future application.

We study the translocation dynamics of a semiflexible polymer through a nanopore from the cis into the trans compartment containing attractive binding particles (BPs) using the Langevin dynamics simulation in two dimensions. The binding particles accelerate the threading process in two ways: (i) reducing the back-sliding of the translocated monomer, and (ii) providing the pulling force toward the translocation direction. We observe that for certain binding strength (${\epsilon }_c$) and concentration ($\rho$) of the BPs, the translocation is faster than the ideal ratcheting condition as elucidated by Simon, Peskin, and Oster [M. Simon, C. S. Peskin, and G. F. Oster, Proc. Natl. Acad. Sci. USA 89, 3770 (1992)]. The asymmetry produced by the BPs at the trans-side leads to similarities of this process to that of a driven translocation with an applied force inside the pore manifested in various physical quantities. Furthermore, we provide an analytic expression for the force experienced by the translocating chain as well as for the scaled mean first passage time (MFPT), for which we observe that for various combinations of $N, \epsilon$, and $\rho$ the scaled MFPT $\left(\langle \tau \rangle /N^{1.5}{\rho }^{-0.8}\right)$ collapses onto the same master plot. Based on the analysis of our simulation data, we provide plausible arguments with regard to how the scaling theory of driven translocation can be generalized for such a directed diffusion process by replacing the externally applied force with an effective force.

We study the stabilization properties of dipolar Bose-Einstein condensate by temporal modulation of short-range two-body interaction. Through both analytical and numerical methods, we analyze the mean-field Gross-Pitaevskii equation with short-range two-body and long-range, nonlocal, dipolar interaction terms. We derive the equation of motion and effective potential of the dipolar condensate by variational method. We show that there is an enhancement of the condensate stability due to the inclusion of dipolar interaction in addition to the two-body contact interaction. We also show that the stability of the dipolar condensate increases in the presence of time varying two-body contact interaction; the temporal modification of the contact interaction prevents the collapse of dipolar Bose-Einstein condensate. Finally we confirm the semi-analytical prediction through the direct numerical simulations of the governing equation.

We perform a two-parameter bifurcation study of the driven-damped regularized long-wave equation by varying the amplitude and phase of the driver. Increasing the amplitude of the driver brings the system to the regime of spatiotemporal chaos (STC), a chaotic state with a large number of degrees of freedom. Several global bifurcations are found, including codimension-two bifurcations and homoclinic bifurcations involving three-tori and the manifolds of steady waves, leading to the formation of chaotic saddles in the phase space. We identify four distinct routes to STC; they depend on the phase of the driver and involve boundary and interior crises, intermittency, the Ruelle–Takens scenario, the Feigenbaum cascade, an embedded saddle-node, homoclinic, and other bifurcations. This study elucidates some of the recently reported dynamical phenomena.

A mixture of dodecanethiol-capped Au nanoparticles (AuNPs) and the amphiphilic fatty acid, stearic acid, spread as a monomolecular layer on water surface, is observed with Brewster angle microscopy (BAM) to form a two-dimensional network of AuNP clusters through demixing, at concentration of AuNPs by weight $(\overline{\rho })>10\%$ and the surface pressure $(\pi )\ge 10\mathrm{mN}{\mathrm{m}}^{-1}$. For $\pi =15\mathrm{mN}{\mathrm{m}}^{-1}$, the number of nodes $\left(n\right)$ remains unchanged till $\sim 2$ hours and then changes over to a lower $n$ state, where the pattern consists of almost perfect circles with greater in-plane thickness of the AuNP lamellae. For the higher $n$ state the mean-square fluctuation of BAM intensity remains flat and then decays as $f\left(\xi \right)={\xi }^{2\alpha }$ with $\alpha \sim 0.6$ (correlated fluctuations) over the length scales of $400\mu \text{m}$–$6\mu \text{m}$ and below $6\mu \text{m}$, respectively. For the lower $n$ state the fluctuation decays almost over the entire length scale with $\alpha =0.3$, indicating emergence of aperiodicity from quasiperiodicity and a changeover to anticorrelated fluctuations. These patterns can be looked at as two distinct chaotic trajectories in the $I\text{−}{I}^{\prime }$ phase space of the system $(I$ being the scattered light intensity at any position of the pattern and $I^{\prime }$ its gradient) with characteristic Lyapunov exponents.

In continuous attractor neural networks (CANNs), spatially continuous information such as orientation, head direction, and spatial location is represented by Gaussian-like tuning curves that can be displaced continuously in the space of the preferred stimuli of the neurons. We investigate how short-term synaptic depression (STD) can reshape the intrinsic dynamics of the CANN model and its responses to a single static input. In particular, CANNs with STD can support various complex firing patterns and chaotic behaviors. These chaotic behaviors have the potential to encode various stimuli in the neuronal system.

