We investigate the behavior of a mixture of asymmetric colloidal dumbbells and emulsion droplets by means of kinetic Monte Carlo simulations. The evaporation of the droplets and the competition between droplet-colloid attraction and colloid-colloid interactions lead to the formation of clusters built up of colloid aggregates with both closed and open structures. We find that stable packings and hence complex colloidal structures can be obtained by changing the relative size of the colloidal spheres and/or their interfacial tension with the droplets.

We carry out constant volume simulations of steady-state shear-driven rheology in a simple model of bidisperse soft-core frictionless disks in two dimensions, using a dissipation law that gives rise to Bagnoldian rheology. We discuss in detail the critical scaling ansatz for the shear-driven jamming transition and carry out a detailed scaling analysis of our resulting data for pressure $p$ and shear stress $\sigma$. Our analysis determines the critical exponent $\beta$ that describes the algebraic divergence of the Bagnold transport coefficients ${lim}_{\dot{\gamma }\to 0}p/{\dot{\gamma }}^2,\sigma /{\dot{\gamma }}^2\sim {({\varphi }_J-\varphi )}^{-\beta }$ as the jamming transition ${\varphi }_J$ is approached from below. For the low strain rates considered in this work, we show that it is still necessary to consider the leading correction-to-scaling term in order to achieve a self-consistent analysis of our data, in which the critical parameters become independent of the size of the window of data used in the analysis. We compare our resulting value $\beta \approx 5.0\pm 0.4$ against previous numerical results and competing theoretical models. Our results confirm that the shear-driven jamming transition in Bagnoldian systems is well described by a critical scaling theory and we relate this scaling theory to the phenomenological constituent laws for dilatancy and friction.

Most of the existing numerical and theoretical investigations on the electrohydrodynamics of a viscous drop have focused on the creeping Stokes flow regime, where nonlinear inertia effects are neglected. In this work we study the inertia effects on the electrodeformation of a viscous drop under a DC electric field using a novel second-order immersed interface method. The inertia effects are quantified by the Ohnesorge number $\text{Oh}$, and the electric field is characterized by an electric capillary number ${\text{Ca}}_E$. Below the critical ${\text{Ca}}_E$, small to moderate electric field strength gives rise to steady equilibrium drop shapes. We found that, at a fixed ${\text{Ca}}_E$, inertia effects induce larger deformation for an oblate drop than a prolate drop, consistent with previous results in the literature. Moreover, our simulations results indicate that inertia effects on the equilibrium drop deformation are dictated by the direction of normal electric stress on the drop interface: Larger drop deformation is found when the normal electric stress points outward, and smaller drop deformation is found otherwise. To our knowledge, such inertia effects on the equilibrium drop deformation has not been reported in the literature. Above the critical ${\text{Ca}}_E$, no steady equilibrium drop deformation can be found, and often the drop breaks up into a number of daughter droplets. In particular, our Navier-Stokes simulations show that, for the parameters we use, (1) daughter droplets are larger in the presence of inertia, (2) the drop deformation evolves more rapidly compared to creeping flow, and (3) complex distribution of electric stresses for drops with inertia effects. Our results suggest that normal electric pressure may be a useful tool in predicting drop pinch-off in oblate deformations.

Spectral kinetic energy transfer by advective processes in turbulent premixed reacting flows is examined using data from a direct numerical simulation of a statistically planar turbulent premixed flame. Two-dimensional turbulence kinetic-energy spectra conditioned on the planar-averaged reactant mass fraction are computed through the flame brush and variations in the spectra are connected to terms in the spectral kinetic energy transport equation. Conditional kinetic energy spectra show that turbulent small-scale motions are suppressed in the burnt combustion products, while the energy content of the mean flow increases. An analysis of spectral kinetic energy transfer further indicates that, contrary to the net down-scale transfer of energy found in the unburnt reactants, advective processes transfer energy from small to large scales in the flame brush close to the products. Triadic interactions calculated through the flame brush show that this net up-scale transfer of energy occurs primarily at spatial scales near the laminar flame thermal width. The present results thus indicate that advective processes in premixed reacting flows contribute to energy backscatter near the scale of the flame.

