We study the collective motion of a dense suspension of active swimmers in a viscous fluid medium. The swimmers are modeled as soft spheres moving in a highly viscous fluid medium. The magnitude of the propelling thrust exerted by each particle is taken to be a constant and the direction is aligned to its velocity. Depending on the magnitude of the exerted thrust, several nonequilibrium steady states are observed. The transitions between the steady states are characterized using the total dissipation as a function of the magnitude of the thrust. The transitions between the nonequilibrium states are characterized by changes in exponent at low thrust values. At high thrust values, hysteretic transitions between ordered and disordered states are observed.

A recent model for monodisperse granular suspensions is used to analyze transport properties in spatially inhomogeneous states close to the simple (or uniform) shear flow. The kinetic equation is based on the inelastic Boltzmann (for low-density gases) with the presence of a viscous drag force that models the influence of the interstitial gas phase on the dynamics of grains. A normal solution is obtained via a Chapman-Enskog-like expansion around a (local) shear flow distribution which retains all the hydrodynamic orders in the shear rate. To first order in the expansion, the transport coefficients characterizing momentum and heat transport around shear flow are given in terms of the solutions of a set of coupled linear integral equations which are approximately solved by using a kinetic model of the Boltzmann equation. To simplify the analysis, the steady-state conditions when viscous heating is compensated by the cooling terms arising from viscous friction and collisional dissipation are considered to get the explicit forms of the set of generalized transport coefficients. The shear-rate dependence of some of the transport coefficients of the set is illustrated for several values of the coefficient of restitution.

Recently, a theoretical framework aimed at separating the roles of dynamics and topology in multidimensional systems has been developed [Gao et al., Nature (London) 530, 307 (2016)]. The validity of their method is assumed to hold depending on two main hypotheses: (i) The network determined by the the interaction between pairs of nodes has negligible degree correlations; (ii) the node activities are uniform across nodes on both the drift and the pairwise interaction functions. Moreover, the authors consider only positive (mutualistic) interactions. Here we show the conditions proposed by Gao and collaborators [Nature (London) 530, 307 (2016)] are neither sufficient nor necessary to guarantee that their method works in general and validity of their results are not independent of the model chosen within the class of dynamics they considered. Indeed we find that a new condition poses effective limitations to their framework and we provide quantitative predictions of the quality of the one-dimensional collapse as a function of the properties of interaction networks and stable dynamics using results from random matrix theory. We also find that multidimensional reduction may work also for an interaction matrix with a mixture of positive and negative signs, opening up an application of the framework to food webs, neuronal networks, and social and economic interactions.

In order to grow and replicate, living cells must express a diverse array of proteins, but the process by which proteins are made includes a great deal of inherent randomness. Understanding this randomness—whether it arises from the discrete stochastic nature of chemical reactivity (“intrinsic” noise), or from cell-to-cell variability in the concentrations of molecules involved in gene expression, or from the timings of important cell-cycle events like DNA replication and cell division (“extrinsic” noise)—remains a challenge. In this article we analyze a model of gene expression that accounts for several extrinsic sources of noise, including those associated with chromosomal replication, cell division, and variability in the numbers of RNA polymerase, ribonuclease E, and ribosomes. We then attempt to fit our model to a large proteomics and transcriptomics data set and find that only through the introduction of a few key correlations among the extrinsic noise sources can we accurately recapitulate the experimental data. These include significant correlations between the rate of mRNA degradation (mediated by ribonuclease E) and the rates of both transcription (RNA polymerase) and translation (ribosomes) and, strikingly, an anticorrelation between the transcription and the translation rates themselves.

We have studied the collective motion of polar active particles confined to ellipsoidal surfaces. The geometric constraints lead to the formation of vortices that encircle surface points of constant curvature (umbilics). We have found that collective motion patterns are particularly rich on ellipsoids with four umbilics where vortices tend to be located near pairs of umbilical points to minimize their interaction energy. Our results provide a perspective on the migration of living cells, which most likely use the information provided from the curved substrate geometry to guide their collective motion.

