A system of hard rods confined into a pore with slit geometry (two parallel planar substrates) is studied theoretically in the regime of high packing fraction. In this regime the bulk system exhibits a nematic phase as well as a smectic-$A$ (spatially layered) phase. When the system is confined, strong commensuration effects between the layer spacing and the pore width bring about a rich phenomenology, with a phase diagram showing layering and capillary transitions. The latter include capillary smectization transitions whereby a confined smectic phase occurs at conditions of saturation different from those of the corresponding bulk fluid. These transitions are seen to be intimately connected with layering transitions involving discontinuous changes in the number of layers inside the pore. This rich phenomenology is obtained by use of a sophisticated density-functional, Onsager-theory-based approach, especially suited to deal with strongly inhomogeneous fluids. The theory allows for a unified description of ordering and phase behavior of the fluid in confined geometry, and permits us to correlate the above behavior with the wetting properties of the fluid on a single substrate.

Transient heating of tissues leading to cellular stress or death is very common in medicine and biology. In procedures involving a mild (below $70°\mathrm{C}$) and prolonged (minutes) heating, such as hyperthermal tumor therapy, the cellular response to thermal stress is relatively well studied. However, there is practically no data on cell viability at higher temperatures and shorter exposures, while the demand for this knowledge is growing. Two main reasons motivate this research: (i) a growing number of laser therapies and surgical procedures involving pulsed heating, and (ii) cellular viability data at short exposures to high temperatures provide a unique insight into the understanding of processes leading to thermally induced cellular death. We designed a technique and performed a study of cell viability under pulses of heat from $0.3\text{to}100\mathrm{ms}$ in duration with peak temperatures as high as $130°\mathrm{C}$. We found that the threshold of cellular death in this range can be accurately approximated by the Arrhenius law with the activation energy of $1\mathrm{eV}$, a significantly lower value than was reported in studies based on multisecond exposures.

We report on a simple model of spatially extended antitumor system with a fluctuation in growth rate, which can undergo a nonequilibrium phase transition. Three states as excited, subexcited and nonexcited states of a tumor are defined to describe its growth. The multiplicative noise is found to have opposite effects: The positive effect on a nonexcited tumor and the negative effect on an excited tumor.

Wikipedia is a popular web-based encyclopedia edited freely and collaboratively by its users. In this paper we present an analysis of Wikipedias in several languages as complex networks. The hyperlinks pointing from one Wikipedia article to another are treated as directed links while the articles represent the nodes of the network. We show that many network characteristics are common to different language versions of Wikipedia, such as their degree distributions, growth, topology, reciprocity, clustering, assortativity, path lengths, and triad significance profiles. These regularities, found in the ensemble of Wikipedias in different languages and of different sizes, point to the existence of a unique growth process. We also compare Wikipedias to other previously studied networks.

Recent experimental results for covalent glasses suggest the existence of an intermediate phase attributed to the self-organization of the glass network resulting from the tendency to minimize its internal stress. However, the exact nature of this experimentally measured phase remains unclear. We modified a previously proposed model of self-organization by generating a uniform sampling of stress-free networks. In our model, studied on a diluted triangular lattice, an unusual intermediate phase appears, in which both rigid and floppy networks have a chance to occur, a result also observed in a related model on a Bethe lattice by Barré et al. [Phys. Rev. Lett. 94, 208701 (2005)]. Our results for the bond-configurational entropy of self-organized networks, which turns out to be only about 2% lower than that of random networks, suggest that a self-organized intermediate phase could be common in systems near the rigidity percolation threshold.

We consider the problem of constructing facilities such as hospitals, airports, or malls in a country with a nonuniform population density, such that the average distance from a person’s home to the nearest facility is minimized. We review some previous approximate treatments of this problem that indicate that the optimal distribution of facilities should have a density that increases with population density, but does so slower than linearly, as the two-thirds power. We confirm this result numerically for the particular case of the United States with recent population data using two independent methods, one a straightforward regression analysis, the other based on density-dependent map projections. We also consider strategies for linking the facilities to form a spatial network, such as a network of flights between airports, so that the combined cost of maintenance of and travel on the network is minimized. We show specific examples of such optimal networks for the case of the United States.

