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Although much empirical evidence has demonstrated that p53 plays a key role in tumor suppression, the dynamics and function of the regulatory network centered on p53 have not yet been fully understood. Here, we develop a Boolean network model to reproduce the two-phase dynamics of the p53 network in response to DNA damage. In particular, we map the fates of cells into two types of Boolean attractors, and we find that the apoptosis attractor does not exist for minor DNA damage, reflecting that the cell is reparable. As the amount of DNA damage increases, the basin of the repair attractor shrinks, accompanied by the rising of the apoptosis attractor and the expansion of its basin, indicating that the cell becomes more irreparable with more DNA damage. For severe DNA damage, the repair attractor vanishes, and the apoptosis attractor dominates the state space, accounting for the exclusive fate of death. Based on the Boolean network model, we explore the significance of links, in terms of the sensitivity of the two-phase dynamics, to perturbing the weights of links and removing them. We find that the links are either critical or ordinary, rather than redundant. This implies that the p53 network is irreducible, but tolerant of small mutations at some ordinary links, and this can be interpreted with evolutionary theory. We further devised practical control schemes for steering the system into the apoptosis attractor in the presence of DNA damage by pinning the state of a single node or perturbing the weight of a single link. Our approach offers insights into understanding and controlling the p53 network, which is of paramount importance for medical treatment and genetic engineering.

We study a reduced electrostatic fluid model for the tokamak scrape-off layer, which incorporates temperature gradient and vorticity gradient as two free energy fields. Two scenarios of field coupling are addressed: (1) sheath condition; (2) vortex wave coupling. For the sheath condition induced field coupling, the poloidal $\mathbf{E} \times \mathbf{B}$ flow shear is coupled with the temperature gradient. Combining an eigenmode analysis and the nonlinear phase dynamics approach, our findings indicate that in the absence of a vorticity gradient, the overall effect of the sheath condition induced flow shear can either stabilize or destabilize the interchange mode, depending on the competition between the flow shear suppression and the temperature gradient driving. This is different from the case where the gradient drive and shear damping are decoupled. When the field coupling is mediated by wave interactions, by setting an idealized step-like temperature and vorticity profiles, a joint mode forms through resonant interaction between the interfacial waves driven by the temperature and vorticity gradients, respectively. Near the phase locking condition, the joint mode can be more unstable than pure temperature gradient driven mode.

Swarmalators are entities with the simultaneous presence of swarming and synchronization that reveal emergent collective behavior due to the fascinating bidirectional interplay between phase and spatial dynamics. Although different coupling topologies have already been considered, here we introduce time-varying competitive phase interaction among swarmalators where the underlying connectivity for attractive and repulsive coupling varies depending on the vision (sensing) radius. Apart from investigating some fundamental properties like conservation of center of position and collision avoidance, we also scrutinize the cases of extreme limits of vision radius. The concurrence of attractiveâ€"repulsive competitive phase coupling allows the exploration of diverse asymptotic states, like static Ď€, and mixed phase wave states, and we explore the feasible routes of those states through a detailed numerical analysis. In sole presence of attractive local coupling, we reveal the occurrence of static cluster synchronization where the number of clusters depends crucially on the initial distribution of positions and phases of each swarmalator. In addition, we analytically calculate the sufficient condition for the emergence of the static synchronization state. We further report the appearance of the static ring phase wave state and evaluate its radius theoretically. Finally, we validate our findings using Stuartâ€"Landau oscillators to describe the phase dynamics of swarmalators subject to attractive local coupling. [ABSTRACT FROM AUTHOR]

We present an analytical electric field expression to simultaneously control the population and phase dynamics of two-level quantum systems. The presented electric field is obtained by a reverse engineering technique after the desired population and phase evolution pathways of the system have been specified. Upon application of this laser field, the system is driven from an arbitrary quantum state superposition to the desired population distribution; meanwhile the phase of one of the states proceeds according to a predefined path. The robustness of the engineered electric field is demonstrated by numerical simulations on the example of the 3s 3p transition of atomic sodium. Furthermore, the limitations of the presented technique, which arise due to the application of the rotating wave approximation, are thoroughly analyzed and discussed. [ABSTRACT FROM AUTHOR]

