Classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The scheme is then used to determine transitions that can be applied in a lattice-based kinetic Monte Carlo (KMC) atomistic simulation model. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements are considered as local transition events constrained in potential energy wells over certain local time periods. These processes are represented by Markov chains of multidimensional Boolean valued functions in three-dimensional lattice space. The events inhibited by the barriers under a certain level are regarded as thermal fluctuations of the canonical ensemble and accepted freely. Consequently, the fluctuating system evolution process is implemented as a Markov chain of equivalence class objects. It is shown that the process can be characterized by the acceptance of metastable local transitions. The method is applied to a problem of Au and Ag cluster growth on a rippled surface. The simulation predicts the existence of a morphology-dependent transition time limit from a local metastable to stable state for subsequent cluster growth by accretion. Excellent agreement with observed experimental results is obtained.

We investigate thermal and isothermal symmetric liquid-vapor separations via a fast Fourier transform thermal lattice Boltzmann (FFT-TLB) model. Structure factor, domain size, and Minkowski functionals are employed to characterize the density and velocity fields, as well as to understand the configurations and the kinetic processes. Compared with the isothermal phase separation, the freedom in temperature prolongs the spinodal decomposition (SD) stage and induces different rheological and morphological behaviors in the thermal system. After the transient procedure, both the thermal and isothermal separations show power-law scalings in domain growth, while the exponent for thermal system is lower than that for isothermal system. With respect to the density field, the isothermal system presents more likely bicontinuous configurations with narrower interfaces, while the thermal system presents more likely configurations with scattered bubbles. Heat creation, conduction, and lower interfacial stresses are the main reasons for the differences in thermal system. Different from the isothermal case, the release of latent heat causes the changing of local temperature, which results in new local mechanical balance. When the Prandtl number becomes smaller, the system approaches thermodynamical equilibrium much more quickly. The increasing of mean temperature makes the interfacial stress lower in the following way: $\sigma ={\sigma }_0{[(T_c-T)/(T_c-T_0)]}^{3/2}$, where $T_c$ is the critical temperature and ${\sigma }_0$ is the interfacial stress at a reference temperature $T_0$, which is the main reason for the prolonged SD stage and the lower growth exponent in the thermal case. Besides thermodynamics, we probe how the local viscosities influence the morphology of the phase separating system. We find that, for both the isothermal and thermal cases, the growth exponents and local flow velocities are inversely proportional to the corresponding viscosities. Compared with the isothermal case, the local flow velocity depends not only on viscosity but also on temperature.

A general analytic solution to the fractional advection diffusion equation is obtained in plane parallel geometry. The result is an infinite series of spatial Fourier modes which decay according to the Mittag-Leffler function, which is cast into a simple closed-form expression in Laplace space using the Poisson summation theorem. An analytic expression for the current measured in a time-of-flight experiment is derived, and the sum of the slopes of the two respective time regimes on logarithmic axes is demonstrated to be $-2$, in agreement with the well-known result for a continuous time random-walk model. The sensitivity of current and particle number density to the variation of experimentally controlled parameters is investigated in general, and the results applied to analyze selected experimental data.

We consider a molecular aggregate consisting of $N$ identical monomers. Each monomer comprises two electronic levels and a single harmonic mode. The monomers interact with each other via dipole-dipole forces. The monomer vibrational modes are bilinearly coupled to a bath of harmonic oscillators. This is a prototypical model for the description of coherent exciton transport, from quantum dots to photosynthetic antennae. We derive an exact quantum master equation for such systems. Computationally, the master equation may be useful for the testing of various approximations employed in theories of quantum transport. Physically, it offers a plausible explanation of the origins of long-lived coherent optical responses of molecular aggregates in dissipative environments.

