Recently Mazenko and Das and Mazenko [Phys. Rev. E 81, 061102 (2010); J. Stat. Phys. 149, 643 (2012); J. Stat. Phys. 152, 159 (2013); Phys. Rev. E 83, 041125 (2011)] introduced a nonequilibrium field-theoretical approach to describe the statistical properties of a classical particle ensemble starting from the microscopic equations of motion of each individual particle. We use this theory to investigate the transition from those microscopic degrees of freedom to the evolution equations of the macroscopic observables of the ensemble. For the free theory, we recover the continuity and Jeans equations of a collisionless gas. For a theory containing two-particle interactions in a canonical perturbation series, we find the macroscopic evolution equations to be described by the Born-Bogoliubov-Green-Kirkwood-Yvon hierarchy with a truncation criterion depending on the order in perturbation theory. This establishes a direct link between the classical and the field-theoretical approaches to kinetic theory that might serve as a starting point to investigate kinetic theory beyond the classical limits.

The high mechanical stiffness of single-nanoparticle-thick membranes is believed to result from the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with a nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl $\left({\mathrm{CH}}_3\right)$ ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Moreover, the particular end group (COOH or ${\mathrm{CH}}_3$) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.

We study two intertwined globally coupled networks of noisy Kuramoto phase oscillators that have the same natural frequency but differ in their perception of the mean field and their contribution to it. Such a give-and-take mechanism is given by asymmetric in- and out-coupling strengths which can be both positive and negative. We uncover in this minimal network of networks intriguing patterns of discordance, where the ensemble splits into two clusters separated by a constant phase lag. If it differs from $\pi$, then traveling wave solutions emerge. We observe a second route to traveling waves via traditional one-cluster states. Bistability is found between the various collective states. Analytical results and bifurcation diagrams are derived with a reduced system.

The time-independent lattice Boltzmann algorithm (TILBA) is developed to calculate the hydrodynamic interactions between two particles in a Stokes flow. The TILBA is distinguished from the traditional lattice Boltzmann method in that a background matrix (BGM) is generated prior to the calculation. The BGM, once prepared, can be reused for calculations for different scenarios, and the computational cost for each such calculation will be significantly reduced. The advantage of the TILBA is that it is easy to code and can be applied to any particle shape without complicated implementation, and the computational cost is independent of the shape of the particle. The TILBA is validated and shown to be accurate by comparing calculation results obtained from the TILBA to analytical or numerical solutions for certain problems.

Out-of-equilibrium systems exhibit domain walls between different states. These walls, depending on the type of connected states, can display rich spatiotemporal dynamics. In this Rapid Communication, we investigate the asymmetrical counterpropagation of fronts in an in-plane-switching cell filled with a nematic liquid crystal. Experimentally, we characterize the different front shapes and propagation speeds. These fronts present dissimilar elastic deformations that are responsible for their asymmetric speeds. Theoretically, using a phenomenological model, we describe the observed dynamics with fair agreement.

Motivated by the recent proposed models of the information engine [Proc. Natl. Acad. Sci. USA 109, 11641 (2012)] and the information refrigerator [Phys. Rev. Lett. 111, 030602 (2013)], we propose a minimal model of the information pump and the information eraser based on enzyme kinetics. This device can either pump molecules against the chemical potential gradient by consuming the information to be encoded in the bit stream or (partially) erase the information initially encoded in the bit stream by consuming the Gibbs free energy. The dynamics of this model is solved exactly, and the “phase diagram” of the operation regimes is determined. The efficiency and the power of the information machine is analyzed. The validity of the second law of thermodynamics within our model is clarified. Our model offers a simple paradigm for the investigating of the thermodynamics of information processing involving the chemical potential in small systems.

