We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers’ radius of gyration, $R_G$, and that of the region containing the knot, $R_{G,k}$, are small compared to the distance $b$ between the obstacles, the knot is weakly localized and $R_G$ scales as in a good solvent with an amplitude that depends on knot type. In an intermediate regime where $R_G>b>R_{G,k}$, the geometry of the polymer becomes branched. When $R_{G,k}$ exceeds $b$, the knot delocalizes and becomes also branched. In this regime, $R_G$ is independent of knot type. We discuss the implications of this behavior for gel electrophoresis experiments on knotted DNA in weak fields.

In systems belonging to the universality class of the random field Ising model, the standard hyperscaling relation between critical exponents does not hold, but is replaced with a modified hyperscaling relation. As a result, standard formulations of finite-size scaling near critical points break down. In this work, the consequences of modified hyperscaling are analyzed in detail. The most striking outcome is that the free-energy cost $\Delta F$ of interface formation at the critical point is no longer a universal constant, but instead increases as a power law with system size, $\Delta F\propto L^{\theta }$, with $\theta$ as the violation of hyperscaling critical exponent and $L$ as the linear extension of the system. This modified behavior facilitates a number of numerical approaches that can be used to locate critical points in random field systems from finite-size simulation data. We test and confirm the approaches on two random field systems in three dimensions, namely, the random field Ising model and the demixing transition in the Widom-Rowlinson fluid with quenched obstacles.

Non-Brownian particles suspended in an oscillatory shear flow are studied numerically. In these systems it is often assumed that chaos (due to the long-range nature of the hydrodynamic interaction between particles) plus noise (contact or roughness) lead to irreversible behavior. However, we demonstrate that the long-range hydrodynamic interactions are not a source, nor even a magnifier, of irreversibility when coupled with nonhydrodynamic interactions. Additionally, analysis reveals that the apparent anisotropy of the particle diffusion is due to coupling of the shear flow and transverse diffusion.

Brownian particles drifting through a periodically structured force landscape can become entrained by the landscape’s symmetries. What direction a particular particle takes can depend strongly on subtle variations in its physical properties. Consequently, a homogeneously structured force field can sort a mixture of particles into spatially separated fractions, much as an optical prism refracts light into its component wavelengths. When the force landscape is implemented with structured light fields, such continuous multichannel sorting may be termed prismatic optical fractionation. We describe experimental and numerical studies of colloidal spheres’ transport through periodic arrays of optical tweezers, which reveal an important role for three-dimensional motion in determining a drifting particle’s fate. These studies also demonstrate sorting on the basis of statistically locked-in transport, in which Brownian fluctuations contribute to direction selection.

We report the boiling behavior of pentane emulsified in a yield stress fluid, a colloidal clay (Laponite) suspension. We have observed that a superheated state is easily reached: the emulsion, heated more than $50°\text{C}$ above the alkane boiling point, does not boil. Superheating is made possible by the suppression of heterogeneous nucleation in pentane, resulting from the emulsification process, a phenomenon evidenced decades ago in studies of the superheating of two phase fluids. We have furthermore studied the growth of isolated bubbles nucleated in the emulsion. The rate of increase of the bubble radius with time depends on both the temperature and emulsion volume fraction but, rather unexpectedly, does not depend on the fluid rheology. We show that the bubbles grow by diffusion of the alkane through the aqueous phase between liquid droplets and bubbles, analogously to an Ostwald ripening process. The peculiarity of the process reported here is that a layer depleted in oil droplets forms around the bubble, layer to which the alkane concentration gradient is confined. We successfully describe our experimental results with a simple transfer model.

We have used Brownian dynamics simulations to study the dynamics of a bead-and-spring polymer subject to a flashing ratchet potential. To elucidate the role of hydrodynamic (HD) interactions, simulations were carried out for the cases where HD interactions are present and when they are absent. The average speed of the polymer and its conformational properties were examined upon variation in the polymer length, $N$, and the ratchet spatial period, $L$. Two distinct dynamical regimes were evident. In the low-$N$/high-$L$ regime, the velocity decreases with increasing $N$, and center-of-mass diffusion is a key part of the motional mechanism. By contrast, in the high-$N$/low-$L$ regime, the velocity is insensitive to variation in $N$, and motion is achieved via the coupling of internal modes to the cycling of the ratchet potential. The location of the regimes is correlated with the average conformational state of the polymer. Incorporating HD interactions increases the average polymer velocity for all polymer lengths and ratchet spatial periods considered. The dynamical behavior of polymers in the low-$N$/high-$L$ regime can be understood using simple a theoretical model that yields quantitatively reasonable predictions of the polymer velocity.

