Phase-field-crystal (PFC) modeling has emerged as a computationally efficient tool to address crystal growth phenomena on atomistic length and diffusive time scales. We use a two-dimensional phase-field-crystal model for a binary system based on Elder et al. [Phys. Rev. B 75, 064107 (2007)] to study critical nuclei and their liquid-solid phase boundaries, in particular the nucleus size dependence of the liquid-solid interface tension as well as of the nucleation barrier. Critical nuclei are stabilized in finite systems of various sizes, however, the extracted interface tension as function of the nucleus radius $r$ is independent of system size. We suggest a phenomenological expression to describe the dependence of the extracted interface tension on the nucleus radius $r$ for the liquid-solid system. Moreover, the numerical PFC results show that this dependency can not be fully described by the nonclassical Tolman formula.

Changes observed in the reflection anisotropy spectroscopy (RAS) profiles of monolayers of cytochrome P450 reductase adsorbed at Au(110)–electrolyte interfaces at 0.056 V following the addition of nicotinamide adenine dinucleotide phosphate $\left({\mathrm{NADP}}^{+}\right)$ are explained in terms of a simple model as arising from changes in the orientation of an isoalloxazine ring located in the flavin mononucleotide binding domain of the protein. The model also accounts for the changes observed in the RAS as the potential applied to the Au(110) surface is varied and suggests that differences in the dependence of the RAS profile of the adsorbed protein on the potential applied to the electrode in the absence and presence of ${\mathrm{NADP}}^{+}$ are explicable as arising from a competition between the applied potential acting to reduce the protein and the ${\mathrm{NADP}}^{+}$ to oxidize it.

In this paper the shape equation for axisymmetric vesicles subjected to an ac electric field is derived on the basis of the liquid-crystal model. The equilibrium morphology of a lipid vesicle is determined by the minimization of its free energy in coupled mechanical and ac electric fields. Besides elastic bending, the effects of the osmotic pressure difference, surface tension, Maxwell pressure, and flexoelectric and dielectric properties of phospholipid membrane as well are taken into account. The influences of elastic bending, osmotic pressure difference, and surface tension on the frequency-dependent behavior of a vesicle membrane in an ac electric field are examined. The singularity of the ac electric field is also investigated. Our theoretical results of vesicle deformation agree well with previous experimental and numerical results. The present study provides insights into the physical mechanisms underpinning the frequency-dependent morphological evolution of vesicles in the electric and mechanical fields.

Unstable dynamics characterizes the evolution of most solid tumors. Because of an increased failure of maintaining genome integrity, a cumulative increase in the levels of gene mutation and loss is observed. Previous work suggests that instability thresholds to cancer progression exist, defining phase transition phenomena separating tumor-winning scenarios from tumor extinction or coexistence phases. Here we present an integral equation approach to the quasispecies dynamics of unstable cancer. The model exhibits two main phases, characterized by either the success or failure of cancer tissue. Moreover, the model predicts that tumor failure can be due to either a reduced selective advantage over healthy cells or excessive instability. We also derive an approximate, analytical solution that predicts the front speed of aggressive tumor populations on the instability space.

The fascinating ability of algae, insects, and fishes to survive at temperatures below normal freezing is realized by antifreeze proteins (AFPs). These are surface-active molecules and interact with the diffusive water-ice interface thus preventing complete solidification. We propose a dynamical mechanism on how these proteins inhibit the freezing of water. We apply a Ginzburg-Landau-type approach to describe the phase separation in the two-component system (ice, AFP). The free-energy density involves two fields: one for the ice phase with a low AFP concentration and one for liquid water with a high AFP concentration. The time evolution of the ice reveals microstructures resulting from phase separation in the presence of AFPs. We observed a faster clustering of pre-ice structure connected to a locking of grain size by the action of AFP, which is an essentially dynamical process. The adsorption of additional water molecules is inhibited and the further growth of ice grains stopped. The interfacial energy between ice and water is lowered allowing the AFPs to form smaller critical ice nuclei. Similar to a hysteresis in magnetic materials we observe a thermodynamic hysteresis leading to a nonlinear density dependence of the freezing point depression in agreement with the experiments.

In this work we investigate, by means of direct numerical hyperviscous simulations, how rotation affects the bidimensionalization of a turbulent flow. We study a thin layer of fluid, forced by a two-dimensional forcing, within the framework of the “split cascade” in which the injected energy flows both to small scales (generating the direct cascade) and to large scale (to form the inverse cascade). It is shown that rotation reinforces the inverse cascade at the expense of the direct one, thus promoting bidimensionalization of the flow. This is achieved by a suppression of the enstrophy production at large scales. Nonetheless, we find that, in the range of rotation rates investigated, increasing the vertical size of the computational domain causes a reduction of the flux of the inverse cascade. Our results suggest that, even in rotating flows, the inverse cascade may eventually disappear when the vertical scale is sufficiently large with respect to the forcing scale. We also study how the split cascade and confinement influence the breaking of symmetry induced by rotation.