We study the jamming transition in a model of elastic particles under shear at zero temperature. The key quantity is the relaxation time $\tau$ which is obtained by stopping the shearing and letting energy and pressure decay to zero. At many different densities and initial shear rates we do several such relaxations to determine the average $\tau$. We establish that $\tau$ diverges with the same exponent as the viscosity and determine another exponent from the relation between $\tau$ and the coordination number. Though most of the simulations are done for the model with dissipation due to the motion of particles relative to an affinely shearing substrate, we also examine a model, where the dissipation is instead due to velocity differences of disks in contact, and confirm that the above-mentioned exponent is the same for these two models. We also consider finite size effects on both $\tau$ and the coordination number.

Swelling clay minerals play a key role in the control of water and pollutant migration in natural media such as soils. Moreover, swelling clay particles’ orientational properties in porous media have significant implications for the directional dependence of fluid transfer. Herein we investigate the ability to mimic the organization of particles in natural swelling-clay porous media using a three-dimensional sequential particle deposition procedure [D. Coelho, J.-F. Thovert, and P. M. Adler, Phys. Rev. E 55, 1959 (1997)]. The algorithm considered is first used to simulate disk packings. Porosities of disk packings fall onto a single master curve when plotted against the orientational scalar order parameter value. This relation is used to validate the algorithm used in comparison with existing ones. The ellipticity degree of the particles is shown to have a negligible effect on the packing porosity for ratios ${\ell }_a/{\ell }_b$ less than 1.5, whereas a significant increase in porosity is obtained for higher values. The effect of the distribution of the geometrical parameters (size, aspect ratio, and ellipticity degree) of particles on the final packing properties is also investigated. Finally, the algorithm is used to simulate particle packings for three size fractions of natural swelling-clay mineral powders. Calculated data regarding the distribution of the geometrical parameters and orientation of particles in porous media are successfully compared with experimental data obtained for the same samples. The results indicate that the obtained virtual porous media can be considered representative of natural samples and can be used to extract properties difficult to obtain experimentally, such as the anisotropic features of pore and solid phases in a system.

In this paper, we investigate how changes in the system entropy influence the characteristic time scale of the system molecular dynamics near the glass transition. Independently of any model of thermodynamic evolution of the time scale, against some previous suppositions, we show that the system entropy $S$ is not sufficient to govern the time scale defined by structural relaxation time τ. In the density scaling regime, we argue that the decoupling between τ and $S$ is a consequence of different values of the scaling exponents γ and ${\gamma }_S$ in the density scaling laws, $\tau =f({\rho }^{\gamma }/T)$ and $S=h({\rho }^{{\gamma }_S}/T)$, where ρ and $T$ denote density and temperature, respectively. It implies that the proper relation between τ and $S$ requires supplementing with a density factor, $u$(ρ), i.e., $\tau =g(u\left(\rho \right)w\left(S\right))$. This meaningful finding additionally demonstrates that the density scaling idea can be successfully used to separate physically relevant contributions to the time scale of molecular dynamics near the glass transition. The relation reported by us between τ and $S$ constitutes a general pattern based on nonconfigurational quantities for describing the thermodynamic evolution of the characteristic time scale of molecular dynamics near the glass transition in the density scaling regime, which is a promising alternative to the approaches based as the Adam-Gibbs model on the configurational entropy that is difficult to evaluate in the entire thermodynamic space. As an example, we revise the Avramov entropic model of the dependence τ($T$,ρ), giving evidence that its entropic basis has to be extended by the density dependence of the maximal energy barrier for structural relaxation. We also discuss the excess entropy $S_{\mathrm{ex}}$, the density scaling of which is found to mimic the density scaling of the total system entropy $S$.

