We apply a Boltzmann approach to the kinetic regime of a relativistic Bose-Einstein condensate of scalar bosons by decomposing the one-particle distribution function in a condensate part and a nonzero momentum part of excited modes, leading to a coupled set of evolution equations which are then solved efficiently with an adaptive higher order Runge-Kutta scheme. We compare our results to the partonic cascade Monte Carlo simulation BAMPS for a critical but far from equilibrium case of massless bosons. Motivated by the color glass condensate initial conditions in QCD with a strongly overpopulated initial glasma state, we also discuss the time evolution starting from an overpopulated initial distribution function of massive scalar bosons. In this system a self-similar evolution of the particle cascade with a nonrelativistic turbulent scaling in the infrared sector is observed as well as a relativistic exponent for the direct energy cascade, confirming a weak wave turbulence in the ultraviolet region.

We inquire how structure emerges during the process of protein folding. For this we scrutinize collective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop, and employ various topological techniques, in combination with analytic tools that we deduce from the concept of integrable models and structure of discrete nonlinear Schrödinger equation. The example we consider is an $\alpha$-helical subunit of the HIV envelope glycoprotein gp41. The helical structure is stable when the subunit is part of the biological oligomer. But in isolation, the helix becomes unstable, and the monomer starts deforming. We follow the process computationally. We interpret the evolving structure both in terms of a backbone based Heisenberg spin chain and in terms of a side chain based XY spin chain. We find that in both cases the formation of protein supersecondary structure is akin the formation of a topological Bloch domain wall along a spin chain. During the process we identify three individual Bloch walls and we show that each of them can be modelled with a precision of tenths to several angstroms in terms of a soliton solution to a discrete nonlinear Schrödinger equation.

We study theoretically and by means of molecular dynamics (MD) simulations the generation of mechanical force by grafted polyelectrolytes in an external electric field, which favors its adsorption on the grafting plane. The force arises in deformable bodies linked to the free end of the chain. Varying the field, one controls the length of the nonadsorbed part of the chain and hence the deformation of the target body, i.e., the arising force too. We consider target bodies with a linear force-deformation relation and with a Hertzian one. While the first relation models a coiled Gaussian chain, the second one describes the force response of a squeezed colloidal particle. The theoretical dependences of generated force and compression of the target body on an applied field agree very well with the results of MD simulations. The analyzed phenomenon may play an important role in future nanomachinery, e.g., it may be used to design nanovices to fix nanosized objects.

A two-dimensional hexagonal smectic structure formed by point topological defects and intersecting defect walls was discovered. This unique structure was predicted theoretically about 30 years ago but not observed. For a long time the hexagonal structure was a challenge for experimentalists. A different type of self-organization in smectic films was found and used to form the hexagonal structure. Methods applied for building the hexagonal phase can be used for the formation of complicated liquid-crystal structures.

Plastic events in amorphous solids can be much more than just “shear transformation zones” when the positional degrees of freedom are coupled nontrivially to other degrees of freedom. Here we consider magnetic amorphous solids where mechanical and magnetic degrees of freedom interact, leading to rather complex plastic events whose nature must be disentangled. In this paper we uncover the anatomy of the various contributions to some typical plastic events. These plastic events are seen as Barkhausen noise or other “serrated noises.” Using theoretical considerations we explain the observed statistics of the various contributions to the considered plastic events. The richness of contributions and their different characteristics imply that in general the statistics of these serrated noises cannot be universal, but rather highly dependent on the state of the system and on its microscopic interactions.

The rate of turbulent kinetic energy dissipation in spatially developing, uniformly sheared turbulence is examined experimentally. In the far-downstream fully developed region of the flow, we confirm that the dissipation parameter $C_{\varepsilon }$ is constant. More importantly, however, we find two upstream regions where this parameter could be scaled with the local turbulent Reynolds number as $C_{\varepsilon }=A{\text{Re}}_{\lambda }^{\alpha }$; the exponents in these two regions are, respectively, $\alpha =-0.6$ and $0.5$. The observed changes in scaling laws are explained by consideration of structural changes in the turbulence.

The comparison performed in Berry et al. [Phys. Rev. E 91, 032915 (2015)] between the skill in predicting the El Niño-Southern Oscillation climate phenomenon by the prediction method of Berry et al. and the “past-noise” forecasting method of Chekroun et al. [Proc. Natl. Acad. Sci. USA 108, 11766 (2011)] is flawed. Three specific misunderstandings in Berry et al. are pointed out and corrected.

In this Reply we provide additional results which allow a better comparison of the diffusion forecast and the “past-noise” forecasting (PNF) approach for the El Niño index. We remark on some qualitative differences between the diffusion forecast and PNF, and we suggest an alternative use of the diffusion forecast for the purposes of forecasting the probabilities of extreme events.

