We study, both analytically and numerically, the Boltzmann transport equation for the Hubbard chain with nearest-neighbor hopping and spatially homogeneous initial condition. The time-dependent Wigner function is matrix-valued because of spin. The $H$ theorem holds. The nearest-neighbor chain is integrable, which, on the kinetic level, is reflected by infinitely many additional conservation laws and linked to the fact that there are also nonthermal stationary states. We characterize all stationary solutions. Numerically, we observe an exponentially fast convergence to stationarity and investigate the convergence rate in dependence on the initial conditions.

We report on the dynamical properties of interacting colloids confined to one dimension and subjected to external periodic energy landscapes. We particularly focus on the influence of hydrodynamic interactions on the mean-square displacement. Using Brownian dynamics simulations, we study colloidal systems with two types of repulsive interparticle interactions, namely, Yukawa and superparamagnetic potentials. We find that in the homogeneous case, hydrodynamic interactions lead to an enhancement of the particle mobility and the mean-square displacement at long times scales as $t^{\alpha }$, with $\alpha =\frac{1}{2}+\epsilon$ and $\epsilon$ being a small correction. This correction, however, becomes much more important in the presence of an external field, which breaks the homogeneity of the particle distribution along the line and, therefore, promotes a richer dynamical scenario due to the hydrodynamical coupling among particles. We provide here the complete dynamical scenario in terms of the external potential parameters: amplitude and commensurability.

A perturbation theory is used to calculate bcc solid-liquid interfacial free energies of metallic systems with embedded-atom model potentials. As a reference system for bcc crystals we used a single-occupancy cell, hard-sphere bcc system. Good agreements between the perturbation theory results and the corresponding results from simulations are found. The strategy to extract hard-sphere bcc solid-liquid interfacial free energies may have broader applications for other crystal lattices.

The nature of the reentrant nematic phase has been actively investigated both experimentally and theoretically during the past few decades. Most studies concluded that, as concerning molecular dynamics, a reentrant nematic phase is essentially analogous to a conventional nematic one. Recent computer simulations [Mazza et al., Phys. Rev. Lett. 105, 227802 (2010)], however, predicted molecular translational self-diffusion along the phase director that was dominated by a collective transport mode and was, relative to that observed in a conventional nematic phase, enhanced by an order of magnitude. In the present work, the principal components of the diffusion tensor in a reentrant nematic phase are determined experimentally and compared to those in conventional nematic and smectic-$A$ phases. We find that the temperature dependence of the translational diffusion in the two nematic phases, within experimental error, follows a uniform trend and can be adequately described in terms of available diffusion models in nematics. Hence, we find no evidence for enhanced diffusion but confirm instead the similarity of conventional and reentrant nematic phases with respect to molecular translational dynamics.

The quantum relativistic Buneman instability is investigated theoretically using a collective Klein-Gordon model for the electrons and a cold fluid model for the ions. The growth rate and unstable wave spectrum is investigated in different parameter regimes corresponding to various degrees of relativistic and quantum effects. The results may be important for streaming instabilities involving ion dynamics in very dense plasmas.

We develop modulation theory for undular bores (dispersive shock waves) in the framework of the Gardner, or extended Korteweg–de Vries (KdV), equation, which is a generic mathematical model for weakly nonlinear and weakly dispersive wave propagation, when effects of higher order nonlinearity become important. Using a reduced version of the finite-gap integration method we derive the Gardner-Whitham modulation system in a Riemann invariant form and show that it can be mapped onto the well-known modulation system for the Korteweg–de Vries equation. The transformation between the two counterpart modulation systems is, however, not invertible. As a result, the study of the resolution of an initial discontinuity for the Gardner equation reveals a rich phenomenology of solutions which, along with the KdV-type simple undular bores, include nonlinear trigonometric bores, solibores, rarefaction waves, and composite solutions representing various combinations of the above structures. We construct full parametric maps of such solutions for both signs of the cubic nonlinear term in the Gardner equation. Our classification is supported by numerical simulations.