Supporting-electrolyte solutions comprise chemically inert cations and anions, produced by salt dissolution, together with a reactive ionic species that may be consumed and generated on bounding ion-selective surfaces (e.g., electrodes or membranes). Upon application of an external voltage, a Faraday current is thereby established. It is natural to analyze this ternary-system process through a one-dimensional transport problem, employing the thin Debye-layer limit. Using a simple model of ideal ion-selective membranes, we have recently addressed this problem for moderate voltages [Yariv and Almog, Phys. Rev. Lett. 105, 176101 (2010)], predicting currents that scale as a fractional power of Debye thickness. We address herein the complementary problem of moderate currents. We employ matched asymptotic expansions, separately analyzing the two inner thin Debye layers adjacent to the ion-selective surfaces and the outer electroneutral region outside them. A straightforward calculation following comparable singular-perturbation analyses of binary systems is frustrated by the prediction of negative ionic concentrations near the cathode. Accompanying numerical simulations, performed for small values of Debye thickness, indicate a number unconventional features occurring at that region, such as inert-cation concentration amplification and electric-field intensification. The current-voltage correlation data of the electrochemical cell, obtained from compilation of these simulations, does not approach a limit as the Debye thickness vanishes. Resolution of these puzzles reveals a transformation of the asymptotic structure of the cathodic Debye layer. This reflects the emergence of an internal boundary layer, adjacent to the cathode, wherein field and concentration scaling differs from those of the Gouy-Chapman theory. The two-scale feature of the cathodic Debye layer is manifested through a logarithmic voltage scaling with Debye thickness. Accounting for this scaling, the complied current-voltage data collapses upon a single curve. This curve practically coincides with an asymptotically calculated universal current-voltage relation.

We investigate the jamming transition of frictional particulate systems via discrete element simulations, reporting the existence of new regimes, which are conveniently described in a jamming phase diagram with axes density, shear stress, and friction coefficient. The resulting jammed states are characterized by different mechanical and structural properties and appear not to be “fragile” as speculated. In particular, we find a regime, characterized by extremely long processes, with a diverging time scale, whereby a suspension first flows but then suddenly jams. We link this sudden jamming transition to the presence of impeded dilatancy.

We investigate stability and breakup of a thin liquid film on a solid surface under the action of disjoining pressure. The solid surface is structured by parallel grooves. Air is trapped in the grooves under the liquid film. Our mathematical model takes into account the effect of slip due to the presence of menisci separating the liquid film from the air inside the grooves, the deformation of these menisci due to local variations of pressure in the liquid film, and nonuniformities of the Hamaker constant which measures the strength of disjoining pressure. Both linear stability and strongly nonlinear evolution of the film are analyzed. Surface structuring results in decrease of the fastest growing instability wavelength and the rupture time. It is shown that a simplified description of film dynamics based on the standard formula for effective slip leads to significant deviations from the behavior seen in our simulations. Self-similar decay over several orders of magnitude of the film thickness near the rupture point is observed. We also show that the presence of the grooves can lead to instability in otherwise stable films if the relative groove width is above a critical value, found as a function of disjoining pressure parameters.

The phase transition behavior of the liquid crystal dimer $\alpha ,\omega$-bis(4,4${}^{{}^{\prime }}$-cyanobiphenyl)nonane (CBC9CB), which has been reported to exhibit a nematic-nematic phase transition, has been investigated by means of high-resolution adiabatic scanning calorimetry. This nematic-nematic phase transition is weakly first-order with a latent heat of $0.24\pm 0.01$ kJ kg${}^{-1}$. Mixtures up to 40 wt % with 4-pentyl-4${}^{{}^{\prime }}$-cyanobiphenyl (5CB) liquid crystals have also been investigated, which also show this nematic to nematic phase transition. The transition stays weakly first-order with a decreasing latent heat with increasing concentration of 5CB. For mixtures with more than 40 wt % uniaxial nematic-unknown nematic phase transition was not observed.

