We present a computational study of a simple one-dimensional map with dynamics composed of stretching, permutations of equally sized cells, and diffusion. We observe that the combination of the aforementioned dynamics results in eigenmodes with long-time exponential decay rates. The decay rate of the eigenmodes is shown to be dependent on the choice of permutation and changes nonmonotonically with the diffusion coefficient for many of the permutations. The global mixing rate of the map $M$ in the limit of vanishing diffusivity approximates well the decay rates of the eigenmodes for small diffusivity, however this global mixing rate does not bound the rates for all values of the diffusion coefficient. This counterintuitively predicts a deceleration in the asymptotic mixing rate with an increasing diffusivity rate. The implications of the results on finite time mixing are discussed.

A two-dimensional Lennard-Jones system in a circular and rotating container has been studied by means of molecular dynamics technique. A nonequilibrium transition to the rotating stage has been detected in a delayed time since an instant switching of the frame rotation. This transition is attributed to the increase of the density at the wall because of the centrifugal force. At the same time the phase transition occurs, the inner system changes its configuration of the solid-state type into the liquid type. Impact of angular frequency and molecular roughness on the transport properties of the nonrotating and rotating systems is analyzed.

The morphology of dried blood droplets derives from the deposition of red cells, the main components of their solute phase. Up to now, evaporation-induced convective flows were supposed to be at the base of red cell distribution in blood samples. Here, we present a direct visualization by videomicroscopy of the internal dynamics in desiccating blood droplets, focusing on the role of cell concentration and plasma composition. We show that in diluted suspensions, the convection is promoted by the rich molecular composition of plasma, whereas it is replaced by an outward red blood cell displacement front at higher hematocrits. We also evaluate by ultrasounds the effect of red cell deposition on the temporal evolution of sample rigidity and adhesiveness.

The interaction of a gravity-driven water film with an evolving solid substrate (calcite or ice) results in the formation of fascinating wavy patterns similar both in caves and in ice-falls. Due to their remarkable similarity, we adopt a unified approach in the study of pattern formation of longitudinally oriented organ-pipe-like structures, called flutings. Since the morphogenesis of cave patterns can evolve for millennia, they have an additional value as silent repositories of past climates. Fluting formation is studied with the aid of gradient expansion and center manifold projection. In particular, through gradient expansion, a Benney-type equation accounting for the movable boundary is obtained. The coupling with a wall evolution equation provides a morphodynamic model for fluting formation, explored through linear and nonlinear analyses. In this way, closed relationships for the selected wave number and for the finite amplitude are achieved. However, as finite-amplitude monochromatic waves may be destabilized by nonlinear interactions with other modes, we verify, through center manifold projection, the stability of the fundamental to subharmonic disturbances. Conclusively, we perform numerical simulations of the fully nonlinear equations to validate the theory results.

We study the conductivities $\sigma$ of (i) the equilibrium isochoric state ${\sigma }_{\mathrm{is}}$, (ii) the equilibrium isobaric state ${\sigma }_{\mathrm{ib}}$, and also the (iii) nonequilibrium ultrafast matter state ${\sigma }_{\mathrm{uf}}$ with the ion temperature $T_i$ less than the electron temperature $T_e$. Aluminum, lithium, and carbon are considered, being increasingly complex warm dense matter systems, with carbon having transient covalent bonds. First-principles calculations, i.e., neutral-pseudoatom (NPA) calculations and density-functional theory (DFT) with molecular-dynamics (MD) simulations, are compared where possible with experimental data to characterize ${\sigma }_{\mathrm{ic}}$, ${\sigma }_{\mathrm{ib}}$, and ${\sigma }_{\mathrm{uf}}$. The NPA ${\sigma }_{\mathrm{ib}}$ is closest to the available experimental data when compared to results from DFT with MD simulations, where simulations of about 64–125 atoms are typically used. The published conductivities for Li are reviewed and the value at a temperature of 4.5 eV is examined using supporting x-ray Thomson-scattering calculations. A physical picture of the variations of $\sigma$ with temperature and density applicable to these materials is given. The insensitivity of $\sigma$ to $T_e$ below 10 eV for carbon, compared to Al and Li, is clarified.