Harmonic generation from linearly polarized high-intensity short-pulse laser normally impacting a solid plasma grating is investigated using analytical modeling and particle-in-cell simulation. It is found that when the radiation excited by the relativistic electron quiver motion in the laser fields suitably matches a harmonic of the grating periodicity, it will be significantly enhanced and peak with narrow angular spread in specific directions. The corresponding theory shows that the phenomenon can be attributed to an interference effect of the periodic grating on the excitation.

Statistical mechanical modeling is developed to describe a catalytic conversion reaction $A\to B^c$ or $B^t$ with concentration-dependent selectivity of the products, $B^c$ or $B^t$, where reaction occurs inside catalytic particles traversed by narrow linear nanopores. The associated restricted diffusive transport, which in the extreme case is described by single-file diffusion, naturally induces strong concentration gradients. Furthermore, by comparing kinetic Monte Carlo simulation results with analytic treatments, selectivity is shown to be impacted by strong spatial correlations induced by restricted diffusivity in the presence of reaction and also by a subtle clustering of reactants, $A$.

Persistent homology analysis, a recently developed computational method in algebraic topology, is applied to the study of the phase transitions undergone by the so-called mean-field $\mathit{XY}$ model and by the ${\displaystyle {\varphi }^4}$ lattice model, respectively. For both models the relationship between phase transitions and the topological properties of certain submanifolds of configuration space are exactly known. It turns out that these a priori known facts are clearly retrieved by persistent homology analysis of dynamically sampled submanifolds of configuration space.

The heat flux between parallel surfaces is computed analytically assuming that heat is transferred by particles moving ballistically under the influence of a conservative force field. Particle reflection at the surfaces is governed by a Maxwell-type boundary condition. It is found that the force field can give rise to a substantial reduction, but also to an enhancement of the heat flux, depending on the ratio of the temperatures at the two surfaces. The influence of the accommodation coefficients is studied. An asymmetry introduced by the force field and/or the boundary conditions at the two surfaces causes a significant heat-flux rectification, characteristic for a thermal diode.

We present the symplectic geometry spectrum regression (SGSR) technique as well as a regularized method based on SGSR for prediction of nonlinear time series. The main tool of analysis is the symplectic geometry spectrum analysis, which decomposes a time series into the sum of a small number of independent and interpretable components. The key to successful regularization is to damp higher order symplectic geometry spectrum components. The effectiveness of SGSR and its superiority over local approximation using ordinary least squares are demonstrated through prediction of two noisy synthetic chaotic time series (Lorenz and Rössler series), and then tested for prediction of three real-world data sets (Mississippi River flow data and electromyographic and mechanomyographic signal recorded from human body).

We put forward a hydrodynamic theory of nematic liquid crystals that includes both anisotropic elasticity and dynamic relaxation. Liquid remodeling is encompassed through a continuous update of the shear-stress free configuration. The low-frequency limit of the dynamical theory reproduces the classical Ericksen-Leslie theory, but it predicts two independent identities between the six Leslie viscosity coefficients. One replicates Parodi's relation, while the other—which involves five Leslie viscosities in a nonlinear way—is new. We discuss its significance, and we test its validity against evidence from physical experiments, independent theoretical predictions, and molecular-dynamics simulations.

The study of energetic free-surface flows is challenging because of the large range of interface scales involved due to multiple fragmentations and reconnections of the air-water interface with the formation of drops and bubbles. Because of their complexity the investigation of such phenomena through numerical simulation largely increased during recent years. Actually, in the last decades different numerical models have been developed to study these flows, especially in the context of particle methods. In the latter a single-phase approximation is usually adopted to reduce the computational costs and the model complexity. While it is well known that the role of air largely affects the local flow evolution, it is still not clear whether this single-phase approximation is able to predict global flow features like the evolution of the global mechanical energy dissipation. The present work is dedicated to this topic through the study of a selected problem simulated with both single-phase and two-phase models. It is shown that, interestingly, even though flow evolutions are different, energy evolutions can be similar when including or not the presence of air. This is remarkable since, in the problem considered, with the two-phase model about half of the energy is lost in the air phase while in the one-phase model the energy is mainly dissipated by cavity collapses.