Unicellular organisms exhibit elaborate collective behaviors in response to environmental cues. These behaviors are controlled by complex biochemical networks within individual cells and coordinated through cell-to-cell communication. Describing these behaviors requires new mathematical models that can bridge scales—from biochemical networks within individual cells to spatially structured cellular populations. Here we present a family of “multiscale” models for the emergence of spiral waves in the social amoeba Dictyostelium discoideum. Our models exploit new experimental advances that allow for the direct measurement and manipulation of the small signaling molecule cyclic adenosine monophosphate (cAMP) used by Dictyostelium cells to coordinate behavior in cellular populations. Inspired by recent experiments, we model the Dictyostelium signaling network as an excitable system coupled to various preprocessing modules. We use this family of models to study spatially unstructured populations of “fixed” cells by constructing phase diagrams that relate the properties of population-level oscillations to parameters in the underlying biochemical network. We then briefly discuss an extension of our model that includes spatial structure and show how this naturally gives rise to spiral waves. Our models exhibit a wide range of novel phenomena. including a density-dependent frequency change, bistability, and dynamic death due to slow cAMP dynamics. Our modeling approach provides a powerful tool for bridging scales in modeling of Dictyostelium populations.

X-ray free-electron lasers (XFELs) may allow us to employ the single-particle imaging (SPI) method to determine the structure of macromolecules that do not form stable crystals. Ultrashort pulses of 10 fs and less allow us to outrun complete disintegration by Coulomb explosion and minimize radiation damage due to nuclear motion, but electronic damage is still present. The major contribution to the electronic damage comes from the plasma generated in the sample that is strongly dependent on the amount of Auger ionization. Since the Auger process has a characteristic time scale on the order of femtoseconds, one may expect that its contribution will be significantly reduced for attosecond pulses. Here we study the effect of electronic damage on the SPI at pulse durations from 0.1 to 10 fs and in a large range of XFEL fluences to determine optimal conditions for imaging of biological samples. We analyzed the contribution of different electronic excitation processes and found that at fluences higher than ${10}^{13}–10{}^{15} \mathrm{photons}/\mu {\text{m}}^2$ (depending on the photon energy and pulse duration) the diffracted signal saturates and does not increase further. A significant gain in the signal is obtained by reducing the pulse duration from 10 to 1 fs. Pulses below a duration of 1 fs do not give a significant gain in the scattering signal in comparison with 1-fs pulses. We also study the limits imposed on SPI by Compton scattering.

We propose a generalized stochastic block model to explore the mesoscopic structures in signed networks by grouping vertices that exhibit similar positive and negative connection profiles into the same cluster. In this model, the group memberships are viewed as hidden or unobserved quantities, and the connection patterns between groups are explicitly characterized by two block matrices, one for positive links and the other for negative links. By fitting the model to the observed network, we can not only extract various structural patterns existing in the network without prior knowledge, but also recognize what specific structures we obtained. Furthermore, the model parameters provide vital clues about the probabilities that each vertex belongs to different groups and the centrality of each vertex in its corresponding group. This information sheds light on the discovery of the networks' overlapping structures and the identification of two types of important vertices, which serve as the cores of each group and the bridges between different groups, respectively. Experiments on a series of synthetic and real-life networks show the effectiveness as well as the superiority of our model.

We present an efficient algorithm for simulating percolation transitions of mutually supporting viable clusters on multiplex networks (also known as “catastrophic cascades on interdependent networks”). This algorithm maps the problem onto a solid-on-solid-type model. We use this algorithm to study interdependent agents on duplex Erdös-Rényi (ER) networks and on lattices with dimensions 2, 3, 4, and 5. We obtain surprising results in all these cases, and we correct statements in the literature for ER networks and for two-dimensional lattices. In particular, we find that $d=4$ is the upper critical dimension and that the percolation transition is continuous for $d\le 4$ but—at least for $d\ne 3$—not in the universality class of ordinary percolation. For ER networks we verify that the cluster statistics is exactly described by mean-field theory but find evidence that the cascade process is not. For $d=5$ we find a first-order transition as for ER networks, but we find also that small clusters have a nontrivial mass distribution that scales at the transition point. Finally, for $d=2$ with intermediate-range dependency links we propose a scenario that differs from that proposed in W. Li et al. [Phys. Rev. Lett. 108, 228702 (2012)].