To simulate a diffusion process, a usual approach is to discretize the time in the associated stochastic differential equation. This is the approach used in the Euler method. In the present work we consider a one-dimensional diffusion process where the terms occurring, within the stochastic differential equation, prevent the process entering a region. The outcome is a naturally occurring boundary (which may be absorbing or reflecting). A complication occurs in a simulation of this situation. The term involving a random variable, within the discretized stochastic differential equation, may take a trajectory across the boundary into a “forbidden region.” The naive way of dealing with this problem, which we refer to as the “standard” approach, is simply to reset the trajectory to the boundary, based on the argument that crossing the boundary actually signifies achieving the boundary. In this work we show, within the framework of the Euler method, that such resetting introduces a spurious force into the original diffusion process. This force may have a significant influence on trajectories that come close to a boundary. We propose a corrected numerical scheme, for simulating one-dimensional diffusion processes with naturally occurring boundaries. This involves correcting the standard approach, so that an exact property of the diffusion process is precisely respected. As a consequence, the proposed scheme does not introduce a spurious force into the dynamics. We present numerical test cases, based on exactly soluble one-dimensional problems with one or two boundaries, which suggest that, for a given value of the discrete time step, the proposed scheme leads to substantially more accurate results than the standard approach. Alternatively, the standard approach needs considerably more computation time to obtain a comparable level of accuracy to the proposed scheme, because the standard approach requires a significantly smaller time step.

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

A single-cone finite-difference lattice scheme is developed for the (2+1)-dimensional Dirac equation in presence of general electromagnetic textures. The latter is represented on a (2+1)-dimensional staggered grid using a second-order-accurate finite difference scheme. A Peierls-Schwinger substitution to the wave function is used to introduce the electromagnetic (vector) potential into the Dirac equation. Thereby, the single-cone energy dispersion and gauge invariance are carried over from the continuum to the lattice formulation. Conservation laws and stability properties of the formal scheme are identified by comparison with the scheme for zero vector potential. The placement of magnetization terms is inferred from consistency with the one for the vector potential. Based on this formal scheme, several numerical schemes are proposed and tested. Elementary examples for single-fermion transport in the presence of in-plane magnetization are given, using material parameters typical for topological insulator surfaces.

Tracking experiments in dense biological tissues reveal a diversity of sources for local energy injection at the cell scale. The effect of cell motility has been largely studied, but much less is known about the effect of the observed volume fluctuations of individual cells. We consider a microscopic model of “actively deforming” particles where local fluctuations of the particle size constitute a unique source of motion. We demonstrate that collective motion can emerge under the sole influence of such active volume fluctuations. We interpret the onset of diffusive motion as a nonequilibrium first-order phase transition, which arises at a well-defined amplitude of self-deformation. This behavior contrasts with the glassy dynamics produced by self-propulsion, but resembles the mechanical response of soft solids under mechanical deformation. It thus constitutes an example of an active yielding transition.

We report a transition from a disordered state to an ordered state in the flow of nearly monodisperse granular matter flowing in an inclined channel with planar slide walls and a bumpy base, using discrete element method simulations. For low particle-sidewall friction coefficients, the flowing particles are disordered, however, for high sidewall friction, an ordered state is obtained, characterized by a layering of the particles and hexagonal packing of the particles in each layer. The extent of ordering, quantified by the local bond-orientational order parameter, varies in the cross section of the channel, with the highest ordering near the sidewalls. The flow transition significantly affects the local rheology—the effective friction coefficient is lower, and the packing fraction is higher, in the ordered state compared to the disordered state. A simple model, incorporating the extent of local ordering, is shown to describe the rheology of the system.

Emergent statistical attributes, and therefore the equations of state, of an assembly of interacting charge carriers embedded within a complex molecular environment frequently exhibit a variety of anomalies, particularly in the high-density (equivalently, the concentration) regime, which are not well understood, because they do not fall under the low-concentration phenomenologies of Debye-Hückel-Onsager and Poisson-Nernst-Planck, including their variants. To go beyond, we here use physical concepts and mathematical tools from quantum scattering theory, transport theory with the Stosszahlansatz of Boltzmann, and classical electrodynamics (Lorentz gauge) and obtain analytical expressions both for the average and the frequency-wave vector-dependent longitudinal and transverse current densities, diffusion coefficient, and the charge density, and therefore the analytical expressions for (a) the chemical potential, activity coefficient, and the equivalent conductivity for strong electrolytes and (b) the current-voltage characteristics for ion-transport processes in complex molecular environments. Using a method analogous to the notion of Debye length and thence the electrical double layer, we here identify a pair of characteristic length scales (longitudinal and the transverse), which, being wave vector and frequency dependent, manifestly exhibit nontrivial fluctuations in space-time. As a unifying theme, we advance a quantity (inverse length dimension), $g_{\mathrm{scat}}^{\left(\mathrm{a}\right)}$, which embodies all dynamical interactions, through various quantum scattering lengths, relevant to molecular species a, and the analytical behavior which helps us to rationalize the properties of strong electrolytes, including anomalies, in all concentration regimes. As an example, the behavior of $g_{\mathrm{scat}}^{\left(\mathrm{a}\right)}$ in the high-concentration regime explains the anomalous increase of the Debye length with concentration, as seen in a recent experiment on electrolyte solutions. We also put forth an extension of the standard diffusion equation, which manifestly incorporates the effects arising from the underlying microscopic collisions among constituent molecular species. Furthermore, we show a nontrivial connection between the current-voltage characteristics of electrolyte solutions and the Landauer's approach to electrical conduction in mesoscopic solids and thereby establish a definite conceptual bridge between the two disjoint subjects. For numerical insight, we present results on the aqueous solution of KCl as an example of strong electrolyte, and the transport (conduction as well as diffusion) of ${\mathrm{K}}^{+}$ ions in water, as an example of ion transport across the voltage-gated channels in biological cells.