We derive and analyze the dynamic equations for polar liquid crystals in two spatial dimensions in the framework of classical dynamical density functional theory (DDFT). Translational density variations, polarization, and quadrupolar order are used as order-parameter fields. The results are critically compared with those obtained using the macroscopic approach of time-dependent Ginzburg-Landau (GL) equations for the analogous order-parameter fields. We demonstrate that, for both the microscopic DDFT and the macroscopic GL approach, the resulting dissipative dynamics can be derived from a dissipation function. We obtain microscopic expressions for all diagonal contributions and for many of the cross-coupling terms emerging from a GL approach. Thus, we establish a bridge between molecular correlations and macroscopic modeling for the dissipative dynamics of polar liquid crystals.

Athermal solutions (from dilute to concentrated) of semiflexible macromolecules confined in a film of thickness $D$ between two hard walls are studied by means of grand-canonical lattice Monte Carlo simulation using the bond fluctuation model. This system exhibits two phase transitions as a function of the thickness of the film and polymer volume fraction. One of them is the bulk isotropic-nematic first-order transition, which ends in a critical point on decreasing the film thickness. The chemical potential at this transition decreases with decreasing film thickness (“capillary nematization”). The other transition is a continuous (or very weakly first-order) transition in the layers adjacent to the hard planar walls from the disordered phase, where the bond vectors of the macromolecules show local ordering (i.e., “preferential orientation” along the $x$ or $y$ axes of the simple cubic lattice, but no long-range orientational order occurs), to a quasi-two-dimensional nematic phase (with the director at each wall being oriented along either the $x$ or $y$ axis), while the bulk of the film is still disordered. When the chemical potential or monomer density increase, respectively, the thickness of these surface-induced nematic layers grows, causing the disappearance of the disordered region in the center of the film.

We measured the distribution of a forward swimming strain of Caulobacter crescentus near a surface using a three-dimensional tracking technique based on dark field microscopy and found that the swimming bacteria accumulate heavily within a micrometer from the surface. We attribute this accumulation to frequent collisions of the swimming cells with the surface, causing them to align parallel to the surface as they continually move forward. The extent of accumulation at the steady state is accounted for by balancing alignment caused by these collisions with the rotational Brownian motion of the micrometer-sized bacteria. We performed a simulation based on this model, which reproduced the measured results. Additional simulations demonstrate the dependence of accumulation on swimming speed and cell size, showing that longer and faster cells accumulate more near a surface than shorter and slower ones do.

We investigated the effects of solvents on the intrinsic propensity of peptide backbone conformations based on molecular dynamics simulations. The results show that compared with pure water, aqueous urea decreases the helix propensity. In comparison, methanol decreases the polyproline II (PPII) propensity. Such a solvent dependence of the intrinsic propensity of the backbone conformation is correlated with the solvent dependence of the hydration of the backbone groups and the formation probability of the local intrapeptide hydrogen bonds. Aqueous urea which has low ability to stabilize the local intrapeptide hydrogen bonds disfavors the helical conformation. Whereas, methanol which has low ability to hydrate the backbone groups disfavors the polyproline II conformation. In addition, the solvent effects can be further modulated by the side chains of the peptides. The solvent effects of the intrinsic propensity of peptide backbone conformations observed in this work suggest that changing the intrinsic propensity of the protein backbone conformations can partly contribute to the solvent-induced protein structure and dynamics variations. These results will be useful in understanding the solvent dependence of the conformational distributions of the unfolded proteins or peptides (or intrinsically disordered proteins) in which the global tertiary interactions are less important than that in the well-folded proteins.

We study a coarse-grained protein model whose primary characteristics are (i) a tubelike geometry to describe the self-avoidance effects of the polypeptide chain and (ii) an energy function based on a one-dimensional structural representation. The latter specifies the connectivity of a sequence in a given conformation, so that the energy function, rather than favoring the formation of specific native pairwise contacts, promotes the establishment of a specific target connectivity for each amino acid. We show that the resulting dynamics is in good agreement with both experimental observations and the results of all-atoms simulations. In contrast to the latter, our coarse-grained approach provides the possibility to explore longer time scales and thus enables one to access, albeit in less detail, larger regions of the conformational space. We illustrate our approach by its application to the villin headpiece domain, a three-helix protein, by studying its folding behavior and determining heat capacities and free-energy landscapes in various reaction coordinates.