We study foam flow in an elementary model porous medium consisting of a convergent and a divergent channel positioned side by side and possessing a fixed joint porosity. Configurations of converging or diverging channels are ubiquitous at the pore scale in porous media, as all channels linking pores possess a converging and diverging part. The resulting flow kinematics imposes asymmetric bubble deformations in the two channels, which modulate foam-wall friction and strongly impact the flux distribution. We measure, as well as quantitatively predict, the ratio of the fluxes in the two channels as a function of the channel widths by modeling pressure drops of both viscous and capillary origins. This study reveals the crucial importance of boundary-induced bubble deformation on the mobility of a flowing foam, resulting in particular in flow irreversibility.

We consider an axisymmetric liquid film on a horizontal cylindrical surface subjected to axial harmonic oscillation in the high-frequency limit. We derive and analyze the nonlinear evolution equation describing the nonlinear dynamics of this physical system in terms of the averaged film thickness. The method used for the derivation of the evolution equation is based on long-wave theory and the separation of the relevant fields into fast and slow components. We carry out the linear stability analysis for a film of a constant thickness which shows that axial forcing of the cylinder may result in either stabilization or destabilization of the axisymmetric flow with respect to the unforced one, depending on the choice of the parameter set. The analysis is extended to the weakly nonlinear stage and it reveals that the system bifurcates subcritically from the equilibrium.

Very recently, interferometric methods have been proposed to measure the full statistics of work performed on a driven quantum system [Dorner et al., Phys. Rev. Lett. 110, 230601 (2013) and Mazzola et al., Phys. Rev. Lett. 110, 230602 (2013)]. The advantage of such schemes is that they replace the necessity to make projective measurements by performing phase estimation on an appropriately coupled ancilla qubit. These proposals are one possible route to the tangible experimental exploration of quantum thermodynamics, a subject which is the center of much current attention due to the current control of mesoscopic quantum systems. In this Rapid Communication we demonstrate that a modification of the phase estimation protocols can be used in order to measure the heat distribution of a quantum process. In addition, we demonstrate how our scheme maybe implemented using ion trap technology. Our scheme should pave the way for experimental explorations of the Landauer principle and hence the intricate energy to information conversion in mesoscopic quantum systems.

We compute the structure and kinetics of two systems of low-valence particles with three or six freely oriented bonds in two dimensions. The structure of clusters formed by trivalent particles is complex with loops and holes, while hexavalent particles self-organize into regular and compact structures. We identify the elementary structures which compose the clusters of trivalent particles. At initial stages of clustering, the clusters of trivalent particles grow with a power-law time dependence. Yet at longer times fusion and fission of clusters equilibrates and clusters form a heterogeneous phase with polydispersed sizes. These results emphasize the role of valence in the kinetics and stability of finite-size clusters.

We treat a chaotic Hamiltonian scattering system with three degrees of freedom where the chaotic invariant set is of low dimension. Then the chaos and its structure are not visible in scattering functions plotted along one-dimensional lines in the set of asymptotic initial conditions. We show that an asymptotic observer can nevertheless see the structure of the chaotic set in an appropriate scattering function on the two-dimensional impact parameter plane and in the doubly differential cross section. Rainbow singularities in the cross section carry over the symbolic dynamics of the chaotic set into the cross section. A smooth image of the fractal structure of the chaotic set can be reconstructed on the domain of the cross section.

The present work investigates the acceleration of test particles, relevant to the solar-wind problem, in balanced and imbalanced magnetohydrodynamic turbulence (terms referring here to turbulent states possessing zero and nonzero cross helicity, respectively). These turbulent states, obtained numerically by prescribing the injection rates for the ideal invariants, are evolved dynamically with the particles. While the energy spectrum for balanced and imbalanced states is known, the impact made on particle heating is a matter of debate, with different considerations giving different results. By performing direct numerical simulations, resonant and nonresonant particle accelerations are automatically considered and the correct turbulent phases are taken into account. For imbalanced turbulence, it is found that the acceleration rate of charged particles is reduced and the heating rate diminished. This behavior is independent of the particle gyroradius, although particles that have a stronger adiabatic motion (smaller gyroradius) tend to experience a larger heating.

We develop a unified treatment of pumping and nonequilibrium thermodynamics. We show that the pumping current generated through an adiabatic mechanical operation in equilibrium can be expressed in terms of the stationary distribution of the corresponding driven nonequilibrium system. We also show that the total transfer in pumping can be evaluated from the work imported to the driven counterpart. These findings lead us to a unified viewpoint for pumping and nonequilibrium thermodynamics.

