Max Planck Institute for the Physics of Complex Systems

An information theoretic measure is derived that quantifies the statistical coherence between systems evolving in time. The standard time delayed mutual information fails to distinguish information that is actually exchanged from shared information due to common history and input signals. In our new approach, these influences are excluded by appropriate conditioning of transition probabilities. The resulting transfer entropy is able to distinguish effectively driving and responding elements and to detect asymmetry in the interaction of subsystems.

In sexually reproducing organisms, embryos specify germ cells, which ultimately generate sperm and eggs. In Caenorhabditis elegans, the first germ cell is established when RNA and protein-rich P granules localize to the posterior of the one-cell embryo. Localization of P granules and their physical nature remain poorly understood. Here we show that P granules exhibit liquid-like behaviors, including fusion, dripping, and wetting, which we used to estimate their viscosity and surface tension. As with other liquids, P granules rapidly dissolved and condensed. Localization occurred by a biased increase in P granule condensation at the posterior. This process reflects a classic phase transition, in which polarity proteins vary the condensation point across the cell. Such phase transitions may represent a fundamental physicochemical mechanism for structuring the cytoplasm.

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary to understand the consequences of liquid-like states for biological functions.

Modern nanotechnology allows one to scale down various important devices (sensors, chips, fibers, etc.) and thus opens up new horizons for their applications. The efficiency of most of them is based on fundamental physical phenomena, such as transport of wave excitations and resonances. Short propagation distances make phase-coherent processes of waves important. Often the scattering of waves involves propagation along different paths and, as a consequence, results in interference phenomena, where constructive interference corresponds to resonant enhancement and destructive interference to resonant suppression of the transmission. Recently, a variety of experimental and theoretical work has revealed such patterns in different physical settings. The purpose of this review is to relate resonant scattering to Fano resonances, known from atomic physics. One of the main features of the Fano resonance is its asymmetric line profile. The asymmetry originates from a close coexistence of resonant transmission and resonant reflection and can be reduced to the interaction of a discrete (localized) state with a continuum of propagation modes. The basic concepts of Fano resonances are introduced, their geometrical and/or dynamical origin are explained, and theoretical and experimental studies of light propagation in photonic devices, charge transport through quantum dots, plasmon scattering in Josephson-junction networks, and matter-wave scattering in ultracold atom systems, among others are reviewed.

Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species 1–4 . To address this issue, the international Genome 10K (G10K) consortium 5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

The paradigm of deterministic chaos has influenced thinking in many fields of science. Chaotic systems show rich and surprising mathematical structures. In the applied sciences, deterministic chaos provides a striking explanation for irregular behaviour and anomalies in systems which do not seem to be inherently stochastic. The most direct link between chaos theory and the real world is the analysis of time series from real systems in terms of nonlinear dynamics. Experimental technique and data analysis have seen such dramatic progress that, by now, most fundamental properties of nonlinear dynamical systems have been observed in the laboratory. Great efforts are being made to exploit ideas from chaos theory wherever the data displays more structure than can be captured by traditional methods. Problems of this kind are typical in biology and physiology but also in geophysics, economics, and many other sciences.

We present a full-potential band-structure scheme based on the linear combination of overlapping nonorthogonal orbitals. The crystal potential and density are represented as a lattice sum of local overlapping nonspherical contributions. The decomposition of the exchange and correlation potential into local parts is done using a technique of partitioning of unity resulting in local shape functions, which add exactly to unity in the whole crystal and which are very easily treated numerically. The method is all-electron, which means that core relaxation is properly taken into account. Nevertheless, the eigenvalue problem is reduced to the dimension of a minimum valence orbital basis only. Calculations on sp and transition metals give results comparable to other full-potential methods. The calculations on the diamond lattice demonstrate the applicability of our approach to open structures. The consequent local description of all real-space functions allows the treatment of substitutional disordered materials.

Although fluorescence microscopy provides a crucial window into the physiology of living specimens, many biological processes are too fragile, are too small, or occur too rapidly to see clearly with existing tools. We crafted ultrathin light sheets from two-dimensional optical lattices that allowed us to image three-dimensional (3D) dynamics for hundreds of volumes, often at subsecond intervals, at the diffraction limit and beyond. We applied this to systems spanning four orders of magnitude in space and time, including the diffusion of single transcription factor molecules in stem cell spheroids, the dynamic instability of mitotic microtubules, the immunological synapse, neutrophil motility in a 3D matrix, and embryogenesis in Caenorhabditis elegans and Drosophila melanogaster. The results provide a visceral reminder of the beauty and the complexity of living systems.

