Based on the idea conveyed in the author’s prior study [Fluct. Noise Lett. 6, L147 (2006)], a physical approach for the description of neuronal dynamics under the influence of ion channel noise is developed in the realm of Nelson’s stochastic mechanics when open to dissipative environments. The formalism therein is scrutinized using a special membrane with some tailored properties giving the Rose-Hindmarsh dynamics in the deterministic limit. Led by the presence of multiple number of gates in an ion channel, a dual viewpoint of channel noise is established. Then, stochastic mechanics is adopted to model those channel fluctuations emerging from the uncertainty in accessing the permissible topological states of open gates. A mutual interaction between the above fluctuations and the noise, emerging from the stochasticity in the movement of gating particles between the inner and the outer faces of the membrane, is portrayed within a system plus reservoir strategy. Induced by the interaction, renormalizations of the membrane capacitance and of a membrane voltage dependent potential are found to arise. Consequently, the equations of motion, for the expectation values of the variables and the pair correlation functions, are obtained in the collective membrane voltage space.

An efficient Bayesian inference method for problems that can be mapped onto dense graphs is presented. The approach is based on message passing where messages are averaged over a large number of replicated variable systems exposed to the same evidential nodes. An assumption about the symmetry of the solutions is required for carrying out the averages; here we extend the previous derivation based on a replica-symmetric- (RS)-like structure to include a more complex one-step replica-symmetry-breaking-like (1RSB-like) ansatz. To demonstrate the potential of the approach it is employed for studying critical properties of the Ising linear perceptron and for multiuser detection in code division multiple access (CDMA) under different noise models. Results obtained under the RS assumption in the noncritical regime give rise to a highly efficient signal detection algorithm in the context of CDMA; while in the critical regime one observes a first-order transition line that ends in a continuous phase transition point. Finite size effects are also observed. While the 1RSB ansatz is not required for the original problems, it was applied to the CDMA signal detection problem with a more complex noise model that exhibits RSB behavior, resulting in an improvement in performance.

We study the stable attractors of a class of continuous dynamical systems that may be idealized as networks of Boolean elements, with the goal of determining which Boolean attractors, if any, are good approximations of the attractors of generic continuous systems. We investigate the dynamics in simple rings and rings with one additional self-input. An analysis of switching characteristics and pulse propagation explains the relation between attractors of the continuous systems and their Boolean approximations. For simple rings, “reliable” Boolean attractors correspond to stable continuous attractors. For networks with more complex logic, the qualitative features of continuous attractors are influenced by inherently non-Boolean characteristics of switching events.

We study the effects of confinement between two parallel walls on a two dimensional fluid with competing interactions which lead to the formation of particle microdomains at the thermodynamic equilibrium (microphases or microseparation). The possibility to induce structural changes of the morphology of the microdomains is explored, under different confinement conditions and temperatures. In the presence of neutral walls, a switch from stripes of particles to circular clusters (droplets) occurs as the temperature decreases, which does not happen in bulk. While the passage from droplets to stripes, as the density increases, is a well-known phenomenon, the change of the stripes into droplets as an effect of temperature is rather unexpected. Depending on the wall separation and on the wall-fluid interaction parameters, the stripes can switch from parallel to perpendicular to the walls and also a mixed morphology can be stable.

The nearest-neighbor-interaction ferromagnetic Ashkin-Teller model is investigated on a square lattice through a powerful computational method for dealing with correlation functions in magnetic systems. This technique, which is based on damage-spreading numerical simulations, makes use of exact relations involving special kinds of damage and correlation functions, as well as the corresponding order parameters of the model. The computation of correlation functions, which represents usually a hard task in standard Monte Carlo simulations, due to large fluctuations, turns out to be much simpler within the present approach. We concentrate our analysis along the Baxter line, well known for its continuously varying critical exponents; seven different points along this line are investigated. The critical exponents associated with correlation functions along the Baxter line are successfully evaluated, by means of numerical methods, within damage-spreading simulations. The efficiency of this method is confirmed through precise estimates of the critical exponents associated with the order parameters (magnetization and polarization), as well as with their corresponding correlation functions, in spite of the small lattice sizes considered.

We use recently introduced three-point dynamic susceptibilities to obtain an experimental determination of the temperature evolution of the number of molecules $N_{\mathrm{corr}}$ that are dynamically correlated during the structural relaxation of supercooled liquids. We first discuss in detail the physical content of three-point functions that relate the sensitivity of the averaged two-time dynamics to external control parameters (such as temperature or density), as well as their connection to the more standard four-point dynamic susceptibility associated with dynamical heterogeneities. We then demonstrate that these functions can be experimentally determined with good precision. We gather available data to obtain the temperature dependence of $N_{\mathrm{corr}}$ for a large number of supercooled liquids over a wide range of relaxation time scales from the glass transition up to the onset of slow dynamics. We find that $N_{\mathrm{corr}}$ systematically grows when approaching the glass transition. It does so in a modest manner close to the glass transition, which is consistent with an activation-based picture of the dynamics in glassforming materials. For higher temperatures, there appears to be a regime where $N_{\mathrm{corr}}$ behaves as a power-law of the relaxation time. Finally, we find that the dynamic response to density, while being smaller than the dynamic response to temperature, behaves similarly, in agreement with theoretical expectations.

