We study the dynamical proprieties of phase synchronization and intermittent behavior of neural systems using a network of networks structure based on an experimentally obtained human connectome for healthy and Alzheimer-affected brains. We consider a network composed of 78 neural subareas (subnetworks) coupled with a mean-field potential scheme. Each subnetwork is characterized by a small-world topology, composed of 250 bursting neurons simulated through a Rulkov model. Using the Kuramoto order parameter we demonstrate that healthy and Alzheimer-affected brains display distinct phase synchronization and intermittence properties as a function of internal and external coupling strengths. In general, for the healthy case, each subnetwork develops a substantial level of internal synchronization before a global stable phase-synchronization state has been established. For the unhealthy case, despite the similar internal subnetwork synchronization levels, we identify higher levels of global phase synchronization occurring even for relatively small internal and external coupling. Using recurrence quantification analysis, namely the determinism of the mean-field potential, we identify regions where the healthy and unhealthy networks depict nonstationary behavior, but the results denounce the presence of a larger region or intermittent dynamics for the case of Alzheimer-affected networks. A possible theoretical explanation based on two locally stable but globally unstable states is discussed.

A question in evolutionary biology is why the number of males is approximately equal to that of females in many species, and Fisher's theory of equal investment answers that it is the evolutionarily stable state. The Fisherian mechanism can be given a concrete form by a genetic model based on the following assumptions: (1) Males and females mate at random. (2) An allele acts on the father to determine the expected progeny sex ratio. (3) The offspring inherits the allele from either side of the parents with equal probability. The model is known to achieve the 1:1 sex ratio due to the invasion of mutant alleles with different progeny sex ratios. In this study, however, we argue that mutation plays a more subtle role in that fluctuations caused by mutation renormalize the sex ratio and thereby keep it away from $1:1$ in general. This finding shows how the sex ratio is affected by mutation in a systematic way, whereby the effective mutation rate can be estimated from an observed sex ratio.

Active swarms, consisting of individual agents which consume energy to move or produce work, are known to generate a diverse range of collective behaviors. Many examples of active swarms are biological in nature (e.g., fish shoals and bird flocks) and have been modeled extensively by numerical simulations. Such simulations of swarms usually assume that the swarm is homogeneous; that is, every agent has exactly the same dynamical properties. However, many biological swarms are highly heterogeneous, such as multispecies communities of micro-organisms in soil, and individual species may have a wide range of different physical properties. Here we explore heterogeneity by developing a simple model for the dynamics of a swarm of motile heterogeneous rodlike bacteria in the absence of hydrodynamic effects. Using molecular dynamics simulations of active rods confined within a two-dimensional rectangular channel, we first explore the case of homogeneous swarms and show that the key parameter governing both dynamics is ratio of the motility force to the steric force. Next we explore heterogeneous or mixed swarms in which the constituent self-propelled rods have a range of motilities and steric interactions. Our results show that the confining boundaries play a strong role in driving the segregation of mixed populations.

A spin-glass transition has been investigated for a long time but we have not reached a conclusion yet due to difficulties in the simulation studies. They are slow dynamics, strong finite-size effects, and sample-to-sample dependencies. We found that a size of the spin-glass order reaches a lattice boundary within a very short Monte Carlo step. A competition between the spin-glass order and a boundary condition causes these difficulties. Once the boundary effect was removed, physical quantities exhibited quite normal behaviors. They became self-averaging in a limit of large replica numbers. These findings suggest that the nonequilibrium relaxation method is a good choice for solving the difficulties if a lattice size and a replica number are set sufficiently large. A dynamic scaling analysis on nonequilibrium relaxation functions gave a result that the spin-glass transition and the chiral-glass transition occurs at the same temperature in the Heisenberg model in three dimensions. The estimated critical exponent $\nu$ agrees with the experimental result.

In this work a phase field-lattice Boltzmann model for incompressible two-phase flows is presented. In this model, the interface tracking equation is a linear combination of the local and nonlocal Allen-Cahn equations. We also propose a multiple-relaxation-time lattice Boltzmann model for solving the hybrid Allen-Cahn equation. The second-order convergence rate of the present model in space is validated by simulating the diagonal translation of circular interface. Three other numerical tests, including static bubble immersed in another fluid, bubble rising under gravity, and droplet splashing on a thin liquid film, are simulated to verify the performance of the present model in reducing the numerical dispersion. The numerical results indicate that the order parameter fluctuation can be reduced by one order of magnitude in bulk region.

