Intracellular transport based on molecular motors and its regulation are crucial to the functioning of cells. Filamentary tracks of the cells are abundantly decorated with nonmotile microtubule-associated proteins, such as tau. Motivated by experiments on kinesin-tau interactions [Dixit et al., Science 319, 1086 (2008)] we developed a stochastic model of interacting single-headed motor proteins KIF1A that also takes into account the interactions between motor proteins and tau molecules. Our model reproduces experimental observations and predicts significant effects of tau on bound time and run length which suggest an important role of tau in regulation of kinesin-based transport.

Some physical properties of hydrated biomolecules, e.g., the occurrence of a boson peak, have been recognized to resemble those of glassy states. The present work shows that quantum fluctuations play a fundamental role in describing the glassy state of biomolecules, particularly at lower hydration levels. There is a linear relationship between the quantumness and the slope of the temperature dependence of the boson peak frequency, which is used to classify the extent of quantum contributions to the glassy state of glasses in general. Lastly, we demonstrate that the boson peak two-band spectral structure that is observed in some cases can be directly linked to the anisotropy of the elastic properties of the material. The amino acid L-cysteine is studied in detail. The findings are compared with previously reported data for other macromolecules.

The message passing approach of Karrer and Newman [Phys. Rev. E 82, 016101 (2010)] is an exact and practicable representation of susceptible-infected-recovered dynamics on finite trees. Here we show that, assuming Poisson contact processes, a pair-based moment-closure representation [Sharkey, J. Math. Biol. 57, 311 (2008)] can be derived from their equations. We extend the applicability of both representations and discuss their relative merits. On arbitrary time-independent networks, as was shown for the message passing formalism, the pair-based moment-closure equations also provide a rigorous lower bound on the expected number of susceptibles at all times.

We investigate the tendency for financial instruments to form clusters when there are multiple factors influencing the correlation structure. Specifically, we consider a stock portfolio which contains companies from different industrial sectors, located in several different countries. Both sector membership and geography combine to create a complex clustering structure where companies seem to first be divided based on sector, with geographical subclusters emerging within each industrial sector. We argue that standard techniques for detecting overlapping clusters and communities are not able to capture this type of structure and show how robust regression techniques can instead be used to remove the influence of both sector and geography from the correlation matrix separately. Our analysis reveals that prior to the 2008 financial crisis, companies did not tend to form clusters based on geography. This changed immediately following the crisis, with geography becoming a more important determinant of clustering structure.

The effect of compressibility on the mixing of Lagrangian tracers is analyzed in chaotic stirred flows. Mixing is studied in terms of the finite-time Lyapunov exponents. Mixing and clustering of passive tracers surrounded by Lagrangian coherent structures is observed to increase with compressibility intensity. The role of the stirring rate and compressibility on mixing and clustering has been analyzed.

We report the first experimental observation of extreme multistability in a controlled laboratory investigation. Extreme multistability arises when infinitely many attractors coexist for the same set of system parameters. The behavior was predicted earlier on theoretical grounds, supported by numerical studies of models of two coupled identical or nearly identical systems. We construct and couple two analog circuits based on a modified coupled Rössler system and demonstrate the occurrence of extreme multistability through a controlled switching to different attractor states purely through a change in initial conditions for a fixed set of system parameters. Numerical studies of the coupled model equations are in agreement with our experimental findings.

Here we show that a nonlinear resonance between oceanic surface waves caused by small seabed features (the so-called Bragg resonance) can be utilized to create the equivalent of lenses and curved mirrors for surface gravity waves. Such gravity wave lenses, which are merely small changes to the seafloor topography and therefore are surface noninvasive, can focus or defocus the energy of incident waves toward or away from any desired focal point. We further show that for a broadband incident wave spectrum (i.e., a wave group composed of a multitude of different-frequency waves), a polychromatic topography (occupying no more than the area required for a monochromatic lens) can achieve a broadband lensing effect. Gravity wave lenses can be utilized to create localized high-energy wave zones (e.g., for wave energy harvesting or creating artificial surf zones) as well as to disperse waves in order to create protected areas (e.g., harbors or areas near important offshore facilities). In reverse, lensing of oceanic waves may be caused by natural seabed features and may explain the frequent appearance of very high amplitude waves in certain bodies of water.

Model equations for describing and efficiently computing the radiation profiles of tightly spherically focused higher-order electromagnetic beams of vortex nature are derived stemming from a vectorial analysis with the complex-source-point method. This solution, termed as a high-order quasi-Gaussian (qG) vortex beam, exactly satisfies the vector Helmholtz and Maxwell's equations. It is characterized by a nonzero integer degree and order ($n$,$m$), respectively, an arbitrary waist $w_0$, a diffraction convergence length known as the Rayleigh range $z_R$, and an azimuthal phase dependency in the form of a complex exponential corresponding to a vortex beam. An attractive feature of the high-order solution is the rigorous description of strongly focused (or strongly divergent) vortex wave fields without the need of either the higher-order corrections or the numerically intensive methods. Closed-form expressions and computational results illustrate the analysis and some properties of the high-order qG vortex beams based on the axial and transverse polarization schemes of the vector potentials with emphasis on the beam waist.

