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Physical Review. E

Pierre A Haas, Raymond E Goldstein
The embryos of the green alga Volvox carteri are spherical sheets of cells that turn themselves inside out at the close of their development through a programme of cell shape changes. This process of inversion is a model for morphogenetic cell sheet deformations; it starts with four lips opening up at the anterior pole of the cell sheet, flipping over and peeling back to invert the embryo. Experimental studies have revealed that inversion is arrested if some of these cell shape changes are inhibited, but the mechanical basis for these observations has remained unclear...
November 2018: Physical Review. E
Lukas Ophaus, Svetlana V Gurevich, Uwe Thiele
The conserved Swift-Hohenberg equation (or phase-field-crystal [PFC] model) provides a simple microscopic description of the thermodynamic transition between fluid and crystalline states. Combining it with elements of the Toner-Tu theory for self-propelled particles, Menzel and Löwen [Phys. Rev. Lett. 110, 055702 (2013)PRLTAO0031-900710.1103/PhysRevLett.110.055702] obtained a model for crystallization (swarm formation) in active systems. Here, we study the occurrence of resting and traveling localized states, i...
August 2018: Physical Review. E
Dongkyu Kim, Dong-Hee Kim
Learning with an artificial neural network encodes the system behavior in a feed-forward function with a number of parameters optimized by data-driven training. An open question is whether one can minimize the network complexity without loss of performance to reveal how and why it works. Here we investigate the learning of the phase transition in the Ising model and find that having two hidden neurons can be enough for an accurate prediction of critical temperature. We show that the networks learn the scaling dimension of the order parameter while being trained as a phase classifier, demonstrating how the machine learning exploits the Ising universality to work for different lattices of the same criticality within a single set of trainings in one lattice geometry...
August 2018: Physical Review. E
V Yu Shishkov, E S Andrianov, A A Pukhov, A P Vinogradov, A A Lisyansky
We study the evolution of an open quantum system described by a dynamical semigroup having the Lindblad superoperator as a generator. This generator may have an eigenfunction with a zero eigenvalue referred to as a constant of motion (COM). An open quantum system has a unique stationary state if and only if it has no COMs. A system with multiple stationary states has a basis of COMs, any COM of the system is a linear combination of the basis COMs. The basis divides the space of system states into subspaces...
August 2018: Physical Review. E
Parth Rakesh Desai, Siddhartha Das
We conduct molecular dynamics (MD) simulations and develop scaling laws to quantify the lubrication behavior of weakly interpenetrated polymer brush bilayers in the presence of an external shear force. The weakly interpenetrated regime is characterized by 1<d_{g}/d_{0}<2, where d_{g} is the gap between the opposing surfaces (where the brushes are grafted) and d_{0} is the unperturbed brush height. MD simulations predict that in the shear thinning regime, characterized by a larger shear force or a large Weissenberg number (W), R_{g}^{2}∼W^{0...
August 2018: Physical Review. E
Yu-Han Ma, Dazhi Xu, Hui Dong, Chang-Pu Sun
Efficiency at maximum power has been investigated extensively, yet the practical control scheme to achieve it remains elusive. We fill this gap with a stepwise Carnot-like cycle, which consists of the discrete isothermal process (DIP) and adiabatic process. With DIP, we validate the widely adopted assumption of the C/t relation of the irreversible entropy generation S^{(ir)} and show the explicit dependence of the coefficient C on the fluctuation of the speed of tuning energy levels as well as the microscopic coupling constants to the heat baths...
August 2018: Physical Review. E
Wonjung Lee
Because the existence of cheap emulators can give rise to potentially drastic computational savings as compared to direct numerical simulations of complex turbulence models, the study of reduced models has good practical relevance, and the guidelines regarding their construction from the true dynamical system model are much in demand. In accordance with this contemporary trend in science and engineering, we provide a new approach for the rigorous derivation of the linear reduced model with memory from the one-dimensional Majda-McLaughlin-Tabak (MMT) prototypical wave turbulence in thermal equilibrium...
August 2018: Physical Review. E
N Roy, P Sanz-Leon, P A Robinson
The spatiotemporal spectrum of feedback-driven fluctuations of brain connectivity is investigated using nonlinear neural field theory of the corticothalamic system. Weakly nonlinear dynamics of neural feedbacks are expanded in terms of first order perturbations of neural activity relative to a fixed point. Susceptibilities are used to quantify the change in connectivity per unit change in presynaptic or postsynaptic activity caused by nonlinear feedbacks such as facilitation, depression, sensitization, potentiation, and the effects of discrete eigenmode structure are included for a spherical brain geometry...
August 2018: Physical Review. E
Theo Gibbs, Jacopo Grilli, Tim Rogers, Stefano Allesina
Random matrix theory successfully connects the structure of interactions of large ecological communities to their ability to respond to perturbations. One of the most debated aspects of this approach is that so far studies have neglected the role of population abundances on stability. While species abundances are well studied and empirically accessible, studies on stability have so far failed to incorporate this information. Here we tackle this question by explicitly including population abundances in a random matrix framework...
August 2018: Physical Review. E
M H Jin, B Zheng, L Xiong, N J Zhou, L Wang
With the stochastic Landau-Lifshitz-Gilbert (sLLG) equation, critical dynamic behaviors far from equilibrium or stationary around the order-disorder and pinning-depinning phase transitions in anisotropic magnetic films are investigated. From the dynamic relaxation with and without an external field, the Curie temperature and critical exponents of the order-disorder phase transition are accurately determined. For the pinning-depinning phase transition induced by quenched disorder, the nonstationary creep motion of domain wall activated by finite temperatures is simulated, and the thermal rounding exponent is extracted...