In a recent letter (Friedrich et al 2012 Phys. Rev. Lett. 109 138102), a minimal model swimmer has been proposed that propels itself at low Reynolds numbers by the revolving motion of a pair of spheres. The motion of the two spheres can synchronize by virtue of a hydrodynamic coupling that depends on the motion of the swimmer, but is rather independent of direct hydrodynamic interactions. This novel synchronization mechanism could account for the synchronization of a pair of flagella, e.g. in the green algae Chlamydomonas. In this paper, we discuss in detail how swimming and synchronization depend on the geometry of the model swimmer and compute the swimmer design for optimal synchronization. Our analysis highlights the role of broken symmetries in swimming and synchronization. [ABSTRACT FROM AUTHOR]

We study the mean-field dynamics and the reduced-dimension character of two-mode Bose-Einstein condensates (BECs) in highly anisotropic traps. By means of perturbative techniques, we show that the tightly confined (transverse) degrees of freedom can be decoupled from the dynamical equations at the expense of introducing additional effective three-body, attractive, intra- and inter-mode interactions into the dynamics of the loosely confined (longitudinal) degrees of freedom. These effective interactions are mediated by changes in the transverse wave function. The perturbation theory is valid as long as the nonlinear scattering energy is small compared to the transverse energy scales. This approach leads to reduced-dimension mean-field equations that optimally describe the evolution of a two-mode condensate in general quasi-one-dimensional (1D) and quasi-two-dimensional geometries.We use this model to investigate the relative phase and density dynamics of a two-mode, cigar- shaped 87Rb BEC. We study the relative-phase dynamics in the context of a nonlinear Ramsey interferometry scheme, which has recently been proposed as a novel platform for high-precision interferometry. Numerical integration of the coupled, time-dependent, three-dimensional, two-mode Gross-Pitaevskii equations for various atom numbers shows that this model gives a considerably more refined analytical account of the mean-field evolution than an idealized quasi-1D description. [ABSTRACT FROM AUTHOR]

We present a novel approach for recovery of the directional connectivity of a small oscillator network by means of the phase dynamics reconstruction from multivariate time series data. The main idea is to use a triplet analysis instead of the traditional pairwise one. Our technique reveals an effective phase connectivity which is generally not equivalent to a structural one. We demonstrate that by comparing the coupling functions from all possible triplets of oscillators, we are able to achieve in the reconstruction a good separation between existing and non-existing connections, and thus reliably reproduce the network structure. [ABSTRACT FROM AUTHOR]

This tutorial introduces the theoretical and experimental basics of electromagnetically induced transparency (EIT) in thermal alkali vapors. We first give a brief phenomenological description of EIT in simple three-level systems of stationary atoms and derive analytical expressions for optical absorption and dispersion under EIT conditions. Then we focus on how the thermal motion of atoms affects various parameters of the EIT system. Specifically, we analyze the Doppler broadening of optical transitions, ballistic versus diffusive atomic motion in a limited-volume interaction region, and collisional depopulation and decoherence. Finally, we discuss the common trade-offs important for optimizing an EIT experiment and give a brief 'walk-through' of a typical EIT experimental setup. We conclude with a brief overview of current and potential EIT applications. [ABSTRACT FROM AUTHOR]