We investigate slow nonequilibrium dynamical processes in a two-dimensional $q$-state Potts model with both ferromagnetic and $\pm J$ couplings. Dynamical properties are characterized by means of the mean-flipping time distribution. This quantity is known for clearly unveiling dynamical heterogeneities. Using a two-times protocol we characterize the different time scales observed and relate them to growth processes occurring in the system. In particular we target the possible relation between the different time scales and the spatial heterogeneities originated in the ground-state topology, which are associated to the presence of a backbone structure. We perform numerical simulations using an approach based on graphis processing units (GPUs) which permits us to reach large system sizes. We present evidence supporting both the idea of a growing process in the preasymptotic regime of the glassy phases and the existence of a backbone structure behind this process.

Effects of size and charge asymmetry between oppositely charged ions or particles on spatial inhomogeneities are studied for a large range of charge and size ratios. We perform a stability analysis of the primitive model of ionic systems with respect to periodic ordering using the collective variables–based theory. We extend previous studies [Ciach et al., Phys. Rev. E 75, 051505 (2007)] in several ways. First, we employ a nonlocal approximation for the reference hard-sphere fluid which leads to the Percus-Yevick pair direct correlation functions for the uniform case. Second, we use the Weeks-Chandler-Anderson regularization scheme for the Coulomb potential inside the hard core. We determine the relevant order parameter connected with the periodic ordering and analyze the character of the dominant fluctuations along the $\lambda$ lines. We show that the above-mentioned modifications produce large quantitative and partly qualitative changes in the phase diagrams obtained previously. We discuss possible scenarios of the periodic ordering for the whole range of size and charge ratios of the two ionic species, covering electrolytes, ionic liquids, charged globular proteins or nanoparticles in aqueous solutions, and charge-stabilized colloids.

We develop a relativistic variational model for a nematic liquid crystal interacting with an electromagnetic field. The constitutive relation for a general anisotropic uniaxial diamagnetic and dielectric medium is analyzed. We discuss light wave propagation in this moving uniaxial medium, for which the corresponding optical metrics are identified explicitly. A Lagrangian for the coupled system of a nematic liquid crystal and the electromagnetic field is constructed, from which a complete set of equations of motion for the system is derived. The canonical energy-momentum and spin tensors are systematically obtained. We compare our results with those within the nonrelativistic models. As an application of our general formalism, we discuss the so-called Abraham-Minkowski controversy on the momentum of light in a medium.

We investigate the chain conformation of ring polymers confined to a cylindrical nanochannel using both theoretical analysis and three-dimensional Langevin dynamics simulations. We predict that the longitudinal size of a ring polymer scales with the chain length and the diameter of the channel in the same manner as that for linear chains based on scaling analysis and Flory-type theory. Moreover, Flory-type theory also gives the ratio of the longitudinal sizes for a ring polymer and a linear chain with identical chain length. These theoretical predictions are confirmed by numerical simulations. Finally, our simulation results show that this ratio first decreases and then saturates with increasing the chain stiffness, which explains the discrepancy in experiments. Our results have biological significance.

The helix-coil transition in peptides is a critical structural transition leading to functioning proteins. Peptide chains have a large number of possible configurations that must be accounted for in statistical mechanical investigations. Using hydrogen bond and local helix propensity interaction terms, we develop a method for obtaining and incorporating the degeneracy factor that allows the exact calculation of the partition function for a peptide as a function of chain length. The partition function is used in calculations for engineered peptide chains of various lengths that allow comparison with a variety of different types of experimentally measured quantities, such as fraction of helicity as a function of both temperature and chain length, heat capacity, and denaturation studies. When experimental sensitivity in helicity measurements is properly accounted for in the calculations, the calculated curves fit well with the experimental curves. We determine values of interaction energies for comparison with known biochemical interactions, as well as quantify the difference in the number of configurations available to an amino acid in a random coil configuration compared to a helical configuration.