We demonstrate that a compact manometer experiment allows direct observation of a delay to the classical electric-field-induced Freedericksz transition produced by flow in a highly dispersive nematic liquid crystal layer. The Ericksen-Leslie equations are used to show that a flow aligning torque generated in the nematic layer under Poiseuille flow competes with the orthogonal electric-field reorientation torque. This model fully reproduces the experimental results using only self-consistently determined viscosity values, and predicts a more generally applicable expression for the dependence of the delay $E_c\propto \sqrt{\zeta /\mathrm{\Delta }{\chi }_e}$ on the shear rate $\zeta$ and on the electric susceptibility anisotropy $\mathrm{\Delta }{\chi }_e$.

Two-reservoir thermochemical engines are established by using near-independent particles (including Maxwell-Boltzmann, Fermi-Dirac, and Bose-Einstein particles) as the working substance. Particle and heat fluxes can be formed based on the temperature and chemical potential gradients between two different reservoirs. A rectangular-type energy filter with width $\mathrm{\Gamma }$ is introduced for each engine to weaken the coupling between the particle and heat fluxes. The efficiency at maximum power of each particle system decreases monotonously from an upper bound ${\eta }^{+}$ to a lower bound ${\eta }^{-}$ when $\mathrm{\Gamma }$ increases from 0 to $\infty$. It is found that the ${\eta }^{+}$ values for all three systems are bounded by ${\eta }_{\mathrm{C}}/2\le {\eta }^{+}\le {\eta }_{\mathrm{C}}/\left(2-{\eta }_{\mathrm{C}}\right)$ due to strong coupling, where ${\eta }_{\mathrm{C}}$ is the Carnot efficiency. For the Bose-Einstein system, it is found that the upper bound is approximated by the Curzon-Ahlborn efficiency: ${\eta }_{\mathrm{CA}}=1-\sqrt{1-{\eta }_{\mathrm{C}}}$. When $\mathrm{\Gamma }\to \infty$, the intrinsic maximum powers are proportional to the square of the temperature difference of the two reservoirs for all three systems, and the corresponding lower bounds of efficiency at maximum power can be simplified in the same form of ${\eta }^{-}={\eta }_{\mathrm{C}}/\left[1+a_0\left(2-{\eta }_{\mathrm{C}}\right)\right]$.

We present a dynamic off-equilibrium method for the study of continuous transitions, which represents a dynamic generalization of the usual equilibrium cumulant method. Its main advantage is that critical parameters are derived from numerical data obtained much before equilibrium has been attained. Therefore, the method is particularly useful for systems with long equilibration times, like spin glasses. We apply it to the three-dimensional Ising spin-glass model, obtaining accurate estimates of the critical exponents and of the critical temperature with a limited computational effort.

Thermal rectification and negative differential thermal conductance were realized in harmonic chains in this work. We used the generalized Caldeira-Leggett model to study the heat flow. In contrast to most previous studies considering only the linear system-bath coupling, we considered the nonlinear system-bath coupling based on recent experiment [Eichler et al., Nat. Nanotech. 6, 339 (2011)]. When the linear coupling constant is weak, the multiphonon processes induced by the nonlinear coupling allow more phonons transport across the system-bath interface and hence the heat current is enhanced. Consequently, thermal rectification and negative differential thermal conductance are achieved when the nonlinear couplings are asymmetric. However, when the linear coupling constant is strong, the umklapp processes dominate the multiphonon processes. Nonlinear coupling suppresses the heat current. Thermal rectification is also achieved. But the direction of rectification is reversed compared to the results of weak linear coupling constant.

We study analytically the dynamics and the microstructural changes of a host medium caused by a driven tracer particle moving in a confined, quiescent molecular crowding environment. Imitating typical settings of active microrheology experiments, we consider here a minimal model comprising a geometrically confined lattice system (a two-dimensional striplike or a three-dimensional capillary-like system) populated by two types of hard-core particles with stochastic dynamics (a tracer particle driven by a constant external force and bath particles moving completely at random). Resorting to a decoupling scheme, which permits us to go beyond the linear-response approximation (Stokes regime) for arbitrary densities of the lattice gas particles, we determine the force-velocity relation for the tracer particle and the stationary density profiles of the host medium particles around it. These results are validated a posteriori by extensive numerical simulations for a wide range of parameters. Our theoretical analysis reveals two striking features: (a) We show that, under certain conditions, the terminal velocity of the driven tracer particle is a nonmonotonic function of the force, so in some parameter range the differential mobility becomes negative, and (b) the biased particle drives the whole system into a nonequilibrium steady state with a stationary particle density profile past the tracer, which decays exponentially, in sharp contrast with the behavior observed for unbounded lattices, where an algebraic decay is known to take place.