We calculate the observed luminosity and spectrum following the emergence of a relativistic shock wave from a stellar edge. Shock waves propagating at 0.6 < Γsh β sh, where Γsh is the shock Lorentz factor, and β sh is its associated reduced velocity, heat the stellar envelope to temperatures exceeding ∼50 keV, allowing for a vigorous production of electron and positron pairs. Pairs significantly increase the electron-scattering optical depth and regulate the temperature through photon generation, producing distinct observational signatures in the escaping emission. Assuming Wien equilibrium, we find analytic expressions for the temperature and pair density profiles in the envelope immediately after shock passage, and compute the emission during the expansion phase. Our analysis shows that, in pair-loaded regions, photons are produced at a roughly uniform rest-frame energy of ∼200 keV, and reinforce previous estimates that the shock breakout signal will be detected as a short burst of energetic γ -ray photons, followed by a longer phase of X-ray emission. We test our model on a sample of low-luminosity gamma-ray bursts using a closure relation between the γ -ray burst duration, the radiation temperature, and the γ -ray isotropic equivalent energy, and find that some of the events are consistent with the relativistic shock breakout model. Finally, we apply our results to explosions in white dwarfs and neutron stars, and find that typical type Ia supernovae emit ∼1041 erg in the form of ∼1 MeV photons. [ABSTRACT FROM AUTHOR]

We analyze the circumgalactic medium (CGM) for eight commonly-used cosmological codes in the AGORA collaboration. The codes are calibrated to use identical initial conditions, cosmology, heating and cooling, and star formation thresholds, but each evolves with its own unique code architecture and stellar feedback implementation. Here, we analyze the results of these simulations in terms of the structure, composition, and phase dynamics of the CGM. We show properties such as metal distribution, ionization levels, and kinematics are effective tracers of the effects of the different code feedback and implementation methods, and as such they can be highly divergent between simulations. This is merely a fiducial set of models, against which we will in the future compare multiple feedback recipes for each code. Nevertheless, we find that the large parameter space these simulations establish can help disentangle the different variables that affect observable quantities in the CGM, e.g., showing that abundances for ions with higher ionization energy are more strongly determined by the simulation’s metallicity, while abundances for ions with lower ionization energy are more strongly determined by the gas density and temperature.

There are still essential aspects regarding cathodes requiring a comprehensive understanding. These include identifying the underlying phenomena that prevent reaching the theoretical capacity, explaining irreversible losses, and determining the cut-off potentials at which batteries should be cycled. We address these inquiries by investigating the cell’s capacity and phase dynamics by looking into the transport properties of electrons. This approach underlines the crucial role of electrons in influencing battery performance, similar to their significance in other materials and devices such as transistors, thermoelectrics, or superconductors. We use lithium iron phosphate LFP as a case study to demonstrate that understanding the electrochemical cycling behavior of a battery cell, particularly a Li//LFP configuration, hinges on factors like the total local potentials used to calculate chemical potentials, electronic density of states (DOS), and charge carrier densities. Our findings reveal that the stable plateau potential difference is 3.42 V, with maximum charge and minimum discharge potentials at 4.12 V and 2.80 V, respectively. The study illustrates the dynamic formation of metastable phases at a plateau voltage exceeding 3.52 V. Moreover, we establish that determining the working chemical potentials of elements like Li and Al can be achieved by combining their workfunction and DOS analysis. Additionally, we shed light on the role of carbon black beyond conductivity enhancement. Through Density functional theory (DFT) calculations and experimental methods involving scanning Kelvin probe (SKP) and electrochemical analysis, we comprehensively examine various materials, including Li, C, Al, Cu, LFP, FePO _4 , Li _0.25 FePO _4 , polyvinylidene fluoride, and Li _6 PS _5 Cl. The insights derived from this study, which solely rely on electrical properties, have broad applicability to all cathodes and batteries. They provide valuable information for efficiently selecting optimal formulations and conditions for cycling batteries.