Metamaterials enable the emergence of novel physical properties due to the existence of an underlying subwavelength structure. Here, we use the Faraday instability to shape the fluid-air interface with a regular pattern. This pattern undergoes an oscillating secondary instability and exhibits spontaneous vibrations that are analogous to transverse elastic waves. By locally forcing these waves, we fully characterize their dispersion relation and show that a Faraday pattern presents an effective shear elasticity. We propose a physical mechanism combining surface tension with the Faraday structured interface that quantitatively predicts the elastic wave phase speed, revealing that the liquid interface behaves as an elastic metamaterial.

We study experimentally and computationally the dynamics of granular flow during impacts where intruders strike a collection of disks from above. In the regime where granular force dynamics are much more rapid than the intruder motion, we find that the particle flow near the intruder is proportional to the instantaneous intruder speed; it is essentially constant when normalized by that speed. The granular flow is nearly divergence free and remains in balance with the intruder, despite the latter's rapid deceleration. Simulations indicate that this observation is insensitive to grain properties, which can be explained by the separation of time scales between intergrain force dynamics and intruder dynamics. Assuming there is a comparable separation of time scales, we expect that our results are applicable to a broad class of dynamic or transient granular flows. Our results suggest that descriptions of static-in-time granular flows might be extended or modified to describe these dynamic flows. Additionally, we find that accurate grain-grain interactions are not necessary to correctly capture the granular flow in this regime.

The chemical master equation (CME) is the exact mathematical formulation of chemical reactions occurring in a dilute and well-mixed volume. The reaction-diffusion master equation (RDME) is a stochastic description of reaction-diffusion processes on a spatial lattice, assuming well mixing only on the length scale of the lattice. It is clear that, for the sake of consistency, the solution of the RDME of a chemical system should converge to the solution of the CME of the same system in the limit of fast diffusion: Indeed, this has been tacitly assumed in most literature concerning the RDME. We show that, in the limit of fast diffusion, the RDME indeed converges to $a$ master equation but not necessarily the CME. We introduce a class of propensity functions, such that if the RDME has propensities exclusively of this class, then the RDME converges to the CME of the same system, whereas if the RDME has propensities not in this class, then convergence is not guaranteed. These are revealed to be elementary and nonelementary propensities, respectively. We also show that independent of the type of propensity, the RDME converges to the CME in the simultaneous limit of fast diffusion and large volumes. We illustrate our results with some simple example systems and argue that the RDME cannot generally be an accurate description of systems with nonelementary rates.

Out-of-equilibrium behavior is explored in the one-dimensional anisotropic $XY$ model. Initially preparing the system in the isotropic $XX$ model with a linearly varying magnetic field to create a domain-wall magnetization profile, dynamics is generated by rapidly changing the exchange interaction anisotropy and external magnetic field. Relaxation to a nonequilibrium steady state is studied analytically at the critical transverse Ising point, where correlation functions may be computed in closed form. For arbitrary values of anisotropy and external field, an effective generalized Gibbs' ensemble is shown to accurately describe observables in the long-time limit. Additionally, we find spatial oscillations in the exponentially decaying, transverse spin-spin correlation functions with wavelength set by the magnetization jump across the initial domain wall. This wavelength depends only weakly on anisotropy and magnetic field in contrast to the current, which is highly dependent on these parameters.

Groth and Ghil [Phys. Rev. E 84, 036206 (2011)] developed a modified varimax rotation aimed at enhancing the ability of the multivariate singular spectrum analysis (M-SSA) to characterize phase synchronization in systems of coupled chaotic oscillators. Due to the special structure of the M-SSA eigenvectors, the modification proposed by Groth and Ghil imposes a constraint in the rotation of blocks of components associated with the different subsystems. Accordingly, here we call it a structured varimax rotation (SVR). The SVR was presented as successive pairwise rotations of the eigenvectors. The aim of this paper is threefold. First, we develop a closed matrix formulation for the entire family of structured orthomax rotation criteria, for which the SVR is a special case. Second, this matrix approach is used to enable the use of known singular value algorithms for fast computation, allowing a simultaneous rotation of the M-SSA eigenvectors (a Python code is provided in the Appendix). This could be critical in the characterization of phase synchronization phenomena in large real systems of coupled oscillators. Furthermore, the closed algebraic matrix formulation could be used in theoretical studies of the (modified) M-SSA approach. Third, we illustrate the use of the proposed singular value algorithm for the SVR in the context of the two benchmark examples of Groth and Ghil: the Rössler system in the chaotic (i) phase-coherent and (ii) funnel regimes. Comparison with the results obtained with Kaiser's original (unstructured) varimax rotation (UVR) reveals that both SVR and UVR give the same result for the phase-coherent scenario, but for the more complex behavior (ii) only the SVR improves on the M-SSA.