We investigate the elastic behavior and damage of weakly cemented granular media under external load with ultrasound. The cementation controlled experiments are performed by freezing the capillary liquid at the bead contact in a dense glass or polymeric [poly(methyl methacrylate)] bead pack wet by tetradecane of volume fraction ϕ = 0.1%–4%. When the pendular rings are solidified, an abrupt increase by a factor of 2 in the compressional wave velocity is observed. We interpret the data in terms of effective medium models in which the contact stiffnesses are derived by either a bonded contact model [P. J. Digby, J. Appl. Mech. 48, 803 (1981)] or a cemented contact model [J. Dvorkin, A. Nur, and H. Yin, Mech. Mater. 18, 351 (1994)]. The former fails to quantitatively account for the results with a soft cement relative to the grain, whereas the latter considering the mechanical properties of the cement does apply. Moreover, we monitor the irreversible behavior of the cemented granular packs under moderate uniaxial loading (<1.3 MPa) with the correlation method of ultrasound scattering. The damage of the cemented materials is accompanied by a compressional wave velocity decrease up to 60%, likely due to the fractures induced at the grain-cement interfaces.

A compression algorithm is introduced for multideterminant wave functions which can greatly reduce the number of determinants that need to be evaluated in quantum Monte Carlo calculations. We have devised an algorithm with three levels of compression, the least costly of which yields excellent results in polynomial time. We demonstrate the usefulness of the compression algorithm for evaluating multideterminant wave functions in quantum Monte Carlo calculations, whose computational cost is reduced by factors of between about 2 and over 25 for the examples studied. We have found evidence of sublinear scaling of quantum Monte Carlo calculations with the number of determinants when the compression algorithm is used.

A gas of inelastic rough spheres admits a spatially homogeneous base state which turns into a hydrodynamic state after a finite relaxation time. We show that this relaxation time is hardly dependent on the degree of inelasticity but increases dramatically with decreasing roughness. An accurate description of translational-rotational velocity correlations at all times is also provided. At a given inelasticity, the roughness parameter can be tuned to produce a huge distortion from the Maxwellian distribution function. The results are obtained from a Grad-like solution of the Boltzmann-Enskog equation complemented by Monte Carlo and molecular dynamics simulations.

We present a powerful semiclassical expression to evaluate off-diagonal matrix elements of the evolution operator between quantum states constructed in the neighborhood of unstable short periodic orbits, which is valid up to the Heisenberg time. The expression is much easier to evaluate than the Van Vleck propagator and consists of a sum over the set of heteroclinic orbits, where each term of the series is computed by canonical invariants. Here we introduce relevant canonical invariants of heteroclinic orbits and with them at hand, the semiclassical expression is derived. Finally, our formula is successfully verified in the hyperbola billiard.

A logarithmic oscillator has the outstanding property that the expectation value of its kinetic energy is constant for all stationary states. Recently the ansatz that this property can be used to define a Hamiltonian thermostat has been put forward and a suggestion has been made that this logarithmic oscillator weakly coupled to a small system would serve as a thermostat as long as few degrees of freedom are involved as is the case in atomic clusters. We have applied these ideas to a cluster of four Lennard-Jones atoms and inspected two different models of coupling between the cluster and the logarithmic oscillator in three dimensions. In both cases we show that there is a clear generation of kinetic motion of the cluster center of mass, but that kinetic energy due to interatomic vibrations is not significantly affected by coupling to the logarithmic oscillator. This is a failure of the published ansatz, as the logarithmic oscillator is unable to modify the kinetic energy due to vibrations in small atomic clusters.

A thermodynamic formalism is developed for a system of interacting particles under overdamped motion, which has been recently analyzed within the framework of nonextensive statistical mechanics. It amounts to expressing the interaction energy of the system in terms of a temperature $\theta$, conjugated to a generalized entropy $s_q$, with $q=2$. Since $\theta$ assumes much higher values than those of typical room temperatures $T\ll \theta$, the thermal noise can be neglected for this system ($T/\theta \simeq 0$). This framework is now extended by the introduction of a work term $\delta W$ which, together with the formerly defined heat contribution ($\delta Q=\theta d{s}_q$), allows for the statement of a proper energy conservation law that is analogous to the first law of thermodynamics. These definitions lead to the derivation of an equation of state and to the characterization of $s_q$ adiabatic and $\theta$ isothermic transformations. On this basis, a Carnot cycle is constructed, whose efficiency is shown to be $\eta =1-({\theta }_2/{\theta }_1)$, where ${\theta }_1$ and ${\theta }_2$ are the effective temperatures of the two isothermic transformations, with ${\theta }_1>{\theta }_2$. The results for a generalized thermodynamic description of this system open the possibility for further physical consequences, like the realization of a thermal engine based on energy exchanges gauged by the temperature $\theta$.