We study a physical system consisting of a Bose–Einstein condensate confined to a ring shaped lattice potential interrupted by three weak links. The system is assumed to be driven by an effective flux piercing the ring lattice. By employing path integral techniques, we explore the effective quantum dynamics of the system in a pure quantum phase dynamics regime. Moreover, the effects of the density’s quantum fluctuations are studied through exact diagonalization analysis of the spectroscopy of the Bose–Hubbard model. We demonstrate that a clear two-level system emerges by tuning the magnetic flux at degeneracy. The lattice confinement, platform for the condensate, is realized experimentally employing a spatial light modulator. [ABSTRACT FROM AUTHOR]

Large-scale neurophysiological networks are often reconstructed from band-pass filtered time series derived from magnetoencephalography (MEG) data. Common practice is to reconstruct these networks separately for different frequency bands and to treat them independently. Recent evidence suggests that this separation may be inadequate, as there can be significant coupling between frequency bands (interlayer connectivity). A multilayer network approach offers a solution to analyze frequency-specific networks in one framework. We propose to use a recently developed network reconstruction method in conjunction with phase oscillator models to estimate interlayer connectivity that optimally fits the empirical data. This approach determines interlayer connectivity based on observed frequency-specific time series of the phase and a connectome derived from diffusion weighted imaging. The performance of this interlayer reconstruction method was evaluated in-silico. Our reconstruction of the underlying interlayer connectivity agreed to very high degree with the ground truth. Subsequently, we applied our method to empirical resting-state MEG data obtained from healthy subjects and reconstructed two-layered networks consisting of either alpha-to-beta or theta-to-gamma band connectivity. Our analysis revealed that interlayer connectivity is dominated by a multiplex structure, i.e. by one-to-one interactions for both alpha-to-beta band and theta-to-gamma band networks. For theta–gamma band networks, we also found a plenitude of interlayer connections between distant nodes, though weaker connectivity relative to the one-to-one connections. Our work is an stepping stone towards the identification of interdependencies across frequency-specific networks. Our results lay the ground for the use of the promising multilayer framework in this field with more-informed and justified interlayer connections. [ABSTRACT FROM AUTHOR]

Josephson effects are commonly studied in quantum systems in which dissipation or noise can be neglected or do not play a crucial role. In contrast, here we discuss a setup where dissipative interactions do amplify a photonic Josephson current, opening a doorway to dissipation-enhanced sensitivity of quantum-optical interferometry devices. In particular, we study two coupled nanolasers subjected to phase coherent drivings and coupled by a coherent photon tunneling process. We describe this system by means of a Fokker–Planck equation and show that it exhibits an interesting non-equilibrium phase diagram as a function of the coherent coupling between nanolasers. As we increase that coupling, we find a non-equilibrium phase transition between a phase-locked (PL) and a non-phase-locked (NPL) steady-state, in which phase coherence is destroyed by the photon tunneling process. In the coherent, PL regime, an imbalanced photon number population appears if there is a phase difference between the nanolasers, which appears in the steady-state as a result of the competition between competing local dissipative dynamics and the Josephson photo-current. The latter is amplified for large incoherent pumping rates and it is also enchanced close to the lasing phase transition. We show that the Josephson photocurrent can be used to measure optical phase differences. In the quantum limit, the accuracy of the two nanolaser interferometer grows with the square of the photon number and, thus, it can be enhanced by increasing the rate of incoherent pumping of photons into the nanolasers. [ABSTRACT FROM AUTHOR]

Bose–Bose droplets are self-bound objects emerging from a mixture of two interacting Bose–Einstein condensates when their interactions are appropriately tuned. During droplet formation three continuous symmetries of the system's Hamiltonian are broken: translational symmetry and two U(1) symmetries, allowing for arbitrary choice of phases of the mean-field wavefunctions describing the two components. Breaking of these symmetries must be accompanied by appearance of zero-energy excitations in the energy spectrum of the system recovering the broken symmetries. Normal modes corresponding to these excitations are the zero-energy modes. Here we find analytic expressions for these modes and introduce Hamiltonians generating their time evolution—dynamics of the droplet's centers of mass as well as dynamics of the phases of the two droplet's wavefunctions. When internal types of excitations (quasiparticles) are neglected then the very complex system of a quantum droplet is described using only a few 'global' degrees of freedom—the position of the center of mass of the droplet and two phases of two wave-functions, all these being quantum operators. We believe that our work might be useful in describing in a relatively easy way the low energy collisions of quantum droplets in situations where coherent flow of atoms between the droplets takes place. [ABSTRACT FROM AUTHOR]