Population annealing is a sequential Monte Carlo scheme well suited to simulating equilibrium states of systems with rough free energy landscapes. Here we use population annealing to study a binary mixture of hard spheres. Population annealing is a parallel version of simulated annealing with an extra resampling step that ensures that a population of replicas of the system represents the equilibrium ensemble at every packing fraction in an annealing schedule. The algorithm and its equilibration properties are described, and results are presented for a glass-forming fluid composed of a 50/50 mixture of hard spheres with diameter ratio of 1.4:1. For this system, we obtain precise results for the equation of state in the glassy regime up to packing fractions $\phi \approx 0.60$ and study deviations from the Boublik-Mansoori-Carnahan-Starling-Leland equation of state. For higher packing fractions, the algorithm falls out of equilibrium and a free volume fit predicts jamming at packing fraction $\phi \approx 0.667$. We conclude that population annealing is an effective tool for studying equilibrium glassy fluids and the jamming transition.

A replica method for calculation of smectic liquid crystal properties within the Onsager theory has been presented and applied to an exemplary case of two-dimensional perfectly aligned needlelike boomerangs. The method allows one to consider the complete influence of the interaction terms in contrast to the Fourier expansion method which uses mostly first or second order terms of expansion. The program based on the replica algorithm is able to calculate a single representative layer as an equivalent set of layers, depending on the size of the considered width of the sample integration interval. It predicts successfully smectic density distributions, energies, and layer thicknesses for different types of layer arrangement—of the antiferroelectric or of the smectic A order type. Specific features of the algorithm performance and influence of the numerical accuracy on the physical properties are presented. Future applications of the replica method to freely rotating molecules are discussed.

In recent years entanglement measures, such as the von Neumann and the Rényi entropies, provided a unique opportunity to access elusive features of quantum many-body systems. However, extracting entanglement properties analytically, experimentally, or in numerical simulations can be a formidable task. Here, by combining the replica trick and the Jarzynski equality we devise an alternative effective out-of-equilibrium protocol for measuring the equilibrium Rényi entropies. The key idea is to perform a quench in the geometry of the replicas. The Rényi entropies are obtained as the exponential average of the work performed during the quench. We illustrate an application of the method in classical Monte Carlo simulations, although it could be useful in different contexts, such as in quantum Monte Carlo, or experimentally in cold-atom systems. The method is most effective in the quasistatic regime, i.e., for a slow quench. As a benchmark, we compute the Rényi entropies in the Ising universality class in $1+1$ dimensions. We find perfect agreement with the well-known conformal field theory predictions.

We consider a model nondispersive nonlinear optical fiber channel with an additive Gaussian noise. Using Feynman path-integral technique, we find the optimal input signal distribution maximizing the channel's per-sample mutual information at large signal-to-noise ratio in the intermediate power range. The optimal input signal distribution allows us to improve previously known estimates for the channel capacity. We calculate the output signal entropy, conditional entropy, and per-sample mutual information for Gaussian, half-Gaussian, and modified Gaussian input signal distributions. We demonstrate that in the intermediate power range the capacity (the per-sample mutual information for the optimal input signal distribution) is greater than the per-sample mutual information for half-Gaussian input signal distribution considered previously as the optimal one. We also show that the capacity grows as $loglogP$ in the intermediate power range, where $P$ is the signal power.

We present an analysis of the entangling quantum kicked top focusing on the few qubit case and the initial condition dependence of the time-averaged entanglement $S_Q$ for spin-coherent states. We show a very strong connection between the classical phase space and the initial condition dependence of $S_Q$ even for the extreme case of two spin-$1/2$ qubits. This correlation is not related directly to chaos in the classical dynamics. We introduce a measure of the behavior of a classical trajectory which correlates far better with the entanglement and show that the maps of classical and quantum initial-condition dependence are both organized around the symmetry points of the Hamiltonian. We also show clear (quasi-)periodicity in entanglement as a function of number of kicks and of kick strength.

