Theoretical and experimental studies have shown that the fluctuations of in vivo systems break the fluctuation-dissipation theorem. One can thus ask what information is contained in the correlation functions of protein concentrations and how they relate to the response of the reactive network to a perturbation. Answers to these questions are of prime importance to extract meaningful parameters from the in vivo fluorescence correlation spectroscopy data. In this paper we study the fluctuations of the concentration of a reactive species involved in a cyclic network that is in a nonequilibrium steady state perturbed by a noisy force, taking into account both the breaking of detailed balance and extrinsic noises. Using a generic model for the network and the extrinsic noise, we derive a chemical Langevin equation that describes the dynamics of the system, we determine the expressions of the correlation functions of the concentrations, and we estimate the deviation of the fluctuation-dissipation theorem and the range of parameters in which an effective temperature can be defined.

A theory is developed to describe the equilibrium adsorption and self-assembly of patchy colloids in microchannels. The adsorption theory is developed in classical density functional theory, with the adsorbed phase and fluid phase chemical potentials modeled using thermodynamic perturbation theory. Adsorption of nonpatchy colloids in microchannels is typically achieved through nonequilibrium routes such as spin coating and evaporation. These methods are required due to the entropic penalty of adsorption. In this work we propose that the introduction of patches on the colloids greatly enhances the temperature dependent and reversible adsorption of colloids in microchannels. It is shown how bulk fluid density, temperature, patch size, and channel diameter can be manipulated to achieve the adsorption and self-assembly of patchy colloids in microchannels.

We present a theoretical study of the energetics of thin nematic shells with two charge-one-half defects and one charge-one defect. We determine the optimal arrangement: the defects are located on a great circle at the vertices of an isosceles triangle with angles of ${66}^{\circ }$ at the charge-one-half defects and a distinct angle of ${48}^{\circ }$, consistent with experimental findings. We also analyze thermal fluctuations around this ground state and estimate the energy as a function of thickness. We find that the energy of the three-defect shell is close to the energy of other known configurations having two charge-one and four charge-one-half defects. This finding, together with the large energy barriers separating one configuration from the others, explains their observation in experiments as well as their long-time stability.

While the existence of stable knotted and linked vortex lines has been established in many experimental and theoretical systems, their existence in oscillatory systems and systems with nonlocal coupling has remained elusive. Here, we present strong numerical evidence that stable knots and links such as trefoils and Hopf links do exist in simple, complex, and chaotic oscillatory systems if the coupling between the oscillators is neither too short ranged nor too long ranged. In this case, effective repulsive forces between vortex lines in knotted and linked structures stabilize curvature-driven shrinkage observed for single vortex rings. In contrast to real fluids and excitable media, the vortex lines correspond to scroll wave chimeras [synchronized scroll waves with spatially extended (tubelike) unsynchronized filaments], a prime example of spontaneous synchrony breaking in systems of identical oscillators. In the case of complex oscillatory systems, this leads to a topological superstructure combining knotted filaments and synchronization defect sheets.

The equilibrium properties of a single quantum particle (qp) interacting with a classical gas for a wide range of temperatures that explore the system's behavior in the classical as well as in the quantum regime is investigated. Both the qp and the atoms are restricted to sites on a one-dimensional lattice. A path integral formalism developed within the context of the canonical ensemble is utilized, where the qp is represented by a closed, variable-step random walk on the lattice. Monte Carlo methods are employed to determine the system's properties. To test the usefulness of the path integral formalism, the Metropolis algorithm is employed to determine the equilibrium properties of the qp in the context of a square well potential, forcing the qp to occupy bound states. We consider a one-dimensional square well potential where all atoms on the lattice are occupied with one atom with an on-site potential except for a contiguous set of sites of various lengths centered at the middle of the lattice. Comparison of the potential energy, the energy fluctuations, and the correlation function are made between the results of the Monte Carlo simulations and the numerical calculations.

In reconstituting $k$-mer models, extended objects that occupy several sites on a one-dimensional lattice undergo directed or undirected diffusion, and reconstitute—when in contact—by transferring a single monomer unit from one $k$-mer to the other; the rates depend on the size of participating $k$-mers. This polydispersed system has two conserved quantities, the number of $k$-mers and the packing fraction. We provide a matrix product method to write the steady state of this model and to calculate the spatial correlation functions analytically. We show that for a constant reconstitution rate, the spatial correlation exhibits damped oscillations in some density regions separated, from other regions with exponential decay, by a disorder surface. In a specific limit, this constant-rate reconstitution model is equivalent to a single dimer model and exhibits a phase coexistence similar to the one observed earlier in totally asymmetric simple exclusion process on a ring with a defect.

The diagonal entropy was introduced as a good entropy candidate especially for isolated quantum systems out of equilibrium. Here we present an analytical calculation of the average diagonal entropy for systems undergoing unitary evolution and an external perturbation in the form of a cyclic quench. We compare our analytical findings with numerical simulations of various quantum systems. Our calculations elucidate various heuristic relations proposed recently in the literature.