We describe the implementation of methods of nonlinear time series analysis which are based on the paradigm of deterministic chaos. A variety of algorithms for data representation, prediction, noise reduction, dimension and Lyapunov estimation, and nonlinearity testing are discussed with particular emphasis on issues of implementation and choice of parameters. Computer programs that implement the resulting strategies are publicly available as the TISEAN software package. The use of each algorithm will be illustrated with a typical application. As to the theoretical background, we will essentially give pointers to the literature. (c) 1999 American Institute of Physics.

The search for highly efficient and low-cost catalysts is one of the main driving forces in catalytic chemistry. Current strategies for the catalyst design focus on increasing the number and activity of local catalytic sites, such as the edge sites of molybdenum disulfides in the hydrogen evolution reaction (HER). Here, the study proposes and demonstrates a different principle that goes beyond local site optimization by utilizing topological electronic states to spur catalytic activity. For HER, excellent catalysts have been found among the transition-metal monopnictides-NbP, TaP, NbAs, and TaAs-which are recently discovered to be topological Weyl semimetals. Here the study shows that the combination of robust topological surface states and large room temperature carrier mobility, both of which originate from bulk Dirac bands of the Weyl semimetal, is a recipe for high activity HER catalysts. This approach has the potential to go beyond graphene based composite photocatalysts where graphene simply provides a high mobility medium without any active catalytic sites that have been found in these topological materials. Thus, the work provides a guiding principle for the discovery of novel catalysts from the emerging field of topological materials.

The form of energy termed heat that typically derives from lattice vibrations, i.e., phonons, is usually considered as waste energy and, moreover, deleterious to information processing. However, in this Colloquium, an attempt is made to rebut this common view: By use of tailored models it is demonstrated that phonons can be manipulated similarly to electrons and photons, thus enabling controlled heat transport. Moreover, it is explained that phonons can be put to beneficial use to carry and process information. In the first part ways are presented to control heat transport and to process information for physical systems which are driven by a temperature bias. In particular, a toolkit of familiar electronic analogs for use of phononics is put forward, i.e., phononic devices are described which act as thermal diodes, thermal transistors, thermal logic gates, and thermal memories. These concepts are then put to work to transport, control, and rectify heat in physically realistic nanosystems by devising practical designs of hybrid nanostructures that permit the operation of functional phononic devices; the first experimental realizations are also reported. Next, richer possibilities to manipulate heat flow by use of time-varying thermal bath temperatures or various other external fields are discussed. These give rise to many intriguing phononic nonequilibrium phenomena such as, for example, the directed shuttling of heat, geometrical phase-induced heat pumping, or the phonon Hall effect, which may all find their way into operation with electronic analogs.

Weyl semimetals (WSMs) are topological quantum states wherein the electronic bands disperse linearly around pairs of nodes with fixed chirality, the Weyl points. In WSMs, nonorthogonal electric and magnetic fields induce an exotic phenomenon known as the chiral anomaly, resulting in an unconventional negative longitudinal magnetoresistance, the chiral-magnetic effect. However, it remains an open question to which extent this effect survives when chirality is not well-defined. Here, we establish the detailed Fermi-surface topology of the recently identified WSM TaP via combined angle-resolved quantum-oscillation spectra and band-structure calculations. The Fermi surface forms banana-shaped electron and hole pockets surrounding pairs of Weyl points. Although this means that chirality is ill-defined in TaP, we observe a large negative longitudinal magnetoresistance. We show that the magnetoresistance can be affected by a magnetic field-induced inhomogeneous current distribution inside the sample.

For most intracellular structures with larger than molecular dimensions, little is known about the connection between underlying molecular activities and higher order organization such as size and shape. Here, we show that both the size and shape of the amphibian oocyte nucleolus ultimately arise because nucleoli behave as liquid-like droplets of RNA and protein, exhibiting characteristic viscous fluid dynamics even on timescales of < 1 min. We use these dynamics to determine an apparent nucleolar viscosity, and we show that this viscosity is ATP-dependent, suggesting a role for active processes in fluidizing internal contents. Nucleolar surface tension and fluidity cause their restructuring into spherical droplets upon imposed mechanical deformations. Nucleoli exhibit a broad distribution of sizes with a characteristic power law, which we show is a consequence of spontaneous coalescence events. These results have implications for the function of nucleoli in ribosome subunit processing and provide a physical link between activity within a macromolecular assembly and its physical properties on larger length scales.