We consider the nonaxisymmetric modes of instability present in Taylor-Couette flow under the application of helical magnetic fields, mainly for magnetic Prandtl numbers close to the inductionless limit, and conduct a full examination of marginal stability in the resulting parameter space. We allow for the azimuthal magnetic field to be generated by a combination of currents in the inner cylinder and fluid itself and introduce a parameter governing the relation between the strength of these currents. A set of governing eigenvalue equations for the nonaxisymmetric modes of instability are derived and solved by spectral collocation with Chebyshev polynomials over the relevant parameter space, with the resulting instabilities examined in detail. We find that by altering the azimuthal magnetic field profiles the azimuthal magnetorotational instability, nonaxisymmetric helical magnetorotational instability, and Tayler instability yield interesting dynamics, such as different preferred mode types and modes with azimuthal wave number $m>1$. Finally, a comparison is given to the recent WKB analysis performed by Kirillov et al. [Kirillov, Stefani, and Fukumoto, J. Fluid Mech. 760, 591 (2014)] and its validity in the linear regime.

In this study melting of irregular ice crystals was observed in an acoustic levitator. The evolution of the particle shape is captured using a high-speed video system. Several typical phenomena have been discovered: change of the particle shape, appearance of a capillary flow of the melted liquid on the particle surface leading to liquid collection at the particle midsection (where the interface curvature is smallest), and appearance of sharp cusps at the particle tips. No such phenomena can be observed during melting of spherical particles. An approximate theoretical model is developed which accounts for the main physical phenomena associated with melting of an irregular particle. The agreement between the theoretical predictions for the melting time, for the evolution of the particle shape, and the corresponding experimental data is rather good.

The problem of electron-ion temperature relaxation in beryllium plasma at various densities $\left(0.185–18.5\mathrm{g}/{\mathrm{cm}}^3\right)$ and temperatures [$(1.0–8)\times {10}^3$ eV] is investigated by using the generalized Lenard-Balescu theory. We consider the correlation effects between electrons and ions via classical and quantum static local field corrections. The numerical results show that the electron-ion pair distribution function at the origin approaches the maximum when the electron-electron coupling parameter equals unity. The classical result of the Coulomb logarithm is in agreement with the quantum result in both the weak $\left({\mathrm{\Gamma }}_{ee}<{10}^{-2}\right)$ and strong $\left({\mathrm{\Gamma }}_{ee}>1\right)$ electron-electron coupling ranges, whereas it deviates from the quantum result at intermediate values of the coupling parameter $\left({10}^{-2}<{\mathrm{\Gamma }}_{ee}<1\right)$. We find that with increasing density of Be, the Coulomb logarithm will decrease and the corresponding relaxation rate ${\nu }_{ie}$ will increase. In addition, a simple fitting law ${\nu }_{ie}/{\nu }_{ie}^{\left(0\right)}=a{({\rho }_{\text{Be}}/{\rho }_0)}^b$ is determined, where ${\nu }_{ie}^{\left(0\right)}$ is the relaxation rate corresponding to the normal metal density of Be and ${\rho }_0$, $a$, and $b$ are the fitting parameters related to the temperature and the degree of ionization $〈Z〉$ of the system. Our results are expected to be useful for future inertial confinement fusion experiments involving Be plasma.

Plasmas with electromagnetic fields turbulent at sub-Larmor scales are a feature of a wide variety of high-energy-density environments and are essential to the description of many astrophysical and laboratory plasma phenomena. Radiation from particles, whether they are relativistic or nonrelativistic, moving through small-scale magnetic turbulence has spectral characteristics distinct from both synchrotron and cyclotron radiation. The radiation, carrying information on the statistical properties of the magnetic turbulence, is also intimately related to the particle diffusive transport. We have investigated, both theoretically and numerically, the transport of nonrelativistic and trans-relativistic particles in plasmas with high-amplitude isotropic sub-Larmor-scale magnetic turbulence, and its relation to the spectra of radiation simultaneously produced by these particles. Consequently, the diffusive and radiative properties of plasmas turbulent on sub-Larmor scales may serve as a powerful tool to diagnosis laboratory and astrophysical plasmas.

The first law of thermodynamics states that the average total energy current between different reservoirs vanishes at large times. In this paper we examine this fact at the level of the full statistics of two-time measurement protocols, also known as the Full Counting Statistics. Under very general conditions, we establish a tight form of the first law asserting that the fluctuations of the total energy current computed from the energy variation distribution are exponentially suppressed in the large time limit. We illustrate this general result using two examples: the Anderson impurity model and a two-dimensional spin lattice model.

By the effect of aggregating currents, some systems display an effective diffusion coefficient that becomes negative in a range of the order parameter, giving rise to bistability among homogeneous states (HSs). By applying a proper multiplicative noise, localized (pinning) states are shown to become stable at the expense of one of the HSs. They are, however, not static, but their location fluctuates with a variance that increases with the noise intensity. The numerical results are supported by an analytical estimate in the spirit of the so-called solvability condition.