August 2018: Physical Review. E
Márton Pósfai, Raissa M D'Souza
The hierarchy of social organization is a ubiquitous property of animal and human groups, linked to resource allocation, collective decisions, individual health, and even to social instability. Experimental evidence shows that both the intrinsic abilities of individuals and social reinforcement processes impact hierarchies; existing mathematical models, however, focus on the latter. Here, we develop a rigorous model that incorporates both features and explore their synergistic effect on stability and the structure of hierarchy...
August 2018: Physical Review. E
Y Zhao, G J Morales
This analytical and numerical study explores, from a deterministic perspective, the response of a particle in contact with a heat bath to an external force that varies sinusoidally in time. The heat bath is represented as a deterministic Nosé-Hoover thermostat. Such an idealized model encompasses features found in a variety of physical problems in which the coherent influence of an external agent competes against the thermalization tendencies of the surrounding medium, e.g., a charged particle in a thermal plasma that is acted on by a powerful electromagnetic wave...
August 2018: Physical Review. E
B Cheng, T J T Kwan, S A Yi, O L Landen, Y M Wang, C J Cerjan, S H Batha, F J Wysocki
Asymmetric implosion of inertial confinement fusion capsules is known, both experimentally and computationally, to reduce thermonuclear performance. This work shows that low-mode asymmetries degrade performance as a result of a decrease in the hydrodynamic disassembly time of the hot-spot core, which scales with the minimum dimension of the hot spot. The asymmetric shape of a hot spot results in decreased temperatures and areal densities and allows more alpha particles to escape, relative to an ideal spherical implosion, thus reducing alpha-energy deposition in the hot spot...
August 2018: Physical Review. E
Abdorreza Goodarzinick, Mohammad D Niry, Alireza Valizadeh, Matjaž Perc
The robustness of dynamical properties of neuronal networks against structural damages is a central problem in computational and experimental neuroscience. Research has shown that the cortical network of a healthy brain works near a critical state and, moreover, that functional neuronal networks often have scale-free and small-world properties. In this work, we study how the robustness of simple functional networks at criticality is affected by structural defects. In particular, we consider a two-dimensional Ising model at the critical temperature and investigate how its functional network changes with the increasing degree of structural defects...
August 2018: Physical Review. E
Petter Holme
Assume one has the capability of determining whether a node in a network is infectious or not by probing it. Then problem of optimizing sentinel surveillance in networks is to identify the nodes to probe such that an emerging disease outbreak can be discovered early or reliably. Whether the emphasis should be on early or reliable detection depends on the scenario in question. We investigate three objective measures from the literature quantifying the performance of nodes in sentinel surveillance: the time to detection or extinction, the time to detection, and the frequency of detection...
August 2018: Physical Review. E
F Zaccagnino, A Audebert, S J Cox
We describe a numerical model to predict the rheology of two-dimensional dry foams. The model accurately describes soap film curvature and viscous friction with the walls, and includes the transport of surfactant within the films and across the vertices where films meet. It accommodates the changes in foam topology that occur when a foam flows and, in particular, accurately represents the relaxation of the foam following a topological change. The model is validated against experimental data, allowing the prediction of elastic and viscous parameters associated with different surfactant solutions...
August 2018: Physical Review. E
Ryan L Melvin, Jiajie Xiao, Kenneth S Berenhaut, Ryan C Godwin, Freddie R Salsbury
Here we present a time-dependent correlation method that provides insight into how long a system takes to grow into its equal-time (Pearson) correlation. We also show a usage of an extant time-lagged correlation method that indicates the time for parts of a system to become decorrelated, relative to equal-time correlation. Given a completed simulation (or set of simulations), these tools estimate (i) how long of a simulation of the same system would be sufficient to observe the same correlated motions, (ii) if patterns of observed correlated motions indicate events beyond the timescale of the simulation, and (iii) how long of a simulation is needed to observe these longer timescale events...
August 2018: Physical Review. E
Mengying Wang, Ivan C Christov
Low-dimensional dynamical systems are fruitful models for mixing in fluid and granular flows. We study a one-dimensional discontinuous dynamical system (termed "cutting and shuffling" of a line segment), and we present a comprehensive computational study of its finite-time mixing properties including the effect of diffusion. To explore a large parameter space, we introduce fit functions for two mixing metrics of choice: the number of cutting interfaces (a standard quantity in dynamical systems theory of interval exchange transformations) and a mixing norm (a more physical measure of mixing)...
August 2018: Physical Review. E
M Di Pietro Martínez, M Hoyuelos
A mean-field theory for diffusion with interaction was introduced in Phys. Rev. E 92, 062118 (2015)PLEEE81539-375510.1103/PhysRevE.92.062118. Interaction effects are represented with a mean-field potential. Here we show that the potential can be directly related to the activity coefficient. In this context, we obtain an alternative derivation of the Darken equation, that relates collective diffusion coefficient and single particle diffusion coefficient (generally different in the presence of interactions). We also carry out a validation test of the model using, as a case study, effective interactions that reproduce Bose-Einstein statistics...
August 2018: Physical Review. E
Eric Cator, Peter Donnelly, Piet Van Mieghem
We emphasize that correlations between infection states in both the SIS and SIR model are always positive and that the title of the article "Nodal infection in Markovian susceptible-infected-susceptible and susceptible-infected-removed epidemics on networks are non-negatively correlated" [Phys. Rev. E 89, 052802 (2014)PLEEE81539-375510.1103/PhysRevE.89.052802] is correct. The history and motivation that led to the proof is placed in perspective.
August 2018: Physical Review. E
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