We report on self-assembly of ${\text{CoPt}}_3$ particles (diameter 6 nm) into low-dimensional close-packed arrays. This was achieved on substrates coated with a nitrocellulose (NC) thin layer by spreading of a hexane solution containing ${\text{CoPt}}_3$ particles, hexadecylamine, and water. In a first step, the solution film transforms into a bilayer containing a hexane layer located onto a water film. The hexane layer dewets the water layer and the latter dewets the NC covered substrate. Dewetting of the water layer leads to the formation of water droplets. Finally, the particles follow the motion of the contact line of the dewetting water layer and thus assemble into close-packed arrays at the periphery of the water droplets.

We study the coevolution of network structure and node states in a model of multiple state interacting agents. The system displays two transitions, network recombination and fragmentation, governed by time scales that emerge from the dynamics. The recombination transition separates a frozen configuration, composed by disconnected network components whose agents share the same state, from an active configuration, with a fraction of links that are continuously being rewired. The nature of this transition is explained analytically as the maximum of a characteristic time. The fragmentation transition, that appears between two absorbing frozen phases, is an anomalous order-disorder transition, governed by a crossover between the time scales that control the structure and state dynamics.

We have studied the process of creation of solitons and generation of fractal structures in the Korteweg–de Vries (KdV) equation when the relation between the nonlinearity and dispersion is abruptly changed. We observed that when this relation is changed nonadiabatically the solitary waves present in the system lose their stability and split up into ones that are stable for the set of parameters. When this process is successively repeated the trajectories of the solitary waves create a fractal treelike structure where each branch bifurcates into others. This structure is formed until the iteration where two solitary waves overlap just before the breakup. By means of a method based on the inverse scattering transformation, we have obtained analytical results that predict and control the number, amplitude, and velocity of the solitary waves that arise in the system after every change in the relation between the dispersion and the nonlinearity. This complete analytical information allows us to define a recursive $L$ system which coincides with the treelike structure, governed by KdV, until the stage when the solitons start to overlap and is used to calculate the Hausdorff dimension and the multifractal properties of the set formed by the segments defined by each of the two “brothers” solitons before every breakup.

The angular momentum is conserved in fluids with a few exceptions such as ferrofluids. However, it can be violated locally in fluid simulations to reduce computational costs. The effects of this violation are investigated using a particle-based simulation method, multiparticle collision dynamics, which can switch on or off angular-momentum conservation. To this end, we study circular Couette flows between concentric and eccentric cylinders, where nonphysical torques due to the lack of the angular-momentum conservation are found whereas the velocity field is not affected. In addition, in simulations of fluids with different viscosities in contact and star polymers in solvent, incorrect angular velocities occur. These results quantitatively agree with the theoretical predictions based on the macroscopic stress tensor.

The emergence of synchronization is a phenomenon that is ubiquitous in a wide variety of natural systems. Such behavior is also often robust: systems subject to large stochastic fluctuations and which possess a range of internal time scales are capable of exhibiting sustained correlated dynamics. Here we study model chemical reactions and genetic networks that have stochastic oscillatory dynamics, and discuss microscopic mechanisms through which two or more such distinct stochastic processes can be coupled so as to result in the phase synchronization of their dynamical variables. We also consider the effect of time delay in the interaction and show that for suitable choices of the delay parameter, in-phase or antiphase synchronization can occur.

Our recent theory for the glassy dynamics of fluids and suspensions of hard nonspherical objects is applied to several modestly anisotropic shapes. The role of bond length and aspect ratio is studied for diatomics, triatomics, and spherocylinders. As spherical symmetry is broken the ideal kinetic glass transition volume fraction of all objects increases linearly with aspect ratio with the same slope, in surprising agreement with the jamming phase diagram of hard granular ellipsoids. The ideal glass boundary of all shapes is a nonmonotonic function of aspect ratio which is also in qualitative accord with the jamming behavior of spherocylinders and ellipsoids. The maximum glass volume fraction shifts to higher values, and larger aspect ratios, as the object becomes smoother. Suggestions for why the nonequilibrium jamming and kinetic ideal glass formation (dynamical crossover) boundaries are similar are advanced. Beyond the ideal glass volume fraction the nonequilibrium free energy acquires a localization well and entropic barrier. Although its form is highly nonuniversal, if different shapes are compared at constant barrier height then a good collapse is found. Collapse of the volume fraction dependence of the barrier height for different shapes is also predicted for modest shape anisotropy, but increasingly fails as the aspect ratio exceeds 2. For a given volume fraction the mean barrier hopping times are nonmonotonic functions of aspect ratio. The functional form of this dependence, and order of magnitude variation with aspect ratio, is distinct for each object.