Given a system with a finite heat capacity and a heat reservoir, and two values of initial temperatures, $T_{+}$ and $T_{-}(<T_{+})$, we inquire, in which case is the optimal work extraction larger: when the reservoir is an infinite source at $T_{+}$ and the system is a sink at $T_{-}$, or, when the reservoir is an infinite sink at $T_{-}$ and the system acts as a source at $T_{+}$? It is found that in order to compare the total extracted work, and the corresponding efficiency in the two cases, we need to consider three regimes as suggested by an inequality, the so-called arithmetic mean-geometric mean inequality, involving the arithmetic and the geometric means of the two temperature values $T_{+}$ and $T_{-}$. In each of these regimes, the efficiency at total work obeys certain universal bounds, given only in terms of the ratio of initial temperatures. The general theoretical results are exemplified for thermodynamic systems for which internal energy and temperature are power laws of the entropy. The conclusions may serve as benchmarks in the design of heat engines, where we can choose the nature of the finite system, so as to tune the total extractable work and/or the corresponding efficiency.

A model of stochastic evolutionary game dynamics with finite population of size $N+M$ was built. Among these individuals, $N$ individuals update strategies with aspiration updating, while the other $M$ individuals update strategies with imitation updating. In the proposed model, we obtain the expression of the mean fraction of cooperators and analyze some concrete cases. Compared with the standard imitation dynamics, there is always a positive probability to support the formation of cooperation in the system with the aspiration and imitation rules. Moreover, the numerical results indicate that more aspiration-driven individuals lead to a higher mean fraction of imitation-driven cooperators, which means the invasion of the aspiration-driven individuals is conducive to promoting the cooperation of the imitation-driven individuals.

Since the first suggestion of the Jarzynski equality many derivations of this equality have been presented in both the classical and the quantum context. While the approaches and settings differ greatly from one another, they all appear to rely on the condition that the initial state is a thermal Gibbs state. Here, we present an investigation of work distributions in driven isolated quantum systems, starting from pure states that are close to energy eigenstates of the initial Hamiltonian. We find that, for the nonintegrable quantum ladder studied, the Jarzynski equality is fulfilled to a good accuracy.

We investigate the influence of spatially homogeneous multiplicative noise on the formation of localized patterns in the framework of the cubic-quintic complex Ginzburg-Landau equation. We find that for sufficiently large multiplicative noise the formation of stationary and temporally periodic dissipative solitons is suppressed. This result is characterized by a linear relation between the bifurcation parameter and the noise amplitude required for suppression. For the regime associated with exploding dissipative solitons we find a reduction in the number of explosions for larger noise strength as well as a conversion to other types of dissipative solitons or to filling-in and eventually a collapse to the zero solution.

Complex time series are widespread in physics and physiology. Multifractal analysis provides a tool to study the scaling dynamics of such time series. However, the temporal evolution of scaling dynamics has been ignored by traditional tools such as the multifractal spectrum. We present scaling maps that add the time dimension to the study of scaling dynamics. This is particularly important in cases in which the dynamics of the underlying processes change in time or in applications that necessitate real-time detection of scaling dynamics. In addition, we present a methodology for automatic clustering of existing scaling regimes in a signal. We demonstrate the methodology on time-evolving correlated and uncorrelated noise and the output of a physiological control system (i.e., cardiac interbeat intervals) in healthy and pathological states.

The optical properties of several scarab beetles have been previously studied but few attempts have been made to compare beetles in the same genus. To determine whether there is any relation between specimens of the same genus, we have studied and classified seven species from the Chrysina genus. The polarization properties were analyzed with Mueller-matrix spectroscopic ellipsometry and the structural characteristics with optical microscopy and scanning electron microscopy. Most of the Chrysina beetles are green colored or have a metallic look (gold or silver). The results show that the green-colored beetles polarize reflected light mainly at off-specular angles. The gold-colored beetles polarize light left-handed near circular at specular reflection. The structure of the exoskeleton is a stack of layers that form a cusplike structure in the green beetles whereas the layers are parallel to the surface in the case of the gold-colored beetles. The beetle C. gloriosa is green with gold-colored stripes along the elytras and exhibits both types of effects. The results indicate that Chrysina beetles can be classified according to these two major polarization properties.

We report a theory capable of describing conformational transitions for single polymer adsorption in a poor solvent. We show that an additional molecular confinement effect near the contact line can act exactly like line tension, playing a critical role in the behavior of an absorbed polymer chain. Using this theory, distinct conformational states: desorbed globule (DG), surface attached cap (SAC), and adsorbed lens (AL), can be vividly revealed, resembling the drying-wetting transition of a nanodroplet. But the transitions between these states can behave rather differently from those in the usual wetting transitions. The DG-SAC transition is discrete, occurring at the adsorption threshold when the globule size at the desorbed state is equal to the adsorption blob. The SAC-AL transition is smooth for finite chain lengths, but can change to discontinuous in the infinite chain limit, characterized by the different end-to-end exponent 3/8 and the unique crossover exponent 1/4. Distinctive critical exponents near this transition are also determined, indicating that it is an additional universality class of phase transitions. This work also sheds light on nanodrop spreading, wherein the important role played by line tension might simply be a manifestation of the local molecular confinement near the contact line.