We present a systematic analysis of statistical properties of turbulent current and vorticity structures at a given time using cluster analysis. The data stem from numerical simulations of decaying three-dimensional magnetohydrodynamic turbulence in the absence of an imposed uniform magnetic field; the magnetic Prandtl number is taken equal to unity, and we use a periodic box with grids of up to ${1536}^3$ points and with Taylor Reynolds numbers up to 1100. The initial conditions are either an $X$-point configuration embedded in three dimensions, the so-called Orszag-Tang vortex, or an Arn’old-Beltrami-Childress configuration with a fully helical velocity and magnetic field. In each case two snapshots are analyzed, separated by one turn-over time, starting just after the peak of dissipation. We show that the algorithm is able to select a large number of structures (in excess of 8000) for each snapshot and that the statistical properties of these clusters are remarkably similar for the two snapshots as well as for the two flows under study in terms of scaling laws for the cluster characteristics, with the structures in the vorticity and in the current behaving in the same way. We also study the effect of Reynolds number on cluster statistics, and we finally analyze the properties of these clusters in terms of their velocity–magnetic-field correlation. Self-organized criticality features have been identified in the dissipative range of scales. A different scaling arises in the inertial range, which cannot be identified for the moment with a known self-organized criticality class consistent with magnetohydrodynamics. We suggest that this range can be governed by turbulence dynamics as opposed to criticality and propose an interpretation of intermittency in terms of propagation of local instabilities.

We study a model of a lattice gas with orientational degrees of freedom which resemble the formation of hydrogen bonds between the molecules. In this model, which is the simplified version of the Henriques-Barbosa model, no distinction is made between donors and acceptors in the bonding arms. We solve the model in the grand-canonical ensemble on a Husimi lattice built with hexagonal plaquettes with a central site. The ground state of the model, which was originally defined on the triangular lattice, is exactly reproduced by the solution on this Husimi lattice. In the phase diagram, one gas and two liquid [high density liquid (HDL) and low density liquid (LDL)] phases are present. All phase transitions (GAS-LDL, GAS-HDL, and LDL-HDL) are discontinuous, and the three phases coexist at a triple point. A line of temperatures of maximum density in the isobars is found in the metastable GAS phase, as well as another line of temperatures of minimum density appears in the LDL phase, part of it in the stable region and another in the metastable region of this phase. These findings are at variance with simulational results for the same model on the triangular lattice, which suggested a phase diagram with two critical points. However, our results show very good quantitative agreement with the simulations, both for the coexistence loci and the densities of particles and of hydrogen bonds. We discuss the comparison of the simulations with our results.

We present a detailed analysis of two-state trajectories obtained from force-clamp spectroscopy (FCS) of reversibly bonded systems. FCS offers the unique possibility to vary the equilibrium constant in two-state kinetics, for instance, the unfolding and refolding of biomolecules, over many orders of magnitude due to the force dependence of the respective rates. We discuss two different kinds of counting statistics, the event counting usually employed in the statistical analysis of two-state kinetics and additionally the so-called cycle counting. While in the former case all transitions are counted, cycle counting means that we focus on one type of transitions. This might be advantageous in particular if the equilibrium constant is much larger or much smaller than unity because in these situations the temporal resolution of the experimental setup might not allow to capture all transitions of an event-counting analysis. We discuss how an analysis of FCS data for complex systems exhibiting dynamic disorder might be performed yielding information about the detailed force dependence of the transition rates and about the time scale of the dynamic disorder. In addition, the question as to which extent the kinetic scheme can be viewed as a Markovian two-state model is discussed.