Biotechnology advances have allowed investigation of heterogeneity of cellular responses to stimuli on the single-cell level. Functionally, this heterogeneity can compromise cellular responses to environmental signals, and it can also enlarge the repertoire of possible cellular responses and hence increase the adaptive nature of cellular behaviors. However, the mechanism of how this response heterogeneity is generated remains elusive. Here, by systematically analyzing a representative cellular signaling system, we show that (1) the upstream activator always amplifies the downstream burst frequency (BF) but the noiseless activator performs better than the noisy one, remarkably for small or moderate input signal strengths, and the repressor always reduces the downstream BF but the difference in the reducing effect between noiseless and noise repressors is very small; (2) both the downstream burst size and mRNA mean are a monotonically increasing function of the activator strength but a monotonically decreasing function of the repressor strength; (3) for repressor-type input, there is a noisy signal strength such that the downstream mRNA noise arrives at an optimal level, but for activator-type input, the output noise intensity is fundamentally a monotonically decreasing function of the input strength. Our results reveal the essential mechanisms of both signal information decoding and cellular response heterogeneity, whereas our analysis provides a paradigm for analyzing dynamics of noisy biochemical signaling systems.

We consider the symmetry and physical origin of collective displacement modes playing a crucial role in the morphological transformation during the maturation of the HK97 bacteriophage and similar viruses. It is shown that the experimentally observed hexamer deformation and pentamer twist in the HK97 procapsid correspond to the simplest irreducible shear strain mode of a spherical shell. We also show that the icosahedral faceting of the bacteriophage capsid shell is driven by the simplest irreducible radial displacement field. The shear field has the rotational icosahedral symmetry group $I$ while the radial field has the full icosahedral symmetry $I_h$. This difference makes their actions independent. The radial field sign discriminates between the icosahedral and the dodecahedral shapes of the faceted capsid shell, thus making the approach relevant not only for the HK97-like viruses but also for the parvovirus family. In the frame of the Landau-Ginzburg formalism we propose a simple phenomenological model valid for the first reversible step of the HK97 maturation process. The calculated phase diagram illustrates the discontinuous character of the virus shape transformation. The characteristics of the virus shell faceting and expansion obtained in the in vitro and in vivo experiments are related to the decrease in the capsid shell thickness and to the increase of the internal capsid pressure.

Optical properties of DNA:Ag-nanoclusters complexes have been successfully applied experimentally in Chemistry, Physics, and Biology. Nevertheless, the mechanisms behind their optical activity remain unresolved. In this work, we present a time-dependent density functional study of optical absorption in DNA:${\mathrm{Ag}}_4$. In all 23 different complexes investigated, we obtain new absorption peaks in the visible region that are not found in either the isolated ${\mathrm{Ag}}_4$ or isolated DNA base pairs. Absorption from red to green are predominantly of charge-transfer character, from the ${\mathrm{Ag}}_4$ to the DNA fragment, while absorption in the blue-violet range are mostly associated to electronic transitions of a mixed character, involving either DNA-${\mathrm{Ag}}_4$ hybrid orbitals or intracluster orbitals. We also investigate the role of exchange-correlation functionals in the calculated optical spectra. Significant differences are observed between the calculations using the PBE functional (without exact exchange) and the CAM-B3LYP functional (which partly includes exact exchange). Specifically, we observe a tendency of charge-transfer excitations to involve purines bases, and the PBE spectra error is more pronounced in the complexes where the Ag cluster is bound to the purines. Finally, our results also highlight the importance of adding both the complementary base pair and the sugar-phosphate backbone in order to properly characterize the absorption spectrum of DNA:Ag complexes.