A new kind of instability caused by Joule heating near charge-selective surfaces (permselective membranes, electrodes, or systems of micro- and nanochannels) is investigated theoretically using a model based on the Rubinstein-Zaltzman approach. A simple relation is derived for the marginal stability curves: Joule heating can either destabilize or stabilize the steady state, depending on the location of the space charge region relative to the gravity vector. For the destabilizing case, the short-wave Rubinstein-Zaltzman instability is replaced by a long-wave thermal instability. The physical mechanism of the thermal instability is found to be very different from Rayleigh-Bénard convection, and is based on a nonuniform distribution of the electrical conductivity in the electrolyte. The study is complemented by numerical investigations both of linear and nonlinear instabilities near a charge-selective surface. There is a good qualitative agreement with the analytics. A possible explanation of the discrepancy between the experimental data and our previous theoretical voltage-current characteristics is highlighted.

The radiation of a charged-particle bunch moving perpendicularly to a semi-infinite plane grid composed of thin parallel wires is analyzed using the method of averaged boundary conditions (the period of the grid is assumed to be much less than the wavelengths under investigation). We perform an analysis of the volume radiation and surface waves generated by a bunch of finite length. It is shown that the patterns of the volume radiation fundamentally differ from those that arise in the case of an infinite grid. The properties of the surface waves are similar to the properties of Cherenkov radiation in a three-dimensional wire metamaterial. These waves propagate along the wires at the speed of light in a vacuum and do not diminish with distance (if absorption is negligible). The structure of the surface waves allows for the determination of the size and form of the particle bunches.

We study the evolution of localized wave groups in unidirectional water wave envelope equations [the nonlinear Schrödinger (NLSE) and the modified NLSE (MNLSE)]. These localizations of energy can lead to disastrous extreme responses (rogue waves). We analytically quantify the role of such spatial localization, introducing a technique to reduce the underlying partial differential equation dynamics to a simple ordinary differential equation for the wave packet amplitude. We use this reduced model to show how the scale-invariant symmetries of the NLSE break down when the additional terms in the MNLSE are included, inducing a critical scale for the occurrence of extreme waves.

When the amount of entanglement in a quantum system is limited, the relevant dynamics of the system is restricted to a very small part of the state space. When restricted to this subspace the description of the system becomes efficient in the system size. A class of algorithms, exemplified by the time-evolving block-decimation (TEBD) algorithm, make use of this observation by selecting the relevant subspace through a decimation technique relying on the singular value decomposition (SVD). In these algorithms, the complexity of each time-evolution step is dominated by the SVD. Here we show that, by applying a randomized version of the SVD routine (RRSVD), the power law governing the computational complexity of TEBD is lowered by one degree, resulting in a considerable speed-up. We exemplify the potential gains in efficiency at the hand of some real world examples to which TEBD can be successfully applied and demonstrate that for those systems RRSVD delivers results as accurate as state-of-the-art deterministic SVD routines.

The thermal discrete dipole approximation (T-DDA) is a numerical approach for modeling near-field radiative heat transfer in complex three-dimensional geometries. In this work, the convergence of the T-DDA is investigated by comparison against the exact results for two spheres separated by a vacuum gap. The error associated with the T-DDA is reported for various sphere sizes, refractive indices, and vacuum gap thicknesses. The results reveal that for a fixed number of subvolumes, the accuracy of the T-DDA degrades as the refractive index and the sphere diameter to gap ratio increase. A converging trend is observed as the number of subvolumes increases. The large computational requirements associated with increasing the number of subvolumes, and the shape error induced by large sphere diameter to gap ratios, are mitigated by using a nonuniform discretization scheme. Nonuniform discretization is shown to significantly accelerate the convergence of the T-DDA, and is thus recommended for near-field thermal radiation simulations. Errors less than 5% are obtained in 74% of the cases studied by using up to 82 712 subvolumes. Additionally, the convergence analysis demonstrates that the T-DDA is very accurate when dealing with surface polariton resonant modes dominating radiative heat transfer in the near field.