Important aspects in the field of microrheology are studies of the viscosity of fluids within structures with micrometer dimensions and fluid samples where only microliter volumes are available. We have quantitatively investigated the performance and accuracy of a microviscometer based on rotating optical tweezers, which requires as little as one microliter of sample. We have characterized our microviscometer, including effects due to heating, and demonstrated its ability to perform measurements over a large dynamic range of viscosities (at least two orders of magnitude). We have also inserted a probe particle through the membrane of a cell and measured the viscosity of the intramembranous contents. Viscosity measurements of tears have also been made with our microviscometer, which demonstrate its potential use to study unstimulated eye fluid.

This paper is the fifth in a series exploring the physical consequences of the solidity of highly viscous liquids. Paper IV proposed a model where the density field is described by a time-dependent Ginzburg-Landau equation of the nonconserved type with rates in $k$ space of the form ${\Gamma }_0+D{k}^2$. If $a$ is the average intermolecular distance, the model assumes that $D⪢{\Gamma }_0{a}^2$. This inequality expresses a long-wavelength dominance of the dynamics, which implies that the Hamiltonian (free energy) to a good approximation may be taken to be ultralocal, i.e., with the property that equal-time field fluctuations are uncorrelated in space. Paper IV also briefly discussed how to generalize the model by including the molecular orientational fields, the stress tensor fields, and the potential energy density field. In the present paper it is argued that this is the simplest model consistent with the following three experimental facts: (1) Viscous liquids approaching the glass transition do not develop long-range order; (2) the glass has lower compressibility than the liquid; (3) the $\alpha$ process involves several decades of relaxation times shorter than the mean relaxation time. The paper proceeds to list six further experimental facts of viscous liquid dynamics and shows that these follow naturally from the model.

Dynamic heterogeneity in glass formers has been related to their static structure using the concept of dynamic propensity. We reexamine this relationship by analyzing dynamical fluctuations in two atomistic glass formers and two theoretical models. We introduce quantitative statistical indicators which show that the dynamics of individual particles cannot be predicted on the basis of the propensity or by any structural indicator. However, the spatial structure of the propensity field does have predictive power for the spatial correlations associated with dynamic heterogeneity. Our results suggest that the quest for a connection between the static and dynamic properties of glass formers at the particle level is in vain, but they demonstrate that such a connection does exist on larger length scales.

We discuss mechanical buckling instabilities of a rigid film under compression interacting repulsively with a substrate through a thin fluid layer. The buckling occurs at a characteristic wavelength that increases as the one-fourth power of the bending stiffness, such as the gravitational instability studied previously by Milner et al. However, the potential can affect the characteristic buckling wavelength strongly, as predicted by Huang and Suo. If the potential changes sufficiently sharply with thickness, this instability is continuous, with an amplitude varying as the square root of overpressure. We discuss three forms of interaction important for the case of Langmuir monolayers transferred to a substrate: Casimir–van der Waals interaction, screened charged double-layer interaction, and the Sharma potential. We verify these predictions numerically in the van der Waals case.

Conformational behavior of flexible polyelectrolytes in the presence of monovalent cationic surfactants is examined. A simple model is presented for the formation of polyelectrolyte-surfactant complexes in salt-free solutions in the framework of the Debye-Hückel-Bjerrum-Manning and Flory theories, including explicitly the hydrophobic interactions between the associated surfactant molecules on the polyelectrolyte. The distribution of complexes is calculated as a function of the surfactant concentration and a discrete conformational transition between an elongated coil and a compact globule was found, in agreement with experimental observations.

Modular structure is ubiquitous among complex networks. We note that most such systems are subject to multiple structural and functional constraints, e.g., minimizing the average path length and the total number of links, while maximizing robustness against perturbations in node activity. We show that the optimal networks satisfying these three constraints are characterized by the existence of multiple subnetworks (modules) sparsely connected to each other. In addition, these modules have distinct hubs, resulting in an overall heterogeneous degree distribution.

We consider the discrete surface growth process with relaxation to the minimum [F. Family, J. Phys. A 19, L441 (1986)] as a possible synchronization mechanism on scale-free networks, characterized by a degree distribution $P\left(k\right)\sim k^{-\lambda }$, where $k$ is the degree of a node and $\lambda$ its broadness, and compare it with the usually applied Edward-Wilkinson process (EW) [S. F. Edwards and D. R. Wilkinson, Proc. R. Soc. London, Ser. A 381, 17 (1982)]. In spite of both processes belonging to the same universality class for Euclidean lattices, in this work we demonstrate that for scale-free networks with exponents $\lambda <3$ the scaling behavior of the roughness in the saturation cannot be explained by the EW process. Moreover, we show that for these ubiquitous cases the Edward-Wilkinson process enhances spontaneously the synchronization when the system size is increased. This nonphysical result is mainly due to finite size effects due to the underlying network. Contrarily, the discrete surface growth process does not present this flaw and is applicable for every $\lambda$.