The interactions among the elementary components of many complex systems can be qualitatively different. Such systems are therefore naturally described in terms of multiplex or multilayer networks, i.e., networks where each layer stands for a different type of interaction between the same set of nodes. There is today a growing interest in understanding when and why a description in terms of a multiplex network is necessary and more informative than a single-layer projection. Here we contribute to this debate by presenting a comprehensive study of correlations in multiplex networks. Correlations in node properties, especially degree-degree correlations, have been thoroughly studied in single-layer networks. Here we extend this idea to investigate and characterize correlations between the different layers of a multiplex network. Such correlations are intrinsically multiplex, and we first study them empirically by constructing and analyzing several multiplex networks from the real world. In particular, we introduce various measures to characterize correlations in the activity of the nodes and in their degree at the different layers and between activities and degrees. We show that real-world networks exhibit indeed nontrivial multiplex correlations. For instance, we find cases where two layers of the same multiplex network are positively correlated in terms of node degrees, while other two layers are negatively correlated. We then focus on constructing synthetic multiplex networks, proposing a series of models to reproduce the correlations observed empirically and/or to assess their relevance.

We consider four nontrivial ensembles involving Gaussian Wigner and Wishart matrices. These are relevant to problems ranging from multiantenna communication to random supergravity. We derive the matrix probability density, as well as the eigenvalue densities for these ensembles. In all cases the joint eigenvalue density exhibits a biorthogonal structure. A determinantal representation, based on a generalization of Andréief's integration formula, is used to compactly express the $r$-point correlation function of eigenvalues. This representation circumvents the complications encountered in the usual approaches, and the answer is obtained immediately by examining the joint density of eigenvalues. We validate our analytical results using Monte Carlo simulations.

We report on the existence and properties of discrete gap solitons in zigzag arrays of alternating waveguides with positive and negative refractive indices. The zigzag quasi-one-dimensional configuration of the waveguide array introduces strong next-to-nearest neighbor interaction in addition to nearest neighbor coupling. Effective diffraction can be controlled both in size and in sign by the value of the next-to-nearest neighbor coupling coefficient and can even be canceled completely. In the regime where instabilities occur, we found different families of discrete solitons bifurcating from the gap edges of the linear spectrum. We show that both staggered and unstaggered discrete solitons can become highly localized states near the zero diffraction points even for low powers. Stability analysis has shown that the soliton solutions are stable over a wide range of parameters and can exist in focusing, defocusing, and even in an alternating focusing-defocusing array.

The compensated three-dimensional turbulent kinetic energy spectrum exhibits a peculiar bump at wave numbers in the vicinity of the crossover from inertial to viscous regimes due to pile up in turbulent kinetic energy, a phenomenon referred to as the bottleneck effect. The origin of this bump is linked to an inflection point in the second-order structure function in physical space caused by competition between vortex stretching and viscous diffusion mechanisms. The bump location and magnitude are reasonably predicted from a novel analytical solution to the Von Kármán-Howarth equation reflecting the competition between these two mechanisms and accounting for variable structure skewness with decreasing scale.

We consider incompressible Euler flows in terms of the stream function in two dimensions and the vector potential in three dimensions. We pay special attention to the case with singular distributions of the vorticity, e.g., point vortices in two dimensions. An explicit equation governing the velocity potentials is derived in two steps. (i) Starting from the equation for the stream function [Ohkitani, Nonlinearity 21, T255 (2009)], which is valid for smooth flows as well, we derive an equation for the complex velocity potential. (ii) Taking a real part of this equation, we find a dynamical equation for the velocity potential, which may be regarded as a refinement of Bernoulli theorem. In three-dimensional incompressible flows, we first derive dynamical equations for the vector potentials which are valid for smooth fields and then recast them in hypercomplex form. The equation for the velocity potential is identified as its real part and is valid, for example, flows with vortex layers. As an application, the Kelvin-Helmholtz problem has been worked out on the basis the current formalism. A connection to the Navier-Stokes regularity problem is addressed as a physical application of the equations for the vector potentials for smooth fields.

Lacunarity analysis is a scale-dependent method quantifying the translational invariance in patterns. In this work it is used to characterize the distribution of several subsets of atoms in molecular systems. Binary clusters and one-component (ethanol or water) hydrogen-bonded clusters of ethanol-water mixtures with $0-100\mathrm{mol}\%$ ethanol content were analyzed. Molecular dynamics simulations created the configurations, and all were in good agreement with the respective experimental x-ray diffraction data. Lacunarity analysis revealed that the placement of the one-component clusters at low concentration can be described by a multifractal distribution, especially in the case of ethanol. Most of the cases these clusters are not isolated entities, but form islands in binary clusters.