Anomalous nonexponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA base pairs exhibits a slow power-law relaxation attributable to weak Hamiltonian chaos, with parameters similar to experimental data. Here, the relationship is studied between this motion and spectroscopic signals measured in DNA with a small molecular photoprobe inserted into the base-pair stack. To this end, the earlier computational approach in combination with an analytical theory is applied to the experimental DNA fragment. It is found that the intensity of breathing dynamics is strongly increased in the internal base pairs that flank the photoprobe, with anomalous relaxation quantitatively close to that in terminal base pairs. A physical mechanism is proposed to explain the coupling between the relaxation of base-pair breathing and the experimental response signal. It is concluded that the algebraic relaxation observed experimentally is very likely a manifestation of weakly chaotic dynamics of hydrogen-bond breathing in the base pairs stacked to the photoprobe and that the weak nanoscale chaos can represent an ubiquitous hidden source of nonexponential relaxation in ultrafast spectroscopy.

Two-dimensional systems of inverse patchy colloids modeled as disks with a central charge and having their surface decorated with oppositely pointlike charged patches are investigated using molecular dynamics simulations. The self-assembly of the patchy colloids leads to diverse ground state configurations ranging from crystalline arrangements of monomers to linear clusters, ramified linear clusters and to percolated configurations. Two structural phase diagrams are constructed: (1) as a function of the net charge and area fraction, and (2) as a function of the net charge and the range of the pair interaction potential. An interesting reentrant percolation transition is obtained as a function of the net charge of the colloids. We identify distinct mechanisms that lead to the percolation transition.

We investigate the crossing of an energy barrier by a self-propelled particle described by a Rayleigh friction term. We reveal the existence of a sharp transition in the external force field whereby the amplitude dramatically increases. This corresponds to a saddle point transition in the velocity flow phase space, as would be expected for any type of repulsive force field. We use this approach to rationalize the results obtained by Eddi et al. [Phys. Rev. Lett. 102, 240401 (2009)] who studied the interaction between a drop propelled by its accompanying wave field and a submarine obstacle. This wave particle entity can overcome potential barrier, suggesting the existence of a “macroscopic tunneling effect.” We show that the effect of self-propulsion is sufficiently strong to generate crossing of the high-energy barrier. By assuming a random distribution of initial angles, we define a probability distribution to cross the potential barrier that matches with the data of Eddi et al. This probability is similar to the one encountered in statistical physics for Hamiltonian systems, i.e., a Boltzmann exponential law.

Stimuli-responsive materials that modify their shape in response to changes in environmental conditions—such as solute concentration, temperature, pH, and stress—are widespread in nature and technology. Applications include micro- and nanoporous materials used in filtration and flow control. The physiochemical mechanisms that induce internal volume modifications have been widely studied. The coupling between induced volume changes and solute transport through porous materials, however, is not well understood. Here, we consider advective and diffusive transport through a small channel linking two large reservoirs. A section of stimulus-responsive material regulates the channel permeability, which is a function of the local solute concentration. We derive an exact solution to the coupled transport problem and demonstrate the existence of a flow regime in which the steady state is reached via a damped oscillation around the equilibrium concentration value. Finally, the feasibility of an experimental observation of the phenomena is discussed.

Electric field induced deformations in twisted and untwisted planar layers of nematic liquid crystals possessing flexoelectric properties were investigated numerically. The spatially periodic deformations, taking the form of parallel stripes, were found to have smaller free energy than the homogeneous deformations. The structures of distorted layers as well as the evolution of deformations during changes of bias voltage were recognized. The role of flexoelectric properties was analyzed. Calculations taking into account the peculiar elastic properties of the bent-core nematics were also performed. In the untwisted planar layers the stripes were parallel to the initial director orientation. In the twisted layers, two different kinds of periodic deformation were distinguished. They had different structures and different directions with respect to the initial director distribution. The results were consistent with existing experimental data.