Generic inhomogeneous steady states in an asymmetric exclusion process on a ring with a pair of point bottlenecks are studied. We show that, due to an underlying universal feature, measurements of coarse-grained steady-state densities in this model resolve the bottleneck structures only partially. Unexpectedly, it displays localization-delocalization transitions and confinement of delocalized domain walls, controlled by the interplay between particle number conservation and bottleneck competition for moderate particle densities.

We discuss the statistical properties of small mechanothermodynamic systems (one- and two-particle cases) subject to nonlinear coupling and in contact with standard Gaussian reservoirs. We use a method that applies averages in the Laplace-Fourier space, which relates to a generalization of the final-value theorem. The key advantage of this method lies in the possibility of eschewing the explicit computation of the propagator, traditionally required in alternative methods like path integral calculations, which is hardly obtainable in the majority of the cases. For one-particle equilibrium systems we are able to compute the instantaneous (equilibrium) probability density functions of injected and dissipated power as well as the respective large deviation functions. Our thorough calculations explicitly show that for such models nonlinearities are irrelevant in the long-term statistics, which preserve the exact same values as computed for linear cases. Actually, we verify that the thermostatistical effect of the nonlinearities is constricted to the transient towards equilibrium, since it affects the average total energy of the system. For the two-particle system we consider each element in contact with a heat reservoir, at different temperatures, and focus on the problem of heat flux between them. Contrarily to the one-particle case, in this steady state nonequilibrium model we prove that the heat flux probability density function reflects the existence of nonlinearities in the system. An important consequence of that it is the temperature dependence of the conductance, which is unobserved in linear(harmonic) models. Our results are complemented by fluctuation relations for the injected power (equilibrium case) and heat flux (nonequilibrium case).

The surface and bulk properties of a modified ballistic deposition model are investigated. The deposition rule interpolates between nearest- and next-nearest-neighbor ballistic deposition and the random deposition models. The stickiness of the depositing particle is controlled by a parameter and the type of interparticle force. Two such forces are considered: Coulomb and van der Waals type. The interface width shows three distinct growth regions before eventual saturation. The rate of growth depends more strongly on the stickiness parameter than on the type of interparticle force. However, the porosity of the deposits is strongly influenced by the interparticle force.

The interfacial two-dimensional spreading dynamics of quasilinear Vero cell colony fronts in methylcellulose (MC)-containing culture medium, under a constant average front displacement velocity regime, was investigated. Under comparable experimental conditions, the average colony front displacement velocity becomes lower than that reported for a standard culture medium. Initially, the presence of MC in the medium hinders both the colony spreading, due to a gradual change in the average size and shape of cells and their distribution in the colony, and the cell motility in the gelled medium. Furthermore, at longer culture times enlarged cells appear at random in the border region of the colony. These cells behave as obstacles (pinning sites) for the displacement of smaller cells towards the colony front. The dynamic scaling analysis of rough fronts yields the set of exponents $\alpha =0.63\pm 0.04,\beta =0.75\pm 0.05$, and $z=0.84\pm 0.05$, which is close to that expected for a quenched Kardar-Parisi-Zhang model.

Current understanding of the forces directing the folding of integral membrane proteins is very limited compared to the detailed picture available for water-soluble proteins. While mechanistic studies of the folding process in vitro have been conducted for only a small number of membrane proteins, the available evidence indicates that their folding process is thermodynamically driven like that of soluble proteins. In vivo, however, the majority of integral membrane proteins are installed in membranes by dedicated machinery, suggesting that the cellular systems may act to facilitate and regulate the spontaneous physical process of folding. Both the in vitro folding process and the in vivo pathway must navigate an energy landscape dominated by the energetically favorable burial of hydrophobic segments in the membrane interior and the opposition to folding due to the need for passage of polar segments across the membrane. This manuscript describes a simple, exactly solvable model which incorporates these essential features of membrane protein folding. The model is used to compare the folding time under conditions which depict both the in vitro and in vivo pathways. It is proposed that the cellular complexes responsible for insertion of membrane proteins act by lowering the energy barrier for passage of polar regions through the membrane, thereby allowing the chain to more rapidly achieve the folded state.

When a population is engaged in successive prisoner's dilemmas, indirect reciprocity through reputation fosters cooperation through the emergence of moral and action rules. A simplified model has recently been proposed where individuals choose between helping others or not and are judged good or bad for it by the rest of the population. The reputation so acquired will condition future actions. In this model, eight strategies (referred to as “leading eight”) enforce a high level of cooperation, generate high payoffs, and are therefore resistant to invasions by other strategies. Here we show that, by assigning each individual one of two labels that peers can distinguish (e.g., political ideas, religion, and skin color) and allowing moral and action rules to depend on the label, intolerant behaviors can emerge within minorities under sufficient economic stress. We analyze the sets of conditions where this can happen and also discuss the circumstances under which tolerance can be restored. Our results agree with empirical observations that correlate intolerance and economic stress and predict a correlation between the degree of tolerance of a population and its composition and ethical stance.