In terms of the multifractal analysis, we investigate the characteristics of the instantaneous normal modes (INMs) at two mobility edges (MEs) of a simple fluid, where the locations of the MEs in the INM spectrum were identified in a previous work [B. J. Huang and T. M. Wu, Phys. Rev. E 79, 041105 (2009)]. The mass exponents and the singularity spectrum of the INMs are obtained by the box-size and system-size scalings under the typical average. The INM eigenvectors at a ME exhibit a multifractal nature and the multifractal INMs at each ME yield the same results in generalized fractal dimensions and singularity spectrum. Our results indicate that the singularity spectrum of the multifractal INMs agrees well with that of the Anderson model at the critical disorder. This good agreement provides numerical evidence for the universal multifractality at the localization-delocalization transition. For the multifractal INMs, the probability density function and the spatial correlation function of the squared vibrational amplitudes are also calculated. The relation between the probability density function and the singularity spectrum is examined numerically, so are the relations between the critical exponents of the spatial correlation function and the mass exponents of the multifractal INMs.

The primary spacing of a dendritic array grown under transient growth conditions displays a distribution of wavelengths. The average primary spacing is shown, both experimentally and numerically, to evolve between characteristic incubation periods during which the distribution of wavelengths remains essentially stable. Our primary spacing results display a gradual transition period from one spacing range to another, consistent with the fact that the abrupt doubling of spacing predicted by Warren and Langer for an idealized periodic array affects different wavelengths of the distribution at different times. This transition is shown to depend on the rate of change in growth speed using phase-field simulations of directional solidification where the pulling speed is ramped at different rates. In particular, for high rates of change of the pulling speed we observe temporary marginally stable array configurations separated by relatively short lived transitions, while for lower rates of change of the pulling speed the distinction between incubation and transition periods disappears.

We investigate the performance of a variant of Axelrod’s model for dissemination of culture—the Adaptive Culture Heuristic (ACH)—on solving an NP-Complete optimization problem, namely, the classification of binary input patterns of size $F$ by a Boolean Binary Perceptron. In this heuristic, $N$ agents, characterized by binary strings of length $F$ which represent possible solutions to the optimization problem, are fixed at the sites of a square lattice and interact with their nearest neighbors only. The interactions are such that the agents’ strings (or cultures) become more similar to the low-cost strings of their neighbors resulting in the dissemination of these strings across the lattice. Eventually the dynamics freezes into a homogeneous absorbing configuration in which all agents exhibit identical solutions to the optimization problem. We find through extensive simulations that the probability of finding the optimal solution is a function of the reduced variable $F/N^{1/4}$ so that the number of agents must increase with the fourth power of the problem size, $N\propto F^4$, to guarantee a fixed probability of success. In this case, we find that the relaxation time to reach an absorbing configuration scales with $F^6$ which can be interpreted as the overall computational cost of the ACH to find an optimal set of weights for a Boolean binary perceptron, given a fixed probability of success.

The analysis of nonlinear modes in a complex absorbing double-well potential supported by linear gain is presented. Families of the nonlinear modes and their bifurcations are found numerically by means of the properly modified “shooting” method. Linear stability and dynamics of the modes are studied. It is shown that no stable modes exist in the case of attractive nonlinearity, while stable modes, including nonsymmetric ones, are found when the nonlinearity is repulsive. Varying a control parameter (e.g., the height of barrier between the wells) results in switching from one mode to another. Apart from stationary modes we have found pulsating solutions emergent from unstable modes.

We develop a theory of turbulence based on the inviscid Navier-Stokes equation, without using dimensional or phenomenological considerations. The theory allows us to obtain the scaling law and to calculate the scaling exponents of the Lagrangian and Eulerian velocity structure functions in the inertial range. The obtained results are shown to be in very good agreement with numerical simulations and experimental data. The introduction of stochasticity into the equations is discussed in detail. The main equation of the theory obtained directly from the Navier-Stokes equation is analyzed by means of continual integration.

Traveling-wave solutions are discovered in plane Couette flow. They are obtained when the so-called steady hairpin vortex state found recently by Gibson et al. [J. Fluid Mech. 638, 243 (2009)] and Itano and Generalis [Phys. Rev. Lett. 102, 114501 (2009)] is continued to sliding Couette flow geometry between two concentric cylinders by using the radius ratio as a homotopy parameter. It turns out that in the plane Couette flow geometry two traveling waves having the phase velocities with opposite signs are associated with their appearance from the steady hairpin vortex state, where the amplitude of the phase velocities increases gradually from zero as the Reynolds number is increased. The solutions obviously inherit the streaky structure of the hairpin vortex state, but shape preserving flow patterns propagate in the streamwise direction. Other striking features of the solution are asymmetric mean flow profiles and strong quasistreamwise vortices which occupy the vicinity of only the top or bottom moving boundary, depending on the sign of the phase velocity. Furthermore, we find that the pitchfork bifurcation associated with the appearance of the solution becomes imperfect when the flow is perturbed by a Poiseuille flow component.