We study the thermodynamic properties induced by non-reciprocal interactions between stochastic degrees of freedom in time- and space-continuous systems. We show that, under fairly general conditions, non-reciprocal coupling alone implies a steady energy flow through the system, i.e., non-equilibrium. Projecting out the non-reciprocally coupled degrees of freedom renders non-Markovian, one-variable Langevin descriptions with complex types of memory, for which we find a generalized second law involving information flow. We demonstrate that non-reciprocal linear interactions can be used to engineer non-monotonic memory, which is typical for, e.g., time-delayed feedback control, and is automatically accompanied with a nonzero information flow through the system. Furthermore, already a single non-reciprocally coupled degree of freedom can extract energy from a single heat bath (at isothermal conditions), and can thus be viewed as a minimal version of a time-continuous, autonomous 'Maxwell demon'. We also show that for appropriate parameter settings, the non-reciprocal system has characteristic features of active matter, such as a positive energy input on the level of the fluctuating trajectories without global particle transport. [ABSTRACT FROM AUTHOR]

We theoretically investigate Bloch oscillations in a one-dimensional Bose–Hubbard chain, with single-particle losses from the odd lattice sites described by a Lindblad equation. For a single particle the time evolution of the state is completely determined by a non-Hermitian effective Hamiltonian. We analyse the spectral properties of this Hamiltonian for an infinite lattice and link features of the spectrum to observable dynamical effects, such as frequency doubling in breathing modes. We further consider the case of many particles in the mean-field limit leading to complex nonlinear Schrödinger dynamics. Analytic expressions are derived for the generalised nonlinear stationary states and the nonlinear Bloch bands. The interplay of nonlinearity and particle losses leads to peculiar features in the nonlinear Bloch bands, such as the vanishing of solutions and the formation of additional exceptional points. The stability of the stationary states is determined via the Bogoliubov–de Gennes equation and is shown to strongly influence the mean-field dynamics. Remarkably, even far from the mean-field limit, the stability of the nonlinear Bloch bands appears to affect the quantum dynamics. This is demonstrated numerically for a two-particle system. [ABSTRACT FROM AUTHOR]

The 3p43PJ–3p34p3PJ transition in the sulphur atom is investigated in a precision two-photon excitation scheme under Doppler-free and collision-free circumstances yielding an absolute accuracy of 0.0009 cm−1, using a narrowband pulsed laser. This verifies and improves the level separations between amply studied odd parity levels with even parity levels in S I. An improved value for the 3P2–3P1 ground state fine structure splitting is determined at 396.0564 (7) cm−1. A 34S–32S atomic isotope shift was measured from combining time-of-flight mass spectrometry with laser spectroscopy. [ABSTRACT FROM AUTHOR]

We study the quantum tunneling of two one-dimensional quasi-condensates made of alkali-metal atoms, considering two different tunneling configurations: side-by-side and head-to-tail. After deriving the quasiparticle excitation spectrum, we discuss the dynamics of the relative phase following a sudden coupling of the independent subsystems. In particular, we calculate the coherence factor of the system, which, due to the nonzero tunneling amplitude, it exhibits dephasing–rephasing oscillations instead of pure dephasing. These oscillations are enhanced by a higher tunneling energy, and by higher system densities. Our predictions provide a benchmark for future experiments at temperatures below T ≲ 5 nK. [ABSTRACT FROM AUTHOR]