Results are presented from molecular dynamics simulations of Pb(l) nanodroplets containing dispersed Cu nanoparticles (NPs) and spreading on solid surfaces. Three-dimensional simulations are employed throughout, but droplet spreading and pinning are reduced to two-dimensional processes by modeling cylindrical NPs in cylindrical droplets; NPs have radius $R_{\mathrm{NP}}\cong 3\mathrm{nm}$ while droplets have initial $R_0\cong 42\mathrm{nm}$. At low particle loading explored here, NPs in sufficient proximity to the initial solid-droplet interface are drawn into advancing contact lines; entrained NPs eventually bind with the underlying substrate. For relatively low advancing contact angle ${\theta }_{\mathrm{adv}}$, self-pinning on entrained NPs occurs; for higher ${\theta }_{\mathrm{adv}}$, depinning is observed. Self-pinning and depinning cases are compared and forces on NPs at the contact line are computed during a depinning event. Though significant flow in the droplet occurs in close proximity to the particle during depinning, resultant forces are relatively low. Instead, forces due to liquid atoms confined between the particles and substrate dominate the forces on NPs; that is, for the NP size studied here, forces are interface dominated. For pinning cases, a precursor wetting film advances ahead of the pinned contact line but at a significantly slower rate than for a pure droplet. This is because the precursor film is a bilayer of liquid atoms on the substrate surface but it is instead a monolayer film as it crosses over pinning particles; thus, mass delivery to the bilayer structure is impeded.

This work reports an experimental and a numerical study of the interfacial instability in a mercury-ferrofluid system caused by a spatially nonuniform magnetic field against the action of gravity and interfacial tension. The interface evolution is observed to be continuous till its movement is hindered by a physical boundary. In contrast to the behavior of the ferrofluid interface under uniform field, we noted the instability growth to be monotonic under a field gradient. A steepness in the growth curve is noticed during the later stages of the instability, indicating a high magnitude of the growth velocities. Some unique phenomena, such as similarity of the growth at the initial stage, a slope transition in the growth curve at a later stage, and wrapping and pinning of the interface are observed, both in experiments and simulations.

The Reynolds analogy and the extended Reynolds analogy for the Rayleigh problem are considered. For a viscous incompressible fluid we derive the Reynolds analogy as a function of the Prandtl number and the Eckert number. We show that for any positive Eckert number, the Reynolds analogy as a function of the Prandtl number has a maximum. For a monatomic gas in the transitional flow regime, using the direct simulation Monte Carlo method, we investigate the extended Reynolds analogy, i.e., the relation between the shear stress and the energy flux transferred to the boundary surface, at different velocities and temperatures. We find that the extended Reynolds analogy for a rarefied monatomic gas flow with the temperature of the undisturbed gas equal to the surface temperature depends weakly on time and is close to 0.5. We show that at any fixed dimensionless time the extended Reynolds analogy depends on the plate velocity and temperature and undisturbed gas temperature mainly via the Eckert number. For Eckert numbers of the order of unity or less we generalize an extended Reynolds analogy. The generalized Reynolds analogy depends mainly only on dimensionless time for all considered Eckert numbers of the order of unity or less.

Fundamental properties of warm dense matter are described by the dielectric function, which gives access to the frequency-dependent electrical conductivity; absorption, emission, and scattering of radiation; charged particles stopping; and further macroscopic properties. Different approaches to the dielectric function and the related dynamical collision frequency are compared in a wide frequency range. The high-frequency limit describing inverse bremsstrahlung and the low-frequency limit of the dc conductivity are considered. Sum rules and Kramers-Kronig relation are checked for the generalized linear response theory and the standard approach following kinetic theory. The results are discussed in application to aluminum, xenon, and argon plasmas.

We reply to the Comment of Becker, Nelissen, Cleuren, Partoens, and Van den Broeck [Phys. Rev. E 93, 046101 (2016)] on our article [Arita, Krapivsky, and Mallick, Phys. Rev. E 90, 052108 (2014)] about the transport properties of a class of generalized exclusion processes.

Many models of heat engines have been studied with the tools of finite-time thermodynamics and an ensemble of independent quantum systems as the working fluid. Because of their convenient analytical properties, harmonic oscillators are the most frequently used example of a quantum system. We analyze different thermodynamical aspects with the final aim of the optimization of the performance of the engine in terms of the mechanical power provided during a finite-time Otto cycle. The heat exchange mechanism between the working fluid and the thermal reservoirs is provided by the Lindblad formalism. We describe an analytical method to find the limit cycle and give conditions for a stable limit cycle to exist. We explore the power production landscape as the duration of the four branches of the cycle are varied for short times, intermediate times, and special frictionless times. For short times we find a periodic structure with atolls of purely dissipative operation surrounding islands of divergent behavior where, rather than tending to a limit cycle, the working fluid accumulates more and more energy. For frictionless times the periodic structure is gone and we come very close to the global optimal operation. The global optimum is found and interestingly comes with a particular value of the cycle time.