We explore the phenomenon of spiral defect chaos in two types of generalized Swift-Hohenberg model equations that include the effects of long-range drift velocity or mean flow. We use spatially extended domains and integrate the equations for very long times to study the pattern dynamics as the magnitude of the mean flow is varied. The magnitude of the mean flow is adjusted via a real and continuous parameter that accounts for the fluid boundary conditions on the horizontal surfaces in a convecting layer. For weak values of the mean flow, we find that the patterns exhibit a slow coarsening to a state dominated by large and very slowly moving target defects. For strong enough mean flow, we identify the existence of spatiotemporal chaos, which is indicated by a positive leading-order Lyapunov exponent. We compare the spatial features of the mean flow field with that of Rayleigh-Bénard convection and quantify their differences in the neighborhood of spiral defects.

Many biological patterns, from population densities to animal coat markings, can be thought of as heterogeneous spatiotemporal distributions of mobile agents. Many mathematical models have been proposed to account for the emergence of this complexity, but, in general, they have consisted of deterministic systems of differential equations, which do not take into account the stochastic nature of population interactions. One particular, pertinent criticism of these deterministic systems is that the exhibited patterns can often be highly sensitive to changes in initial conditions, domain geometry, parameter values, etc. Due to this sensitivity, we seek to understand the effects of stochasticity and growth on paradigm biological patterning models. In this paper, we extend spatial Fourier analysis and growing domain mapping techniques to encompass stochastic Turing systems. Through this we find that the stochastic systems are able to realize much richer dynamics than their deterministic counterparts, in that patterns are able to exist outside the standard Turing parameter range. Further, it is seen that the inherent stochasticity in the reactions appears to be more important than the noise generated by growth, when considering which wave modes are excited. Finally, although growth is able to generate robust pattern sequences in the deterministic case, we see that stochastic effects destroy this mechanism for conferring robustness. However, through Fourier analysis we are able to suggest a reason behind this lack of robustness and identify possible mechanisms by which to reclaim it.

Large-scale dissipation mechanisms have been routinely employed in numerical simulations of two-dimensional turbulence to absorb energy at large scales, presumably mimicking the quasisteady picture of Kraichnan in an unbounded fluid. Here, “side effects” of such a mechanism—mechanical friction—on the small-scale dynamics of forced two-dimensional Navier-Stokes turbulence are elaborated by both theoretical and numerical analysis. Given a positive friction coefficient $\alpha$, viscous dissipation of enstrophy has been known to vanish in the inviscid limit $\nu \to 0$. This effectively renders the scale-neutral friction the only mechanism responsible for enstrophy dissipation in that limit. The resulting dynamical picture is that the classical enstrophy inertial range becomes a dissipation range in which the dissipation of enstrophy by friction mainly occurs. For each $\alpha >0$, there exists a critical viscosity ${\nu }_c$, which depends on physical parameters, separating the regimes of predominant viscous and frictional dissipation of enstrophy. It is found that ${\nu }_c=[{{\eta }^{\prime }}^{1/3}/\left(C{k}_f^2\right)]\exp [-{{\eta }^{\prime }}^{1/3}/\left(C\alpha \right)]$, where ${\eta }^{\prime }$ is half the enstrophy injection rate, $k_f$ is the forcing wave number, and $C$ is a nondimensional constant (the Kraichnan-Batchelor constant). The present results have important theoretical and practical implications. Apparently, mechanical friction is a poor choice in numerical attempts to address fundamental issues concerning the direct enstrophy transfer in two-dimensional Navier-Stokes turbulence. Furthermore, as relatively strong friction naturally occurs on the surfaces and at lateral boundaries of experimental fluids as well as at the interfaces of shallow layers in geophysical fluid models, the frictional effects discussed in this study are crucial in understanding the dynamics of these systems.