The phase sensitivity curve or phase response curve (PRC) quantifies the oscillator’s reaction to stimulation at a specific phase and is a primary characteristic of a self-sustained oscillatory unit. Knowledge of this curve yields a phase dynamics description of the oscillator for arbitrary weak forcing. Similar, though much less studied characteristic, is the amplitude response that can be defined either using an ad hoc approach to amplitude estimation or via the isostable variables. Here, we discuss the problem of the phase and amplitude response inference from observations using test stimulation. Although PRC determination for noise-free neuronal-like oscillators perturbed by narrow pulses is a well-known task, the general case remains a challenging problem. Even more challenging is the inference of the amplitude response. This characteristic is crucial, e.g. for controlling the amplitude of the collective mode in a network of interacting units—a task relevant to neuroscience. Here, we compare the performance of different techniques suitable for inferring the phase and amplitude response, particularly with application to macroscopic oscillators. We suggest improvements to these techniques, e.g. demonstrating how to obtain the PRC in case of stimuli of arbitrary shape. Our main result is a novel technique denoted by IPID-1, based on the direct reconstruction of the Winfree equation and the analogous first-order equation for isostable dynamics. The technique works for signals with or without well-pronounced marker events and pulses of arbitrary shape; in particular, we consider charge-balanced pulses typical in neuroscience applications. Moreover, this technique is superior for noisy and high-dimensional systems. Additionally, we describe an error measure that can be computed solely from data and complements any inference technique.

Synchronization has been reported for a wide range of self-oscillating systems. However, even though it has been predicted theoretically for several decades, the experimental realization of phase self-oscillation, sometimes called phase trapping, in the high driving regime has been studied only recently. We explored in detail the phase dynamics in a synchronized field emission SiC nanoelectromechanical system with intrinsic feedback. A richer variety of phase behavior has been unambiguously identified, implying phase modulation and inertia. This synchronization regime is expected to have implications for the comprehension of the dynamics of interacting self-oscillating networks and for the generation of frequency modulated signals at the nanoscale. [ABSTRACT FROM AUTHOR]

The dynamics of topological defects in a system of coupled phase oscillators, arranged in one and two-dimensional arrays, was numerically investigated using the Kuramoto model. After a rapid decay of the number of topological defects, a long-time quasi steady state with few topological defects was detected. Two competing time scales governed the dynamics corresponding to the dissipation rate and the coupling quench rate. The density of topological defects scales as a power law function of the coupling quench rate ρ ∼ Cν with ν = 0.25. Reducing the number of topological defects improves the long time coherence and order parameter of the system, enhancing the probability to reach a global minimal loss state that can be mapped to the ground state of a classical XY spin Hamiltonian. [ABSTRACT FROM AUTHOR]

Weconsider competition between layers in adaptive multiplex networks of phase oscillators, where adaptation principles (which cause intra-layer topology evolution) are inspired by real world homophily and homeostasis phenomena. Our model yields the emergence of both scale-free topologies and meso-scale structures in the layers, for an appropriate choice of the control parameters. Wefurther report that the growth of the number of interacting layers leads to a decrease of the global order, due to inter-layer structural competition. However, the increase of the system's scale can effect local synchronization between neighboring (or strongly coupled) nodes. Such unforeseen phenomena is connected with the nature of the competitive mechanism, which implies the rivalry for optimal structure within the whole system, a situation occurring in a variety of natural systems. [ABSTRACT FROM AUTHOR]

Wedescribe an experiment where spin squeezing occurs spontaneously within a standard Ramsey sequence driving a two-component Bose--Einstein condensate (BEC) of87Rb atoms trapped in an elongated magnetic trap. The squeezing is generated by state-dependent collisional interactions, despite the near-identical scattering lengths of the spin states in 87Rb. In our proof-of-principle experiment, we observe a metrological spin squeezing that reaches 1.3 ± 0.4 dB for 5000 atoms, with a contrast of 90 ± 1%. The method may be applied to realize spin-squeezed BEC sources for atom interferometry without the need for cavities, state-dependent potentials or Feshbach resonances. [ABSTRACT FROM AUTHOR]