A lattice Boltzmann (LB) model for multiphase flows is developed that complies with the thermodynamic foundations of kinetic theory. By directly devising the collision term for the LB equation at the discrete level, a self-tuning equation of state is achieved, which can be interpreted as the incorporation of short-range molecular interaction. A pairwise interaction force is introduced to mimic the long-range molecular interaction, which is responsible for interfacial dynamics. The derived pressure tensor is naturally consistent with thermodynamic theory, and surface tension and interface thickness can be independently prescribed. Numerical tests, including static and dynamic cases, are carried out to validate the present model and good results are obtained. As a further application, head-on collision of equal-sized droplets is simulated and the elusive “bouncing” regime is successfully reproduced.

The distribution of particles interacting with Lennard-Jones potentials and confined between parallel graphene sheets is investigated by molecular dynamics simulations. For small separation distances, the particles are densely localized in the central region between the graphene sheets. However, two high-density layers appear as the separation distance increases. The particle distribution also depends on the temperature, tensile force of the graphene sheets, and the initial configuration, and various configurations are observed for large separation. For example, an argon cluster initially located between the graphene sheets changes shape, and a bridge between the parallel walls is formed at low temperature. In contrast to the Lennard-Jones system sandwiched between rigid walls, the flexibility of the graphene sheets strongly affects the distribution of particles in the direction perpendicular to the graphene sheets.

In this study we used a nonequilibrium simulation method to investigate the temperature dependent divergence of thermal conductivity in a one-dimensional momentum conserving system with an asymmetric double well nearest-neighbor interaction potential. We show that across all temperatures thermal conductivity exhibits power-law divergence with the chain length and the value of the divergence exponent ($\alpha$) depends on the temperature of the system. At low and high temperatures $\alpha$ reaches close to $\sim 0.5$ and $\sim 0.33$, respectively. Whereas in the intermediate temperature the divergence of thermal conductivity with the chain length saturates with $\alpha \sim 0.07$. Subsequent analysis showed that the estimated value of $\alpha$ in the intermediate temperature may not have reached its thermodynamic limit. Further calculations of local $\alpha$ revealed that its approach towards the thermodynamic limit is crucially dependent on the temperature of the system. At low and high temperatures local $\alpha$ reaches its thermodynamic limits in shorter chain lengths. On the contrary, in the case of intermediate temperature its progress towards the asymptotic limit is nonmonotonic.

We propose a machine-learning approach based on artificial neural network to efficiently obtain new insights on the role of geometric contributions to the nonequilibrium fluctuations of an adiabatically temperature-driven quantum heat engine coupled to a cavity. Using the artificial neural network we have explored the interplay between bunched and antibunched photon exchange statistics for different engine parameters. We report that beyond a pivotal cavity temperature, the Fano factor oscillates between giant and low values as a function of phase difference between the driving protocols. We further observe that the standard thermodynamic uncertainty relation is not valid when there are finite geometric contributions to the fluctuations but holds true for zero phase difference even in the presence of coherences.

In the present work we explore a prestretched oscillator chain where the nodes interact via a pairwise Lennard-Jones potential. In addition to a homogeneous solution, we identify solutions with one or more (so-called) “breaks,” i.e., jumps. As a function of the canonical parameter of the system, namely, the precompression strain $d$, we find that the most fundamental one-break solution changes stability when the monotonicity of the Hamiltonian changes with $d$. We provide a proof for this (motivated by numerical computations) observation. This critical point separates stable and unstable segments of the one-break branch of solutions. We find similar branches for two- through five-break branches of solutions. Each of these higher “excited state” solutions possesses an additional unstable pair of eigenvalues. We thus conjecture that $k$-break solutions will possess at least $k-1$ (and at most $k$) pairs of unstable eigenvalues. Our stability analysis is corroborated by direct numerical computations of the evolutionary dynamics.