We study the equilibrium and nonequilibrium properties of Boolean decision problems with competing interactions on scale-free networks in an external bias (magnetic field). Previous studies at zero field have shown a remarkable equilibrium stability of Boolean variables (Ising spins) with competing interactions (spin glasses) on scale-free networks. When the exponent that describes the power-law decay of the connectivity of the network is strictly larger than 3, the system undergoes a spin-glass transition. However, when the exponent is equal to or less than 3, the glass phase is stable for all temperatures. First, we perform finite-temperature Monte Carlo simulations in a field to test the robustness of the spin-glass phase and show that the system has a spin-glass phase in a field, i.e., exhibits a de Almeida-Thouless line. Furthermore, we study avalanche distributions when the system is driven by a field at zero temperature to test if the system displays self-organized criticality. Numerical results suggest that avalanches (damage) can spread across the whole system with nonzero probability when the decay exponent of the interaction degree is less than or equal to 2, i.e., that Boolean decision problems on scale-free networks with competing interactions can be fragile when not in thermal equilibrium.

Recent developments in hydraulic fracturing (fracking) have enabled the recovery of large quantities of natural gas and oil from old, low-permeability shales. These developments include a change from low-volume, high-viscosity fluid injection to high-volume, low-viscosity injection. The injected fluid introduces distributed damage that provides fracture permeability for the extraction of the gas and oil. In order to model this process, we utilize a loopless nontrapping invasion percolation previously introduced to model optimal polymers in a strongly disordered medium and for determining minimum energy spanning trees on a lattice. We performed numerical simulations on a two-dimensional square lattice and find significant differences from other percolation models. Additionally, we find that the growing fracture network satisfies both Horton-Strahler and Tokunaga network statistics. As with other invasion percolation models, our model displays burst dynamics, in which the cluster extends rapidly into a connected region. We introduce an alternative definition of bursts to be a consecutive series of opened bonds whose strengths are all below a specified value. Using this definition of bursts, we find good agreement with a power-law frequency-area distribution. These results are generally consistent with the observed distribution of microseismicity observed during a high-volume frack.

The presence of spin-glass (SG) order in highly geometrically frustrated systems is analyzed in a cluster SG model. The model considers infinite-range disordered interactions among cluster magnetic moments and the $J_1\text{−}{J}_2$ model couplings between Ising spins of the same cluster. This model can introduce two sources of frustration: one coming from the disordered interactions and another coming from the $J_1\text{−}{J}_2$ intracluster interactions (intrinsic frustration). The framework of one-step replica symmetry breaking is adopted to obtain a one-cluster problem that is exactly solved. As a main result we create phase diagrams of the temperature $T$ versus intensity of the disorder $J$, where the paramagnetic-SG phase transition occurs at $T_f$ when $T$ decreases for high-$J$ values. For low-$J$ values, the SG order is absent for antiferromagnetic clusters without intrinsic frustration. However, the SG order can be observed within the intracluster intrinsic frustration regime even for lower intensity of disorder. In particular, the results indicate that the presence of small clusters in geometrically frustrated antiferromagnetic systems can help stabilize the SG order within a weak disorder.

We study the surface phase diagram of the three-dimensional kinetic Ising model below the equilibrium critical point subjected to a periodically oscillating magnetic field. Changing the surface interaction strength as well as the period of the external field, we obtain a nonequilibrium surface phase diagram that in parts strongly resembles the corresponding equilibrium phase diagram, with an ordinary transition, an extraordinary transition, and a surface transition. These three lines meet at a special transition point. For weak surface couplings, however, the surface does not order. These results are found to remain qualitatively unchanged when using different single-spin flip dynamics.

The critical exponents are estimated for the gauge glass model in two dimensions, in which only the Kosterlitz-Thouless (KT) phase appears in the low-temperature regime. The nonequilibrium relaxation method is applied to estimate the transition temperature and critical exponents: the static exponent $\eta$ and the dynamical exponent $z$. Since the system exhibits criticality in the whole KT phase, we estimate the exponents on the boundary as well as inside the KT phase. The static exponent $\eta$ depends on both the temperature and the strength of randomness, while the dynamical one $z$ is almost constant throughout the KT phase, including the boundary.

We study the dynamics of a system of coupled oscillators of distributed natural frequencies, by including the features of both thermal noise, parametrized by a temperature, and inertial terms, parametrized by a moment of inertia. For a general unimodal frequency distribution, we report here the complete phase diagram of the model in the space of dimensionless moment of inertia, temperature, and width of the frequency distribution. We demonstrate that the system undergoes a nonequilibrium first-order phase transition from a synchronized phase at low parameter values to an incoherent phase at high values. We provide strong numerical evidence for the existence of both the synchronized and the incoherent phase, treating the latter analytically to obtain the corresponding linear stability threshold that bounds the first-order transition point from below. In the limit of zero noise and inertia, when the dynamics reduces to the one of the Kuramoto model, we recover the associated known continuous transition. At finite noise and inertia but in the absence of natural frequencies, the dynamics becomes that of a well-studied model of long-range interactions, the Hamiltonian mean-field model. Close to the first-order phase transition, we show that the escape time out of metastable states scales exponentially with the number of oscillators, which we explain to be stemming from the long-range nature of the interaction between the oscillators.