In interacting dynamical systems, specific local interaction rules for system components give rise to diverse and complex global dynamics. Long dynamical cycles are a key feature of many natural interacting systems, especially in biology. Examples of dynamical cycles range from circadian rhythms regulating sleep to cell cycles regulating reproductive behavior. Despite the crucial role of cycles in nature, the properties of network structure that give rise to cycles still need to be better understood. Here, we use a Boolean interaction network model to study the relationships between network structure and cyclic dynamics. We identify particular structural motifs that support cycles, and other motifs that suppress them. More generally, we show that the presence of in the interaction network enhances cyclic behavior. In simulating an artificial evolutionary process, we find that motifs that break reflection symmetry are discarded. We further show that dynamical reflection symmetries are over-represented in Boolean models of natural biological systems. Altogether, our results demonstrate a link between symmetry and functionality for interacting dynamical systems, and they provide evidence for symmetry's causal role in evolving dynamical functionality.

Thermodynamic selection is an indirect competition between agents feeding on the same energy resource and obeying the laws of thermodynamics. We examine scenarios of this selection, where the agent is modeled as a heat-engine coupled to two thermal baths and extracting work from the high-temperature bath. The agents can apply different work-extracting, game-theoretical strategies, e.g. the maximum power or the maximum efficiency. They can also have a fixed structure or be adaptive. Depending on whether the resource (i.e. the high-temperature bath) is infinite or finite, the fitness of the agent relates to the work-power or the total extracted work. These two selection scenarios lead to increasing or decreasing efficiencies of the work-extraction, respectively. The scenarios are illustrated via plant competition for sunlight, and the competition between different ATP production pathways. We also show that certain general concepts of game-theory and ecology-the prisoner's dilemma and the maximal power principle-emerge from the thermodynamics of competing agents. We emphasize the role of adaptation in developing efficient work-extraction mechanisms.

The renormalization group (RG) is a class of theoretical techniques used to explain the collective physics of interacting, many-body systems. It has been suggested that the RG formalism may be useful in finding and interpreting emergent low-dimensional structure in complex systems outside of the traditional physics context, such as in biology or computer science. In such contexts, one common dimensionality-reduction framework already in use is information bottleneck (IB), in which the goal is to compress an "input" signal while maximizing its mutual information with some stochastic "relevance" variable . IB has been applied in the vertebrate and invertebrate processing systems to characterize optimal encoding of the future motion of the external world. Other recent work has shown that the RG scheme for the dimer model could be "discovered" by a neural network attempting to solve an IB-like problem. This manuscript explores whether IB and any existing formulation of RG are formally equivalent. A class of soft-cutoff non-perturbative RG techniques are defined by families of non-deterministic coarsening maps, and hence can be formally mapped onto IB, and vice versa. For concreteness, this discussion is limited entirely to Gaussian statistics (GIB), for which IB has exact, closed-form solutions. Under this constraint, GIB has a semigroup structure, in which successive transformations remain IB-optimal. Further, the RG cutoff scheme associated with GIB can be identified. Our results suggest that IB can be used to a notion of "large scale" structure, such as biological function, on an RG procedure.

We introduce a design principle of metasurfaces that can form any desired distribution of magnetic field for high-efficiency wireless power transfer centered at 200 kHz, which can be used to efficiently charge implanted medical devices. This metasurface can improve the power transfer efficiency for both single-user and multi-user cases by over tenfold compared to those without the metasurface. Our design enables a robust field distribution to the positions of the transmitting and receiving coils, as well as the geometric distortions of the metasurface itself, demonstrating feasibilities as a wearable device. With our design, the field distribution and subsequent power division among the multiple users can be readily controlled from equal distribution to any selective user(s). When incorporating a three-dimensional unit cell of the metasurface, we theoretically demonstrate an omnidirectional control of the field orientation to achieve a high-efficiency wireless power transfer for multiple users.

In some scenarios ("anti-coordination games"), individuals are better off choosing different actions than their neighbors while in other scenarios ("coordination games"), it is beneficial for individuals to choose the same strategy as their neighbors. Despite having different incentives and resulting population dynamics, it is largely unknown which collective outcome, anti-coordination or coordination, is easier to achieve. To address this issue, we focus on the distributed graph coloring problem on bipartite graphs. We show that with only two strategies, anti-coordination games (2-colorings) and coordination games (uniform colorings) are dual problems that are equally difficult to solve. To prove this, we construct an isomorphism between the Markov chains arising from the corresponding anti-coordination and coordination games under certain specific individual stochastic decision-making rules. Our results provide novel insights into solving collective action problems on networks.