Nonlinear classical Hamiltonian lattices exhibit generic solutions in the form of discrete breathers. These solutions are time-periodic and (typically exponentially) localized in space. The lattices exhibit discrete translational symmetry. Discrete breathers are not confined to certain lattice dimensions. Necessary ingredients for their occurrence are the existence of upper bounds on the phonon spectrum (of small fluctuations around the groundstate) of the system as well as the nonlinearity in the differential equations. We will present existence proofs, formulate necessary existence conditions, and discuss structural stability of discrete breathers. The following results will be also discussed: the creation of breathers through tangent bifurcation of band edge plane waves; dynamical stability; details of the spatial decay; numerical methods of obtaining breathers; interaction of breathers with phonons and electrons; movability; influence of the lattice dimension on discrete breather properties; quantum lattices — quantum breathers. Finally we will formulate a new conceptual approach capable of predicting whether discrete breathers exist for a given system or not, without actually solving for the breather. We discuss potential applications in lattice dynamics of solids (especially molecular crystals), selective bond excitations in large molecules, dynamical properties of coupled arrays of Josephson junctions, and localization of electromagnetic waves in photonic crystals with nonlinear response.

The rare-earth monopnictide LaBi exhibits exotic magneto-transport properties, including an extremely large and anisotropic magnetoresistance. Experimental evidence for topological surface states is still missing although band inversions have been postulated to induce a topological phase in LaBi. In this work, we have revealed the existence of surface states of LaBi through the observation of three Dirac cones: two coexist at the corners and one appears at the centre of the Brillouin zone, by employing angle-resolved photoemission spectroscopy in conjunction with ab initio calculations. The odd number of surface Dirac cones is a direct consequence of the odd number of band inversions in the bulk band structure, thereby proving that LaBi is a topological, compensated semimetal, which is equivalent to a time-reversal invariant topological insulator. Our findings provide insight into the topological surface states of LaBi's semi-metallicity and related magneto-transport properties.

Dynamics of quantum many-body systems is one of the most complex problems in physics since it involves the time evolution of a large number of particles that interact with each other under the influence of external forces. With ultracold atoms in optical atomic lattices it can be done in a controlled environment by applying a periodic force. This Colloquium covers the experimental and theoretical developments in this exciting field of physics.

An important and incompletely answered question is whether a closed quantum system of many interacting particles can be localized by disorder. The time evolution of simple (unentangled) initial states is studied numerically for a system of interacting spinless fermions in one dimension described by the random-field XXZ Hamiltonian. Interactions induce a dramatic change in the propagation of entanglement and a smaller change in the propagation of particles. For even weak interactions, when the system is thought to be in a many-body localized phase, entanglement shows neither localized nor diffusive behavior but grows without limit in an infinite system: interactions act as a singular perturbation on the localized state with no interactions. The significance for proposed atomic experiments is that local measurements will show a large but nonthermal entropy in the many-body localized state. This entropy develops slowly (approximately logarithmically) over a diverging time scale as in glassy systems.

Clean and interacting periodically driven systems are believed to exhibit a single, trivial "infinite-temperature" Floquet-ergodic phase. In contrast, here we show that their disordered Floquet many-body localized counterparts can exhibit distinct ordered phases delineated by sharp transitions. Some of these are analogs of equilibrium states with broken symmetries and topological order, while others-genuinely new to the Floquet problem-are characterized by order and nontrivial periodic dynamics. We illustrate these ideas in driven spin chains with Ising symmetry.

Floquet engineering, the control of quantum systems using periodic driving, is an old concept in condensed matter physics dating back to ideas such as the inverse Faraday effect. However, there is a renewed interest in this concept owing to ( a) the rapid developments in laser and ultrafast spectroscopy techniques, ( b) discovery and understanding of various “quantum materials” hosting interesting exotic quantum properties, and ( c) communication with different areas of physics such as artificial matter and nonequilibrium quantum statistical physics. Here, starting from a nontechnical introduction with emphasis on the Floquet picture and effective Hamiltonians, we review the recent applications of Floquet engineering in ultrafast, nonlinear phenomena in the solid state. In particular, Floquet topological states and their application to ultrafast spintronics and strongly correlated electron systems are overviewed.

Quantum spin liquids (QSLs) are topological states of matter exhibiting remarkable properties such as the capacity to protect quantum information from decoherence. Whereas their featureless ground states have precluded their straightforward experimental identification, excited states are more revealing and particularly interesting owing to the emergence of fundamentally new excitations such as Majorana fermions. Ideal probes of these excitations are inelastic neutron scattering experiments. These we report here for a ruthenium-based material, alpha-RuCl3, continuing a major search (so far concentrated on iridium materials) for realizations of the celebrated Kitaev honeycomb topological QSL. Our measurements confirm the requisite strong spin-orbit coupling and low-temperature magnetic order matching predictions proximate to the QSL. We find stacking faults, inherent to the highly two-dimensional nature of the material, resolve an outstanding puzzle. Crucially, dynamical response measurements above interlayer energy scales are naturally accounted for in terms of deconfinement physics expected for QSLs. Comparing these with recent dynamical calculations involving gauge flux excitations and Majorana fermions of the pure Kitaev model, we propose the excitation spectrum of alpha-RuCl3 as a prime candidate for fractionalized Kitaev physics.