The theoretical Green-Kubo relation for viscosity is tested using experimentally obtained data. In a dusty plasma experiment, micron-sized dust particles are introduced into a partially ionized argon plasma, where they become negatively charged. They are electrically levitated to form a single-layer Wigner crystal, which is subsequently melted using laser heating. In the liquid phase, these dust particles experience interparticle electric repulsion, laser heating, and friction from the ambient neutral argon gas, and they can be considered to be in a nonequilibrium steady state. Direct measurements of the positions and velocities of individual dust particles are then used to obtain a time series for an off-diagonal element of the stress tensor and its time autocorrelation function. This calculation also requires the interparticle potential, which was not measured experimentally but was obtained using a Debye-Hückel-type model with experimentally determined parameters. Integrating the autocorrelation function over time yields the viscosity for shearing motion among dust particles. The viscosity so obtained is found to agree with results from a previous experiment using a hydrodynamical Navier-Stokes equation. This comparison serves as a test of the Green-Kubo relation for viscosity. Our result is also compared to the predictions of several simulations.

We demonstrate “hidden solvability” of the nonlinear Schrödinger (NLS) equation whose nonlinearity coefficient is spatially modulated by Hermite-Gaussian functions of different orders and the external potential is appropriately chosen. By means of an explicit transformation, this equation is reduced to the stationary version of the classical NLS equation, which makes it possible to use the bright and dark solitons of the latter equation to generate solitary-wave solutions in our model. Special kinds of explicit solutions, such as oscillating solitary waves, are analyzed in detail. The stability of these solutions is verified by means of direct integration of the underlying NLS equation. In particular, our analytical results suggest a way of controlling the dynamics of solitary waves by an appropriate spatial modulation of the nonlinearity strength in Bose-Einstein condensates, through the Feshbach resonance.

We describe an alternative method for performing isothermal-isobaric Monte Carlo simulations of crystalline solids. This method uses thermodynamics to estimate appropriate scaling of coordinates relative to their nominal lattice sites in order to increase the probability of acceptance of volume changes. We test this coordinate scaling with three systems: hard spheres, Lennard-Jones spheres, and hard dumbbells. In all cases, we find that the move allows for both a larger step size and faster convergence of calculated properties, in comparison to the conventional algorithm. The improvement is more dramatic for hard potentials, where compressing the system using the conventional algorithm (even a small amount) will almost always cause an overlap.

The time evolution of the ground state wave function of a zero-temperature Bose-Einstein condensate (BEC) gas is well described by the Hamiltonian Gross-Pitaevskii (GP) equation. Using a set of appropriately interleaved unitary collision-stream operators, a qubit lattice gas algorithm is devised, which on taking moments, recovers the Gross-Pitaevskii (GP) equation under diffusion ordering (time scales as length${}^2$). Unexpectedly, there is a class of initial states whose Poincaré recurrence time is extremely short and which, as the grid resolution is increased, scales with diffusion ordering (and not as length${}^3$). The spectral results of J. Yepez et al. [Phys. Rev. Lett. 103, 084501 (2009).] for quantum turbulence are revised and it is found that it is the compressible kinetic energy spectrum that exhibits three distinct spectral regions: a small-$k$ classical-like Kolmogorov $k^{-5/3}$, a steep semiclassical cascade region, and a large-$k$ quantum vortex spectrum $k^{-3}$. For most evolution times the incompressible kinetic energy spectrum exhibits a somewhat robust quantum vortex spectrum of $k^{-3}$ for an extended range in $k$ with a $k^{-3.4}$ spectrum for intermediate $k$. For linear vortices of winding number 1 there is an intermittent loss of the quantum vortex cascade with its signature seen in the time evolution of the kinetic energy $E_{\mathrm{kin}}\left(t\right)$, the loss of the quantum vortex $k^{-3}$ spectrum in the incompressible kinetic energy spectrum as well as the minimalization of the vortex core isosurfaces that would totally inhibit any Kelvin wave vortex cascade. In the time intervals around these intermittencies the incompressible kinetic energy also exhibits a multicascade spectrum.