We present the calculated prediction and the experimental confirmation that doubly ionized Ag and Sn plasmas can have an index of refraction greater than one for soft x-ray wavelengths. Interferometry experiments conducted using a capillary discharge soft x-ray laser operating at a wavelength of $46.9\mathrm{nm}$ $\left(26.44\mathrm{eV}\right)$ confirm that in few times ionized laser-created plasmas of these elements the anomalous dispersion from bound electrons can dominate the free electron contribution, making the index of refraction greater than one. The results confirm that bound electrons can strongly influence the index of refraction of numerous plasmas over a broad range of soft x-ray wavelengths confirming recent observations. The understanding of index of refraction at short wavelengths will become even more essential during the next decade as x-ray free electron lasers will become available to probe a wider variety of plasmas at higher densities and shorter wavelengths.

In colloidal suspensions, at low volume fraction and temperature, dynamical arrest occurs via the growth of elongated structures that aggregate to form a connected network at gelation. Here we show that, in the region of parameter space where gelation occurs, the stable thermodynamical phase is a crystalline columnar one. Near and above the gelation threshold, the disordered spanning network slowly evolves and finally orders to form the crystalline structure. At higher volume fractions the stable phase is a lamellar one, which seems to have a still longer ordering time.

We consider the nonequilibrium thermodynamics of glasses from various perspectives. For the commonly used equilibriumlike approach based on Gibbs’ fundamental form with an additional pair of conjugate variables, we discuss possible choices of the independent out-of-equilibrium variable and we illustrate some implications by concrete results for a well-known exactly solvable lattice model. The choice of variables is further illuminated from the complementary atomistic perspective offered by the inherent-structure formalism. A general formalism of nonequilibrium thermodynamics is employed (i) to derive the standard equilibriumlike approach, (ii) to formulate two self-contained levels to describe glassy dynamics and thermodynamics, and (iii) to offer guidance for future simulations of glasses. The thermodynamic approach suggests to introduce four-point correlation functions associated with structural rearrangements after imposed deformations, which might offer a possibility to detect a growing length scale at the glass transition without employing any dynamic information.

The effect of noise in a motionless front between a periodic spatial state and an homogeneous one is studied. Numerical simulations show that noise induces front propagation. From the subcritical Swift-Hohenberg equation with noise, we deduce an adequate equation for the envelope and the core of the front. The equation of the core of the front is characterized by an asymmetrical periodic potential plus additive noise. The conversion of random fluctuations into direct motion of the core of the front is responsible of the propagation. We obtain an analytical expression for the velocity of the front, which is in good agreement with numerical simulations.

We report measurements of the fluidization process in vertically vibrated two-dimensional granular packings. An initially close packed granular bed is exposed to sinusoidal container oscillations with gradually increasing amplitude. At first the particles close to the free surface become mobile. When a critical value of the forcing strength is reached the remaining crystal suddenly breaks up and the bed fluidizes completely. This transition leads to discontinuous changes in the density distribution and in the root mean square displacement of the individual particles. Likewise the vertical center of mass coordinate increases by leaps and bounds at the transition. It turns out that the maximum container velocity $v_0$ is the crucial driving parameter determining the state of a fully fluidized system. For particles of various sizes the transition to full fluidization occurs at the same value of $v_0^2∕gd$, where $d$ is the particle diameter and $g$ is the gravitational acceleration. A discontinuous fluidization transition is only observed when the particles are highly elastic.

The dynamical behavior of a one-dimensional inelastic particle system with particles of unequal mass traveling between two walls is investigated. The system is driven by adding energy at one of the walls while the other wall is stationary and does not add energy. By deriving analytic solutions for the periodic orbits of this system, we show that there are a countable infinity of critical mass ratios at which the particle dynamics become highly degenerate in the following sense. As the mass ratio passes through these critical points, large numbers of stable periodic orbits can collapse onto a single trivial orbit. We show that the widely studied equal-mass systems represent one of these critical points and are therefore such a degenerate case. We also show that in the elastic limit the number of orbits that collapse onto the single trivial orbit can become arbitrarily large.

Based on the results of phylogenetic analysis, which showed that flecks are the primitive pattern of the felid family and all other patterns including rosettes and blotches develop from it, we construct a Turing reaction-diffusion model which generates spot patterns initially. Starting from this spotted pattern, we successfully generate patterns of adult leopards and jaguars by tuning parameters of the model in the subsequent phase of patterning.