The ability of cells to move through small spaces depends on the mechanical properties of the cellular cytoskeleton and on nuclear deformability. In mammalian cells, the cytoskeleton is composed of three interacting, semi-flexible polymer networks: actin, microtubules, and intermediate filaments (IF). Recent experiments of mouse embryonic fibroblasts with and without vimentin have shown that the IF vimentin plays a role in confined cell motility. Here, we develop a minimal model of a cell moving through a microchannel that incorporates explicit effects of actin and vimentin and implicit effects of microtubules. Specifically, the model consists of a cell with an actomyosin cortex and a deformable cell nucleus and mechanical linkages between the two. By decreasing the amount of vimentin, we find that the cell speed increases for vimentin-null cells compared to cells with vimentin. The loss of vimentin increases nuclear deformation and alters nuclear positioning in the cell. Assuming nuclear positioning is a read-out for cell polarity, we propose a new polarity mechanism which couples cell directional motion with cytoskeletal strength and nuclear positioning and captures the abnormally persistent motion of vimentin-null cells, as observed in experiments. The enhanced persistence indicates that the vimentin-null cells are more controlled by the confinement and so less autonomous, relying more heavily on external cues than their wild-type counterparts. Our modeling results present a quantitative interpretation for recent experiments and have implications for understanding the role of vimentin in the epithelial-mesenchymal transition.

The ability to create linear systems that manifest broadband nonreciprocal wave propagation would provide for exquisite control over acoustic signals for electronic filtering in communication and noise control. Acoustic nonreciprocity has predominately been achieved by approaches that introduce nonlinear interaction, mean-flow biasing, smart skins, and spatio-temporal parametric modulation into the system. Each approach suffers from at least one of the following drawbacks: the introduction of modulation tones, narrow band filtering, and the interruption of mean flow in fluid acoustics. We now show that an acoustic media that is non-local and active provides a new means to break reciprocity in a linear fashion without these deleterious effects. We realize this media using a distributed network of interlaced subwavelength sensor-actuator pairs with unidirectional signal transport. We exploit this new design space to create a stable metamaterial with non-even dispersion relations and electronically tunable nonreciprocal behavior over a broad range of frequencies.

Floquet engineering or coherent time periodic driving of quantum systems has been successfully used to synthesize Hamiltonians with novel properties. In ultracold atomic systems, this has led to experimental realizations of artificial gauge fields, topological band structures, and observation of dynamical localization, to name just a few. Here we present a Floquet-based framework to stroboscopically engineer Hamiltonians with spatial features and periodicity below the diffraction limit of light used to create them, by time-averaging over various configurations of a 1D optical Kronig-Penney (KP) lattice. The KP potential is a lattice of narrow subwavelength barriers spaced by half the optical wavelength and arises from the nonlinear optical response of the atomic dark state. Stroboscopic control over the strength and position of this lattice requires time-dependent adiabatic manipulation of the dark-state spin composition. We investigate adiabaticity requirements, and shape our time-dependent light fields to respect these requirements. We apply this framework to show that a -spaced lattice can be synthesized using realistic experimental parameters. As an example, we discuss mechanisms that limit lifetimes in these lattices, explore candidate systems with their limitations, and study adiabatic loading into the ground band of these lattices.

The invariant cell initiation mass measured in bacterial growth experiments has been interpreted as a minimal unit of cellular replication. Here we argue that the existence of such minimal units induces a coupling between the rates of stochastic cell division and death. To probe this coupling we tracked live and dead cells in populations treated with a ribosome-targeting antibiotic. We find that the growth exponent from macroscopic cell growth or decay measurements can be represented as the difference of microscopic first-order cell division and death rates. The boundary between cell growth and decay, at which the number of live cells remains constant over time, occurs at the minimal inhibitory concentration (MIC) of the antibiotic. This state appears macroscopically static but is microscopically dynamic: division and death rates exactly cancel at MIC but each is remarkably high, reaching 60% of the antibiotic-free division rate. A stochastic model of cells as collections of minimal replicating units we term 'widgets' reproduces both steady-state and transient features of our experiments. Sub-cellular fluctuations of widget numbers stochastically drive each new daughter cell to one of two alternate fates, division or death. First-order division or death rates emerge as eigenvalues of a stationary Markov process, and can be expressed in terms of the widget's molecular properties. High division and death rates at MIC arise due to low mean and high relative fluctuations of widget number. Isolating cells at the threshold of irreversible death might allow molecular characterization of this minimal replication unit.

Understanding how public cooperation emerges and is maintained is a topic of broad interest, with increasing contributions coming from a synergistic combination of evolutionary game theory and statistical physics. The comprehensive study by Battiston (2017 , in press) improves our understanding of the role of multiplexity in cooperation, revealing that a significant edge overlap across network layers along with benign conditions for cooperation in at least one of the layers is needed to facilitate the emergence of cooperation in the multiplex.