Eukaryotic DNA replication is initiated from multiple sites on the chromosome, but little is known about the global and local regulation of replication. We present a mathematical model for the spatial dynamics of DNA replication, which offers insight into the kinetics of replication in different types of organisms. Most biological experiments involve average quantities over large cell populations (typically $>$${10}^7$ cells) and therefore can mask the cell-to-cell variability present in the system. Although the model is formulated in terms of a population of cells, using mathematical analysis we show that one can obtain signatures of stochasticity in individual cells from averaged quantities. This work generalizes the result by Retkute et al. [Phys. Rev. Lett. 107, 068103 (2011)] to a broader set of parameter regimes.

In this work, a Langevin dynamics model of the diffusion of water in articular cartilage was developed. Numerical simulations of the translational dynamics of water molecules and their interaction with collagen fibers were used to study the quantitative relationship between the organization of the collagen fiber network and the diffusion tensor of water in model cartilage. Langevin dynamics was used to simulate water diffusion in both ordered and partially disordered cartilage models. In addition, an analytical approach was developed to estimate the diffusion tensor for a network comprising a given distribution of fiber orientations. The key findings are that (1) an approximately linear relationship was observed between collagen volume fraction and the fractional anisotropy of the diffusion tensor in fiber networks of a given degree of alignment, (2) for any given fiber volume fraction, fractional anisotropy follows a fiber alignment dependency similar to the square of the second Legendre polynomial of $\cos \left(\theta \right)$, with the minimum anisotropy occurring at approximately the magic angle (${\theta }_{\mathit{MA}}$), and (3) a decrease in the principal eigenvalue and an increase in the transverse eigenvalues is observed as the fiber orientation angle $\theta$ progresses from $0^{\circ }$ to ${90}^{\circ }$. The corresponding diffusion ellipsoids are prolate for $\theta <{\theta }_{\mathit{MA}}$, spherical for $\theta \approx {\theta }_{\mathit{MA}}$, and oblate for $\theta >{\theta }_{\mathit{MA}}$. Expansion of the model to include discrimination between the combined effects of alignment disorder and collagen fiber volume fraction on the diffusion tensor is discussed.

We studied the Bouchaud-Mézard (BM) model, which was introduced to explain Pareto's law in a real economy, on a random network. Using “adiabatic and independent” assumptions, we analytically obtained the stationary probability distribution function of wealth. The results show that wealth condensation, indicated by the divergence of the variance of wealth, occurs at a larger $J$ than that obtained by the mean-field theory, where $J$ represents the strength of interaction between agents. We compared our results with numerical simulation results and found that they were in good agreement.

We investigate the population dynamics in generalized rock-paper-scissors models with an arbitrary number of species $N$. We show that spiral patterns with $N$ arms may develop both for odd and even $N$, in particular in models where a bidirectional predation interaction of equal strength between all species is modified to include one $N$-cyclic predator-prey rule. While the former case gives rise to an interface network with Y-type junctions obeying the scaling law $L\propto t^{1/2}$, where $L$ is the characteristic length of the network and $t$ is the time, the latter can lead to a population network with $N$-armed spiral patterns, having a roughly constant characteristic length scale. We explicitly demonstrate the connection between interface junctions and spiral patterns in these models and compute the corresponding scaling laws. This work significantly extends the results of previous studies of population dynamics and could have profound implications for the understanding of biological complexity in systems with a large number of species.