A simple hydrodynamic model of actin-based propulsion of microparticles in dilute cell-free cytoplasmic extracts is presented. Under the basic assumption that actin polymerization at the particle surface acts as a force dipole, pushing apart the load and the free (nonanchored) actin tail, the propulsive velocity of the microparticle is determined as a function of the tail length, porosity, and particle shape. The anticipated velocities of the cargo displacement and the rearward motion of the tail are in good agreement with recently reported results of biomimetic experiments. A more detailed analysis of the particle-tail hydrodynamic interaction is presented and compared to the prediction of the simplified model.

The dynamics of heterogeneities in a shear thickening, concentrated colloidal suspension is investigated through speckle visibility spectroscopy, a dynamic light scattering technique recently introduced [P. K. Dixon and D. J. Durian, Phys. Rev. Lett. 90, 184302 (2003)]. Formation of shear-induced heterogeneities is observed in the jamming regime, and their relaxation after shear cessation is monitored as a function of the applied shear stress. The relaxation time of these heterogeneities increases when a higher stress is applied.

A simple theoretical approach is proposed for calculation of a solvent-mediated potential (SMP) between two colloid particles immersed in a polymer solvent bath in which the polymer is modeled as a chain with intramolecular degrees of freedom. The present recipe is only concerned with the estimation of the density profile of a polymer site around a single solute colloid particle instead of two solute colloid particles separated by a varying distance as done in existing calculational methods for polymer-SMP. Therefore the present recipe is far simpler for numerical implementation than the existing methods. The resultant predictions for the polymer-SMP and polymer solvent-mediated mean force (polymer-SMMF) are in very good agreement with available simulation data. With the present recipe, change tendencies of the contact value and second virial coefficiency of the SMP as a function of size ratio between the colloid particle and polymer site, the number of sites per chain, and the polymer concentration are investigated in detail. The metastable critical polymer concentration as a function of size ratio and the number of sites per chain is also reported for the first time. To yield the numerical solution of the present recipe at less than $1\min$ on a personal computer, a rapid and accurate algorithm for the numerical solution of the classical density functional theory is proposed to supply rapid and accurate estimation of the density profile of the polymer site as an input into the present formalism.

We present experimental results for spinodal decomposition in polymer mixtures of gelatin and dextran. The domain growth law is found to be consistent with $t^{1∕4}$ growth over extended time regimes. Similar results are obtained from lattice simulations of a polymer mixture. This slow growth arises due to the suppression of the bulk mobility of polymers. In that case, spinodal decomposition is driven by the diffusive transport of material along domain interfaces, which gives rise to a $t^{1∕4}$ growth law.

In this paper we study macroscopic density equations in which the diffusion coefficient depends on a weighted spatial average of the density itself. We show that large differences (not present in the local density-dependence case) appear between the density equations that are derived from different representations of the Langevin equation describing a system of interacting Brownian particles. Linear stability analysis demonstrates that under some circumstances the density equation interpreted with the Ito calculus has pattern solutions that never appear for the kinetic interpretation, which is the other one typically appearing in the context of nonlinear diffusion processes. We also introduce a discrete-time microscopic model of particles that confirms the results obtained at the macroscopic density level.

We suggest a mechanism of connectivity evolution in networks to account for the emergence of scale-free behavior. The mechanism works on a fixed set of nodes and promotes growth from a minimally connected initial topology by the addition of edges. A new edge is added between two nodes depending on the trade-off between a gain and a cost function of local connectivity and communication properties. We report on simulation results that indicate the appearance of power-law distributions of node degrees for selected parameter combinations.

We study heat conduction in a system of hard disks confined to a narrow two-dimensional channel. The system is initially in a high-density solidlike phase. We study, through nonequilibrium molecular dynamics simulations, the dependence of the heat current on an externally applied elongational strain. The strain leads to deformation and failure of the solid and we find that the changes in internal structure can lead to very sharp changes in the heat current. A simple free-volume-type calculation of the heat current in a finite hard-disk system is proposed. This reproduces some qualitative features of the current-strain graph for small strains.