We describe a Fourier transform spectroscopy technique for directly measuring band structures, and apply it to a spin-1 spin-orbit coupled Bose-Einstein condensate. In our technique, we suddenly change the Hamiltonian of the system by adding a spin-orbit coupling interaction and measure populations in different spin states during the subsequent unitary evolution. We then reconstruct the spin and momentum resolved spectrum from the peak frequencies of the Fourier transformed populations. In addition, by periodically modulating the Hamiltonian, we tune the spin-orbit coupling strength and use our spectroscopy technique to probe the resulting dispersion relation. The frequency resolution of our method is limited only by the coherent evolution timescale of the Hamiltonian and can otherwise be applied to any system, for example, to measure the band structure of atoms in optical lattice potentials.

is the causative agent of one of the most common sexually transmitted diseases, gonorrhea. Over the past two decades there has been an alarming increase of reported gonorrhea cases where the bacteria were resistant to the most commonly used antibiotics thus prompting for alternative antimicrobial treatment strategies. The crucial step in this and many other bacterial infections is the formation of microcolonies, agglomerates consisting of up to several thousands of cells. The attachment and motility of cells on solid substrates as well as the cell-cell interactions are primarily mediated by type IV pili, long polymeric filaments protruding from the surface of cells. While the crucial role of pili in the assembly of microcolonies has been well recognized, the exact mechanisms of how they govern the formation and dynamics of microcolonies are still poorly understood. Here, we present a computational model of individual cells with explicit pili dynamics, force generation and pili-pili interactions. We employ the model to study a wide range of biological processes, such as the motility of individual cells on a surface, the heterogeneous cell motility within the large cell aggregates, and the merging dynamics and the self-assembly of microcolonies. The results of numerical simulations highlight the central role of pili generated forces in the formation of bacterial colonies and are in agreement with the available experimental observations. The model can quantify the behavior of multicellular bacterial colonies on biologically relevant temporal and spatial scales and can be easily adjusted to include the geometry and pili characteristics of various bacterial species. Ultimately, the combination of the microbiological experimental approach with the model of bacterial colonies might provide new qualitative and quantitative insights on the development of bacterial infections and thus pave the way to new antimicrobial treatments.

We describe anoveltechniqueforcreatinganartificialmagneticfieldforultracoldatomsusinga periodicallypulsedpairofcounterpropagatingRamanlasersthatdrivetransitionsbetween a pair of internal atomic spin states: a multi-frequency coupling term. In conjunction with a magnetic field gradient, this dynamically generates a rectangular lattice with a non-staggered magnetic flux. For a wide range of parameters, the resulting Bloch bands have non-trivial topology, reminiscent of Landau levels, as quantified by their Chern numbers.

We propose a method to probe the local density of states (LDOS) of atomic systems that provides both spatial and energy resolution. The method combines atomic and tunneling techniques to supply a simple, yet quantitative and operational, definition of the LDOS for both interacting and non-interacting systems: It is the rate at which particles can be siphoned from the system of interest by a narrow energy band of non-interacting states contacted locally to the many-body system of interest. Ultracold atoms in optical lattices are a natural platform for implementing this broad concept to visualize the energy and spatial dependence of the atom density in interacting, inhomogeneous lattices. This includes models of strongly correlated condensed matter systems, as well as ones with non-trivial topologies.

A major application for atomic ensembles consists of a quantum memory for light, in which an optical state can be reversibly converted to a collective atomic excitation on demand. There exists a well-known fundamental bound on the storage error, when the ensemble is describable by a continuous medium governed by the Maxwell-Bloch equations. However, these equations are semi-phenomenological, as they treat emission of the atoms into other directions other than the mode of interest as being independent. On the other hand, in systems such as dense, ordered atomic arrays, atoms interact with each other strongly and spatial interference of the emitted light might be exploited to suppress emission into unwanted directions, thereby enabling improved error bounds. Here, we develop a general formalism that fully accounts for spatial interference, and which finds the maximum storage efficiency for a single photon with known spatial input mode into a collection of atoms with discrete, known positions. As an example, we apply this technique to study a finite two-dimensional square array of atoms. We show that such a system enables a storage error that scales with atom number like , and that, remarkably, an array of just 4 × 4 atoms in principle allows for an error of less than 1%, which is comparable to a disordered ensemble with an optical depth of around 600.

The generation and control of neutron orbital angular momentum (OAM) states and spin correlated OAM (spin-orbit) states provides a powerful probe of materials with unique penetrating abilities and magnetic sensitivity. We describe techniques to prepare and characterize neutron spin-orbit states, and provide a quantitative comparison to known procedures. The proposed detection method directly measures the correlations of spin state and transverse momentum, and overcomes the major challenges associated with neutrons, which are low flux and small spatial coherence length. Our preparation techniques, utilizing special geometries of magnetic fields, are based on coherent averaging and spatial control methods borrowed from nuclear magnetic resonance. The described procedures may be extended to other probes such as electrons and electromagnetic waves.