We introduce thermal fluctuations in the lattice Boltzmann method for nonideal fluids. A fluctuation-dissipation theorem is derived within the Langevin framework and applied to a specific lattice Boltzmann model that approximates the linearized fluctuating Navier-Stokes equations for fluids based on square-gradient free-energy functionals. The obtained thermal noise is shown to ensure equilibration of all degrees of freedom in a simulation to high accuracy. Furthermore, we demonstrate that satisfactory results for most practical applications of fluctuating hydrodynamics can already be achieved using thermal noise derived in the long-wavelength limit.

We derive general properties of the linear-response functions of nonequilibrium steady states in Langevin systems. These correspond to extension of the results which were recently found in Hamiltonian systems [A. Shimizu and T. Yuge, J. Phys. Soc. Jpn. 79, 013002 (2010)]. We discuss one of the properties, the sum rule for the response function, in particular detail. We show that the sum rule for the response function of the velocity holds in the underdamped case, whereas it is violated in the overdamped case. This implies that the overdamped Langevin models should be used with great care. We also investigate the relation of the sum rule to an equality on the energy dissipation in nonequilibrium Langevin systems, which was derived by Harada and Sasa.

Using numerical simulations we examine the velocity fluctuations and velocity-force curve characteristics of a probe particle driven with constant force through a two-dimensional disordered assembly of disks which has a well-defined jamming point J at a density of ${\varphi }_J=0.843$. As $\varphi$ increases toward ${\varphi }_J$, the average velocity of the probe particle decreases and the velocity fluctuations show an increasingly intermittent or avalanchelike behavior. When $\varphi$ is within a few percent of the jamming density, the velocity distributions are exponential, while when $\varphi$ is less than 1% away from jamming, the velocity distributions have a power-law character with exponents in agreement with recent experiments. The velocity power spectra exhibit a crossover from a Lorentzian form to a $1/f$ shape near jamming. We extract a correlation length exponent $\nu$ which is in good agreement with recent shear simulations. For $\varphi >{\varphi }_J$, there is a critical threshold force $F_c$ that must be applied for the probe particle to move through the sample which increases with increasing $\varphi$. The velocity-force curves are linear below jamming, while at jamming they have a power-law form. The onset of the probe motion above ${\varphi }_J$ occurs via a local yielding of the particles around the probe particle which we term a local shear banding effect.

Folding rate prediction is a useful way to find the key factors affecting folding kinetics of proteins. Structural information is more or less required in the present prediction methods, which limits the application of these methods to various proteins. In this work, an “effective length” is defined solely based on the composition of a protein, namely, the number of specific types of amino acids in a protein. A physical theory based on a minimalist model is employed to describe the relation between the folding rates and the effective length of proteins. Based on the resultant relationship between folding rates and effective length, the optimal sets of amino acids are found through the enumeration over all possible combinations of amino acids. This optimal set achieves a high correlation (with the coefficient of 0.84) between the folding rates and the optimal effective length. The features of these amino acids are consistent with our model and landscape theory. Further comparisons between our effective length and other factors are carried out. The effective length is physically consistent with structure-based prediction methods and has the best predictability for folding rates. These results all suggest that both entropy and energetics contribute importantly to folding kinetics. The ability to accurately and efficiently predict folding rates from composition enables the analysis of the kinetics for various kinds of proteins. The underlying physics in our method may be helpful to stimulate further understanding on the effects of various amino acids in folding dynamics.

Polar liquids like water carry a characteristic nanometric length scale, the correlation length of orientation polarizations. Continuum theories that can capture this feature commonly run under the name of “nonlocal” electrostatics since their dielectric response is characterized by a scale-dependent dielectric function $\epsilon \left(q\right)$, where $q$ is the wave vector; the Poisson(-Boltzmann) equation then turns into an integro-differential equation. Recently, “local” formulations have been put forward for these theories and applied to water, solvated ions, and proteins. We review the local formalism and show how it can be applied to a structured liquid in slit and plate geometries, and solve the Poisson-Boltzmann theory for a charged plate in a structured solvent with counterions. Our results establish a coherent picture of the local version of nonlocal electrostatics and show its ease of use when compared to the original formulation.