We describe and explore accelerating oscillatory fronts in sonic vacua with nonlocal interactions. As an example, a chain of particles oscillating in the plane and coupled by linear springs, with fixed ends, is considered. When one end of this system is harmonically excited in the transverse direction, one observes accelerated propagation of the excitation front, accompanied by an almost monochromatic oscillatory tail. Position of the front obeys the scaling law $l\left(t\right)\sim t^{4/3}$. The frequency of the oscillatory tail remains constant, and the wavelength scales as $\lambda \sim t^{1/3}$. These scaling laws result from the nonlocal effects; we derive them analytically (including the scaling coefficients) from a continuum approximation. Moreover, a certain threshold excitation amplitude is required in order to initiate the front propagation. The initiation threshold is evaluated on the basis of a simplified discrete model, further reduced to a completely integrable nonlinear system. Given their simplicity, nonlinear sonic vacua of the type considered herein should be common in periodic lattices.

We study the repartition of monodisperse bubbles at the inlet node of an asymmetric microfluidic loop for low to high bubble densities. In large loops, we evidence a new regime. Contrary to the classical belief, we point out that bubbles are directed not towards the arm having the higher total flow rate but towards the arm with the higher water flow rate at low and moderate relative gas flow rates. At higher rates, they enter the longer arm when they reach close packing in the shorter arm. In small loops, we evidence a clogging regime at high relative gas flow rates. Collisions between bubbles coming from the two arms at the outlet clog the longer arm. We propose a comprehensive analysis allowing us to explain these results.

We consider a continuum model of active viscoelastic matter, whereby an active nematic liquid crystal is coupled to a minimal model of polymer dynamics with a viscoelastic relaxation time ${\tau }_C$. To explore the resulting interplay between active and polymeric dynamics, we first generalize a linear stability analysis (from earlier studies without polymer) to derive criteria for the onset of spontaneous heterogeneous flows (strain rate) and/or deformations (strain). We find two modes of instability. The first is a viscous mode, associated with strain rate perturbations. It dominates for relatively small values of ${\tau }_C$ and is a simple generalization of the instability known previously without polymer. The second is an elastomeric mode, associated with strain perturbations, which dominates at large ${\tau }_C$ and persists even as ${\tau }_C\to \infty$. We explore the dynamical states to which these instabilities lead by means of direct numerical simulations. These reveal oscillatory shear-banded states in one dimension and activity-driven turbulence in two dimensions even in the elastomeric limit ${\tau }_C\to \infty$. Adding polymer can also have calming effects, increasing the net throughput of spontaneous flow along a channel in a type of drag reduction. The effect of including strong antagonistic coupling between the nematic and polymer is examined numerically, revealing a rich array of spontaneously flowing states.

The Nosé-Hoover (NH) equation provides a universal and powerful computer simulation protocol to realize an equilibrium canonical temperature for a target physical system. Here we demonstrate a general formalism to couple such NH equations. We provide a coupled NH equation that is constructed by coupling the NH equation of a target physical system and the NH equation of a temperature system. Thus, in contrast to the conventional single NH equation, the heat-bath temperature is a dynamical variable. The temperature fluctuations are not ad hoc, but instead are generated by the newly defined temperature system, and the statistical distribution of the temperature is completely described with an arbitrarily given probability function. The current equations of motion thus describe the physical system that develops with a predistributed fluctuating temperature, which allows enhanced sampling of the physical system. Since the total system is governed by a prescribed distribution, the equilibrium of the physical system is also reconstructed by reweighting. We have formulated a scheme for specifically setting the distribution of the dynamical inverse temperature and demonstrate the statistical relationship between the dynamical and physical temperatures. The statistical features, dynamical properties, and sampling abilities of the current method are demonstrated via the distributions, trajectories, dynamical correlations, and free energy landscapes for both a model system and a biomolecular system. These results indicated that the current coupled NH scheme works well.

A two-dimensional dense fluid of frictional grains is shown to exhibit time-chaotic, spatially heterogeneous flow in a range of stress values, $\sigma$, chosen in the unstable region of $\mathsf{s}$-shaped flow curves. Stress-controlled simulations reveal a phase diagram with reentrant stationary flow for small and large stress $\sigma$. In between, no steady flow state can be reached, instead the system either jams or displays time-dependent heterogeneous strain rates $\dot{\gamma }(\mathbf{r},t)$. The results of simulations are in agreement with the stability analysis of a simple hydrodynamic model, coupling stress and microstructure which we tentatively associate with the frictional contact network.

A new approach to turbulence closure is presented that eliminates the need to specify a predefined turbulence model and instead provides for fully adaptive, self-optimizing, autonomic closures. The closure is autonomic in the sense that the simulation itself determines the optimal local, instantaneous relation between any unclosed term and resolved quantities through the solution of a nonlinear, nonparametric system identification problem. This nonparametric approach allows the autonomic closure to freely adapt to varying nonlinear, nonlocal, nonequilibrium, and other turbulence characteristics in the flow. Even a simple implementation of the autonomic closure for large eddy simulations provides remarkably more accurate results in a priori tests than do dynamic versions of traditional prescribed closures.