Inelastic neutron scattering is utilized to directly measure inter-nanoparticle spin waves, or magnons, which arise from the magnetic coupling between 8.4 nm ferrite nanoparticles that are self-assembled into a close-packed lattice, yet are physically separated by oleic acid surfactant. The resulting dispersion curve yields a physically-reasonable, non-negative energy gap only when the effective is reduced by the inter-particle spacing. This renormalization strongly indicates that the dispersion is a collective excitation between the nanoparticles, rather than originating from within individual nanoparticles. Additionally, the observed magnons are dispersive, respond to an applied magnetic field, and display the expected temperature-dependent Bose population factor. The experimental results are well explained by a limited parameter model which treats the three-dimensional ordered, magnetic nanoparticles as dipolar-coupled superspins.

The creation of particle-antiparticle pairs from vacuum by a large electric field is at the core of quantum electrodynamics. Despite the wide acceptance that this phenomenon occurs naturally when electric field strengths exceed ≈ 10 Vm, it has yet to be experimentally observed due to the limitations imposed by producing electric fields at this scale. The high degree of experimental control present in ultracold atomic systems allow experimentalists to create laboratory analogs to high-field phenomena. Here we emulated massive relativistic particles subject to large electric field strengths, thereby quantum-simulated particle-antiparticle pair creation, and experimentally explored particle creation from 'the Dirac vacuum'. Data collected from our analog system spans the full parameter regime from low applied field (negligible pair creation) below the Sauter-Schwinger limit, to high field (maximum rate of pair creation) far in excess of the Sauter-Schwinger limit. In our experiment, we perform direct measurements on an analog atomic system and show that this high-field phenomenon is well-characterized by Landau-Zener tunneling, well known in the atomic physics context, and we find full quantitative agreement with theory with no adjustable parameters.

Physical systems with non-trivial topological order find direct applications in metrology (Klitzing 1980 494-7) and promise future applications in quantum computing (Freedman 2001 183-204; Kitaev 2003 2-30). The quantum Hall effect derives from transverse conductance, quantized to unprecedented precision in accordance with the system's topology (Laughlin 1981 B 5632-33). At magnetic fields beyond the reach of current condensed matter experiment, around 10 T, this conductance remains precisely quantized with values based on the topological order (Thouless 1982 405-8). Hitherto, quantized conductance has only been measured in extended 2D systems. Here, we experimentally studied narrow 2D ribbons, just 3 or 5 sites wide along one direction, using ultracold neutral atoms where such large magnetic fields can be engineered (Jaksch and Zoller 2003 56; Miyake 2013 185302; Aidelsburger 2013 185301; Celi 2014 043001; Stuhl 2015 1514; Mancini 2015 1510; An 2017 ). We microscopically imaged the transverse spatial motion underlying the quantized Hall effect. Our measurements identify the topological Chern numbers with typical uncertainty of 5%, and show that although band topology is only properly defined in infinite systems, its signatures are striking even in nearly vanishingly thin systems.

For the past two and a half decades, anomalous heating of trapped ions from nearby electrode surfaces has continued to demonstrate unexpected results. Caused by electric-field noise, this heating of the ions' motional modes remains an obstacle for scalable quantum computation with trapped ions. One of the anomalous features of this electric-field noise is the reported nonmonotonic behavior in the heating rate when a trap is incrementally cleaned by ion bombardment. Motivated by this result, the present work reports on a surface analysis of a sample ion-trap electrode treated similarly with incremental doses of Ar ion bombardment. Kelvin probe force microscopy and x-ray photoelectron spectroscopy were used to investigate how the work functions on the electrode surface vary depending on the residual contaminant coverage between each treatment. It is shown that the as-fabricated Au electrode is covered with a hydrocarbon film that is modified after the first treatment, resulting in work functions and core-level binding energies that resemble that of atomic-like carbon on Au. Changes in the spatial distribution of work functions with each treatment, combined with a suggested phenomenological coverage and surface-potential roughness dependence to the heating, appear to be related to the nonmonotonic behavior previously reported.

We present a general theory for laser-free entangling gates with trapped-ion hyperfine qubits, using either static or oscillating magnetic-field gradients combined with a pair of uniform microwave fields symmetrically detuned about the qubit frequency. By transforming into a 'bichromatic' interaction picture, we show that either or geometric phase gates can be performed. The gate basis is determined by selecting the microwave detuning. The driving parameters can be tuned to provide intrinsic dynamical decoupling from qubit frequency fluctuations. The gates can be implemented in a novel manner which eases experimental constraints. We present numerical simulations of gate fidelities assuming realistic parameters.