Dripping water from a faucet is a typical example exhibiting rich nonlinear phenomena. For such a system, the time stamps at which water drops separate from the faucet can be directly observed in real experiments, and the time series of intervals ${\tau }_n$ between drop separations becomes a subject of analysis. Even if the mass $m_n$ of a drop at the onset of the $n$th separation, which is difficult to observe experimentally, exhibits perfectly deterministic dynamics, it may be difficult to obtain the same information about the underlying dynamics from the time series ${\tau }_n$. This is because the return plot ${\tau }_{n-1}$ vs. ${\tau }_n$ may become a multivalued relation (i.e., it doesn't represent a function describing deterministic dynamics). In this paper, we propose a method to construct a nonlinear coordinate which provides a “surrogate” of the internal state $m_n$ from the time series of ${\tau }_n$. Here, a key of the proposed approach is to use isomap, which is a well-known method of manifold learning. We first apply it to the time series of ${\tau }_n$ generated from the numerical simulation of a phenomenological mass-spring model for the dripping faucet system. It is shown that a clear one-dimensional map is obtained by the proposed approach, whose characteristic quantities such as the Lyapunov exponent, the topological entropy, and the time correlation function coincide with the original dripping faucet system. Furthermore, we also analyze data obtained from real dripping faucet experiments, which also provide promising results.

The steady-state electrohydrodynamics of a leaky dielectric drop in confined domains is investigated analytically. The governing electrohydrodynamic equations are solved for Newtonian and immiscible fluids in the framework of leaky dielectric theory and for the creeping flow regime. The domain confinement strengthens or weakens the electric field, depending on $R>1$ or $R<1$, respectively, where $R={\sigma }_i/{\sigma }_o$ is the ratio of electric conductivity of the drop to that of the surrounding fluid. Similarly, the flow intensity decreases for $R<1$, but it remains unchanged or increases for $R>1$, depending on the interplay of electric and hydrodynamic effects. An expression for the drop deformation for small distortion from the spherical shape is found using the domain perturbation technique. It is shown that below a threshold domain size the confinement effect will lead to the reversal of the tendency of the net normal hydrodynamic stress in deforming the drop to an oblate or a prolate shape, and that below a critical domain size the necessary condition for having an oblate drop will be opposite to the classical one for an unbounded domain.

Thermal transpiration flow of rarefied gases in annular channels is considered where the driving force for the flow is a temperature gradient applied in the channel walls. The influence of gas rarefaction, aspect ratio of the annulus, and surface accommodation coefficient on mass and heat transfer in the process are investigated. An analytical approach to the problem is conducted based on linearized Navier-Stokes-Fourier (NSF) and regularized 13-moment (R13) equations, and a closed-form expression for Knudsen boundary layers is obtained. The results are compared to available solutions of the Boltzmann equation to highlight the advantages of the R13 over the NSF equations in describing nonequilibrium effects in this particular thermally driven flow. Through comparisons with kinetic data, it is shown that R13 equations are valid for moderate Knudsen numbers, i.e., $\mathrm{Kn}<0.5$ where NSF equations fail to describe the flow fields properly.

The time-dependent radiative transport equation is solved for the three-dimensional spatially uniform infinite medium which is illuminated by a point unidirectional source using a spherical harmonics transform under rotation. Apart from the numerical evaluation of a spherical Hankel transform which connects the spatial distance with the radial distance in Fourier space, the dependence on all variables is found analytically. For the special case of a harmonically modulated source, even the spherical Hankel transform can be carried out analytically. Additionally, a special solution for the isotropically scattering infinite medium is given. The Monte Carlo method is used for a successful verification of the derived solution.

General rogue waves in the Davey-Stewartson-I equation are derived by the bilinear method. It is shown that the simplest (fundamental) rogue waves are line rogue waves which arise from the constant background with a line profile and then disappear into the constant background again. It is also shown that multirogue waves describe the interaction of several fundamental rogue waves. These multirogue waves also arise from the constant background and then decay back to it, but in the intermediate times, interesting curvy wave patterns appear. However, higher-order rogue waves exhibit different dynamics. Specifically, only part of the wave structure in the higher-order rogue waves rises from the constant background and then retreats back to it, and this transient wave possesses patterns such as parabolas. But the other part of the wave structure comes from the far distance as a localized lump, which decelerates to the near field and interacts with the transient rogue wave, and is then reflected back and accelerates to the large distance again.