Amphipathic alpha-helical peptides, among other peripheral components of plasma membranes, are promising antimicrobial agents. Partial incorporation of a peptide into a lipid monolayer causes elastic deformations. Deformations induced by two peptides distant from each other are independent; when peptides get closer, interference between the deformations causes effective lateral interaction. We quantified the energy of membrane deformations for arbitrary configuration of two amphipathic peptides on the membrane surface. The global minimum of the deformation energy proved to be achieved when two parallel peptides are in registry at the distance of about 6 nm between the axes of peptides. The energy calculated in the unidimensional approach provides a good approximation for the dependence of the energy of peptides being in the registered configuration upon the distance between them, valid for a broad range of peptide lengths. The effective interactional length of peptides for the unidimensional approach is close to their actual length. If two parallel peptides are shifted along their axes with respect to each other, the interaction energy is also well approximated by the unidimensional potential, within the projection of one peptide onto the other. In the case when the axes of alpha helices cross at a substantial angle, the main contribution to peptide interactions comes from their edges: the effective length of peptides for the unidimensional approach is almost equal to the characteristic length of decay of deformations. Based on the results we obtained it can be concluded that interaction of membrane inclusions is quite adequately described by the potential calculated in the unidimensional approach.

The ordering effects of driven spherocylinder-shaped rods in a colloidal suspension of small spheres confined to a two-dimensional channel geometry are observed via Brownian dynamics simulations without hydrodynamics. To describe the ordering, an order parameter and an expression for a potential of mean force of an equivalent equilibrium system are defined and analyzed. By varying the application point of the external force along the rods and thus the resulting lever, a transition from a preferred orientation parallel to the direction of the force to a preferred orientation perpendicular to the direction of the force was observed. It is shown that this effect can only be found if the spheres and multiple rods are present. Furthermore, a dependency of the order parameter on the absolute value of the force was discovered. The analysis of the potential of mean force further indicates a transition between two different phases of mean orientation. An observation of the flow equilibrium mean velocity in channel direction led to a $s$-shaped progression regarding the lever dependency, also marking a transition between two states linked to the mean orientation of the rods. A finite size analysis was conducted. Its results indicate that the transition between the two orientation states is a general phenomenon of the observed rod-sphere mixture.

We report local roughness exponents, ${\alpha }_{\text{loc}}$, for three interface growth models in one dimension which are believed to belong to the nonlinear molecular-beam-epitaxy (nMBE) universality class represented by the Villain-Lais-Das Sarma (VLDS) stochastic equation. We applied an optimum detrended fluctuation analysis (ODFA) [Luis et al., Phys. Rev. E 95, 042801 (2017)] and compared the outcomes with standard detrending methods. We observe in all investigated models that ODFA outperforms the standard methods providing exponents in the narrow interval ${\alpha }_{\text{loc}}^{}\in [0.96,0.98]$ quantitatively consistent with two-loop renormalization group predictions for the VLDS equation. In particular, these exponent values are calculated for the Clarke-Vvdensky and Das Sarma-Tamborenea models characterized by very strong corrections to the scaling, for which large deviations of these values had been reported. Our results strongly support the absence of anomalous scaling in the nMBE universality class and the existence of corrections in the form ${\alpha }_{\text{loc}}^{}=1-\epsilon$ of the one-loop renormalization group analysis of the VLDS equation.

Peculiar behavior is found in a Si cluster ion, moving with a speed of $\sim 0.22c$ ($c$: speed of light) in a solid Al plasma in the context of cluster-ion beam driven inertial confinement fusion: The Si ion, moving closely behind the forward-moving Si ion for a distance of several Å in the cluster, feels the wake field generated by the forward Si. The acceleration interaction force on the rear Si ion by the forward-moving ion may balance with the deceleration backward force in the longitudinal-moving direction. The forward-moving Si ion would be decelerated, as an isolated ion is decelerated without correlation. However, the deceleration of the rear Si ion, moving behind closely, would be reduced significantly. The rear Si ion may catch up and overtake the forward-moving Si ion in the cluster during the Si cluster-ion interaction with the high-density Al plasma. This peculiar behavior appears when the ions are aligned well longitudinally. The wake field is confined around the Si ion in the forward and transverse directions for a distance smaller than the Si cluster interionic distance $l_c$. However, the tail of the wake field extends beyond $l_c$ due to the Si ion high speed of $\sim 0.22c$. Therefore, the peculiar behavior shown above appears only for the ions in one cluster aligned well longitudinally.