Logarithmic or Sinai-type subdiffusion is usually associated with random force disorder and nonstationary potential fluctuations whose root-mean-squared amplitude grows with distance. We show here that extremely persistent, macroscopic logarithmic diffusion also universally emerges at sufficiently low temperatures in stationary Gaussian random potentials with spatially decaying correlations, known to exist in a broad range of physical systems. Combining results from extensive simulations with a scaling approach we elucidate the physical mechanism of this unusual subdiffusion. In particular, we explain why with growing temperature and/or time a first crossover occurs to standard, power-law subdiffusion, with a time-dependent power-law exponent, and then a second crossover occurs to normal diffusion with a disorder-renormalized diffusion coefficient. Interestingly, the initial, nominally ultraslow diffusion turns out to be much faster than the universal de Gennes–Bässler–Zwanzig limit of the renormalized normal diffusion, which realistically cannot be attained at sufficiently low temperatures and/or for strong disorder. The ultraslow diffusion is also shown to be nonergodic and it displays a local bias phenomenon. Our simple scaling theory not only explains our numerical findings but qualitatively also has a predictive character.

We consider the massless nonlinear Dirac (NLD) equation in $1+1$ dimension with scalar-scalar self-interaction $\frac{g^2}{2}{\left(\overline{\mathrm{\Psi }}\mathrm{\Psi }\right)}^2$ in the presence of three external electromagnetic real potentials $V\left(x\right)$, 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.

With a core-periphery structure of networks, core nodes are densely interconnected, peripheral nodes are connected to core nodes to different extents, and peripheral nodes are sparsely interconnected. Core-periphery structure composed of a single core and periphery has been identified for various networks. However, analogous to the observation that many empirical networks are composed of densely interconnected groups of nodes, i.e., communities, a network may be better regarded as a collection of multiple cores and peripheries. We propose a scalable algorithm to detect multiple nonoverlapping groups of core-periphery structure in a network. We illustrate our algorithm using synthesized and empirical networks. For example, we find distinct core-periphery pairs with different political leanings in a network of political blogs and separation between international and domestic subnetworks of airports in some single countries in a worldwide airport network.

A human pathogen, Neisseria gonorrhoeae (NG), moves on surfaces by attaching and retracting polymeric structures called Type IV pili. The tug-of-war between the pili results in a two-dimensional stochastic motion called twitching motility. In this paper, with the help of real-time NG trajectories, we develop coarse-grained models for their description. The fractal properties of these trajectories are determined and their influence on first passage time and formation of bacterial microcolonies is studied. Our main observations are as follows: (i) NG performs a fast ballistic walk on small time scales and a slow diffusive walk over long time scales with a long crossover region; (ii) there exists a characteristic persistent length $l_p^{*}$, which yields the fastest growth of bacterial aggregates or biofilms. Our simulations reveal that $l_p^{*}\sim L^{0.6}$, where $L\times L$ is the surface on which the bacteria move; (iii) the morphologies have distinct fractal characteristics as a consequence of the ballistic and diffusive motion of the constituting bacteria.