Stabilizing defects in liquid-crystal systems is crucial for many physical processes and applications ranging from functionalizing liquid-crystal textures to recently reported command of chaotic behaviors of active matters. In this work, we perform analytical calculations to study the curvature-driven stability mechanism of defects based on the isotropic nematic disk model that is free of any topological constraint. We show that in a growing spherical disk covering a sphere the accumulation of curvature effect can prevent typical +1 and +1/2 defects from forming boojum textures where the defects are repelled to the boundary of the disk. Our calculations reveal that the movement of the equilibrium position of the +1 defect from the boundary to the center of the spherical disk occurs in a very narrow window of the disk area, exhibiting the first-order phase-transition-like behavior. For the pair of +1/2 defects by splitting a +1 defect, we find the curvature-driven alternating repulsive and attractive interactions between the two defects. With the growth of the spherical disk these two defects tend to approach and finally recombine towards a +1 defect texture. The sensitive response of defects to curvature and the curvature-driven stability mechanism demonstrated in this work in nematic disk systems may have implications towards versatile control and engineering of liquid-crystal textures in various applications.

We use protein folding energy landscape concepts such as golf course and funnel to study re-equilibration in athermal martensites under systematic temperature quench Monte Carlo simulations. On quenching below a transition temperature, the seeded high-symmetry parent-phase austenite that converts to the low-symmetry product-phase martensite, through autocatalytic twinning or elastic photocopying, has both rapid conversions and incubation delays in the temperature-time-transformation phase diagram. We find the rapid (incubation delays) conversions at low (high) temperatures arises from the presence of large (small) size of golf-course edge that has the funnel inside for negative energy states. In the incubating state, the strain structure factor enters into the Brillouin-zone golf course through searches for finite transitional pathways which close off at the transition temperature with Vogel-Fulcher divergences that are insensitive to Hamiltonian energy scales and log-normal distributions, as signatures of dominant entropy barriers. The crossing of the entropy barrier is identified through energy occupancy distributions, Monte Carlo acceptance fractions, heat emission, and internal work. The above ideas had previously been presented for the scalar order parameter case. Here we show similar results are also obtained for vector order parameters.

Iron opacity calculations presently disagree with measurements at an electron temperature of $\sim 180–195$ eV and an electron density of ($2–4)\times {10}^{22}{\mathrm{cm}}^{-3}$, conditions similar to those at the base of the solar convection zone. The measurements use x rays to volumetrically heat a thin iron sample that is tamped with low-$Z$ materials. The opacity is inferred from spectrally resolved x-ray transmission measurements. Plasma self-emission, tamper attenuation, and temporal and spatial gradients can all potentially cause systematic errors in the measured opacity spectra. In this article we quantitatively evaluate these potential errors with numerical investigations. The analysis exploits computer simulations that were previously found to reproduce the experimentally measured plasma conditions. The simulations, combined with a spectral synthesis model, enable evaluations of individual and combined potential errors in order to estimate their potential effects on the opacity measurement. The results show that the errors considered here do not account for the previously observed model-data discrepancies.

In biofluid flow systems, often the flow problems of fluids of complex structures, such as the flow of red blood cells (RBCs) through complex capillary vessels, need to be considered. The smoothed dissipative particle dynamics (SDPD), a particle-based method, is one of the easy and flexible methods to model such complex structure fluids. It couples the best features of the smoothed particle hydrodynamics (SPH) and dissipative particle dynamics (DPD), with parameters having specific physical meaning (coming from SPH discretization of the Navier-Stokes equations), combined with thermal fluctuations in a mesoscale simulation, in a similar manner to the DPD. On the other hand, the immersed boundary method (IBM), a preferred method for handling fluid-structure interaction problems, has also been widely used to handle the fluid-RBC interaction in RBC simulations. In this paper, we aim to couple SDPD and IBM together to carry out the simulations of RBCs in complex flow problems. First, we develop the SDPD-IBM model in details, including the SDPD model for the evolving fluid flow, the RBC model for calculating RBC deformation force, the IBM for treating fluid-RBC interaction, and the solid boundary treatment model as well. We then conduct the verification and validation of the combined SDPD-IBM method. Finally, we demonstrate the capability of the SDPD-IBM method by simulating the flows of RBCs in rectangular, cylinder, curved, bifurcated, and constricted tubes, respectively.