A Langmuir film, consisting of a phospholipid monolayer at the air-water interface, was modeled as a two-dimensional lattice gas corresponding to a ternary mixture of water molecules (w), ordered-chain lipids (o), and disordered-chain lipids (d). The statistical problem is formulated in terms of a spin-1 model, in which the disordered-chain lipid states possess a high degenerescence $\omega \gg 1$, and was termed Doniach lattice gas (DLG). Motivated by some open questions in the analysis of the DLG model at the mean-field approximation (MFA) [Phys. Rev. E 90, 052705 (2014)], we have reconsidered it at the pair-approximation level by solving the model on a Cayley tree of coordination $z$. The attractors of the corresponding discrete-map problem are associated with the thermodynamic solutions on the Bethe lattice (the central region of an asymptotically infinite Cayley tree). To check the thermodynamic stability of the possible phases, the grand-potential density was obtained by the method proposed by Gujrati [Phys. Rev. Lett. 74, 809 (1995)]. In general, the previous MFA results are confirmed at the pair-approximation level, but a novel staggered phase, overlooked in the MFA analysis, was found when the condition ${\epsilon }_{\mathrm{wd}}>\frac{1}{2}({\epsilon }_{\mathrm{ww}}+{\epsilon }_{\mathrm{dd}})$ is satisfied, where ${\epsilon }_{xy}$ represents the nearest-neighbor intermolecular interactions between single-site states $x$ and $y$. Model parameters obtained by fitting to experimental data for the two most commonly studied zwitterionic phospholipids, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), yield phase diagrams consistent with the phase transitions observed on Langmuir films of the same lipids under isothermal compression, which present a liquid-condensed to a liquid-expanded first-order transition line ending at a critical point.

Exclusive interactions between self-driven objects may play crucial roles in their collective behavior, e.g., in collective migration of living cells. Here, such collective behavior is studied based on a simple but sufficient model taking account the exclusion effects, which incorporate the following two distinct kinds of exclusion interactions in two dimensions: The first is the mechanical exclusion wherein two objects mechanically repel each other when they overlap. The second is the scattering exclusion, wherein the directions along which each object tries to move are modulated to avoid overlapping. We propose a theoretical model based on two principles: (1) Each object maintains its own polarity with a fixed strength and attempts to move into the polarity direction and (2) objects interact with each other through the abovementioned exclusions. Based on this model, we look at the difference of consequences and combinatory effects of these two kinds of exclusions. Furthermore, we calculate the polar order of polarity directions without an external directional bias. Our results suggest that the combination of these two kinds of exclusions leads to effectively inelastic scattering of two objects, which eventually gives rise to global polar ordering. We also find that the traveling band can arise by this mechanism of alignment at the intermediate density, as generally seen in collective motion with polar alignment and investigated in various earlier works. Characteristics of transitions among disordered, traveling band, and homogeneously ordered states of the presented model are investigated, and their similarities and differences with those given by the explicit alignment interaction are discussed.

An observation is presented that the ratio of the critical and triple-point temperatures $T_{\text{cr}}/T_{\text{tp}}$ of neon, argon, krypton, and xenon fit within a narrow interval, $T_{\text{cr}}/T_{\text{tp}}=1.803\pm 0.5\%$, and the same applies to the density ratio, $n_{\text{cr}}/n_{\text{tp}}=0.3782\pm 1.7\%$ (of the two remaining noble gases, helium does not have a triple point and, for radon, $n_{\text{tp}}$ is unknown). We explain this peculiar property by the fact that the molecules of noble gases are nearly spherical, as a result of which they satisfy the Enskog-Vlasov (EV) kinetic model based on the approximation of hard spheres. The EV model has also allowed us to identify two more parameter combinations which are virtually the same for all noble gases.

We present an analysis of the stationary distributions of run-and-tumble particles trapped in external potentials in terms of a thermophoretic potential that emerges when trapped active motion is mapped to trapped passive Brownian motion in a fictitious inhomogeneous thermal bath. We elaborate on the meaning of the non-Boltzmann-Gibbs stationary distributions that emerge as a consequence of the persistent motion of active particles. These stationary distributions are interpreted as a class of distributions in nonequilibrium statistical mechanics known as superstatistics. Our analysis provides an original insight on the link between the intrinsic nonequilibrium nature of active motion and the well-known concept of local equilibrium used in nonequilibrium statistical mechanics and contributes to the understanding of the validity of the concept of effective temperature. Particular cases of interest, regarding specific trapping potentials used in other theoretical or experimental studies, are discussed. We point out as an unprecedented effect, the emergence of new modes of the stationary distribution as a consequence of the coupling of persistent motion in a trapping potential that varies highly enough with position.