The dynamics of a magnetic active Brownian particle undergoing three-dimensional Brownian motion, both translation and rotation, under the influence of a uniform magnetic field is investigated. The particle self-propels at a constant speed along its magnetic dipole moment, which reorients due to the interplay between Brownian and magnetic torques, quantified by the Langevin parameter $\alpha$. In this work, the time-dependent active diffusivity and the crossover time (${\tau }^{\mathrm{cross}}$)—from ballistic to diffusive regimes—are calculated through the time-dependent correlation function of the fluctuations of the propulsion direction. The results reveal that, for any value of $\alpha$, the particle undergoes a directional (or ballistic) propulsive motion at very short times ($t\ll {\tau }^{\mathrm{cross}}$). In this regime, the correlation function decreases linearly with time, and the active diffusivity increases with it. It the opposite time limit ($t\gg {\tau }^{\mathrm{cross}}$), the particle moves in a purely diffusive regime with a correlation function that decays asymptotically to zero and an active diffusivity that reaches a constant value equal to the long-time active diffusivity of the particle. As expected in the absence of a magnetic field ($\alpha =0$), the crossover time is equal to the characteristic time scale for rotational diffusion, ${\tau }_{\mathrm{rot}}$. In the presence of a magnetic field ($\alpha >0$), the correlation function, the active diffusivity, and the crossover time decrease with increasing $\alpha$. The magnetic field regulates the regimes of propulsion of the particle. Here, the field reduces the period of time at which the active particle undergoes a directional motion. Consequently, the active particle rapidly reaches a diffusive regime at ${\tau }^{\mathrm{cross}}\ll {\tau }_{\mathrm{rot}}$. In the limit of weak fields ($\alpha \ll 1$), the crossover time decreases quadratically with $\alpha$, while in the limit of strong fields ($\alpha \gg 1$) it decays asymptotically as ${\alpha }^{-1}$. The results are in excellent agreement with those obtained by Brownian dynamics simulations.

Molecular dynamics simulations are carried out to investigate mechanical properties and porous structure of binary glasses subjected to steady shear. The model vitreous systems were prepared via thermal quench at constant volume to a temperature well below the glass transition. The quiescent samples are characterized by a relatively narrow pore size distribution whose mean size is larger at lower glass densities. We find that in the linear regime of deformation, the shear modulus is a strong function of porosity, and the individual pores become slightly stretched while their structural topology remains unaffected. By contrast, with further increasing strain, the shear stress saturates to a density-dependent plateau value, which is accompanied by pore coalescence and a gradual development of a broader pore size distribution with a discrete set of peaks at large length scales.

The theory of turbulent diffusion of chemically reacting gaseous admixtures developed previously [T. Elperin et al., Phys. Rev. E 90, 053001 (2014)] is generalized for large yet finite Reynolds numbers and the dependence of turbulent diffusion coefficient on two parameters, the Reynolds number and Damköhler number (which characterizes a ratio of turbulent and reaction time scales), is obtained. Three-dimensional direct numerical simulations (DNSs) of a finite-thickness reaction wave for the first-order chemical reactions propagating in forced, homogeneous, isotropic, and incompressible turbulence are performed to validate the theoretically predicted effect of chemical reactions on turbulent diffusion. It is shown that the obtained DNS results are in good agreement with the developed theory.

We investigate the partition function zeros of the two-dimensional $p$-state clock model in the complex temperature plane by using the Wang-Landau method. For $p=5$, 6, 8, and 10, we propose a modified energy representation to enumerate exact irregular energy levels for the density of states without any binning artifacts. Comparing the leading zeros between different $p$'s, we provide strong evidence that the upper transition at $p=6$ is indeed of the Berezinskii-Kosterlitz-Thouless (BKT) type in contrast to the claim of the previous Fisher zero study [Phys. Rev. E 80, 042103 (2009)]. We find that the leading zeros of $p=6$ at the upper transition collapse onto the zero trajectories of the larger $p$'s including the $XY$ limit while the finite-size behavior of $p=5$ differs from the converged behavior of $p\ge 6$ within the system sizes examined. In addition, we argue that the nondivergent specific heat in the BKT transition is responsible for the small partition function magnitude that decreases exponentially with increasing system size near the leading zero, fundamentally limiting access to large systems in search for zeros with an estimator under finite statistical fluctuations.

Redfield theory provides a closed kinetic description of a quantum system in weak contact with a very dense reservoir. Landau-Zener theory does the same for a time-dependent driven system in contact with a sparse reservoir. Using a simple model, we analyze the validity of these two theories by comparing their predictions with exact numerical results. We show that despite their a priori different range of validity, these two descriptions can give rise to an identical quantum master equation. Both theories can be used for a nonequilibrium thermodynamic description, which we show is consistent with exact thermodynamic identities evaluated in the full system-reservoir space. We emphasize the importance of properly accounting for the system-reservoir interaction energy and of operating in regimes where the reservoir can be considered as close to ideal.