Nature Physics

Experimental studies of protein folding processes are frequently hampered by the fact that only low resolution structural data can be obtained with sufficient temporal resolution. Molecular dynamics simulations offer a complementary approach, providing extremely high resolution spatial and temporal data on folding processes. The effectiveness of such simulations is currently hampered by continuing questions regarding the ability of molecular dynamics force fields to reproduce the true potential energy surfaces of proteins, and ongoing difficulties with obtaining sufficient sampling to meaningfully comment on folding mechanisms. We review recent progress in the simulation of three common model systems for protein folding, and discuss how recent advances in technology and theory are allowing protein folding simulations to address their current shortcomings.

Long-lived nuclear spin states could greatly enhance the applicability of hyperpolarized nuclear magnetic resonance. Using singlet states between inequivalent spin pairs has been shown to extend the signal lifetime by more than an order of magnitude compared to the spin lattice relaxation time (T 1), but they have to be prevented from evolving into other states. In the most interesting case the singlet is between chemically equivalent spins, as it can then be inherently an eigenstate. However this presents major challenges in the conversion from bulk magnetization to singlet. In the only case demonstrated so far, a reversible chemical reaction to break symmetry was required. Here we present a pulse sequence technique that interconverts between singlet spin order and bulk magnetization without breaking the symmetry of the spin system. This technique is independent of field strength and is applicable to a broad range of molecules.

Adaptation is the essential process by which an organism becomes better suited to its environment. The benefits of adaptation are well documented, but the cost it incurs remains poorly understood. Here, by analysing a stochastic model of a minimum feedback network underlying many sensory adaptation systems, we show that adaptive processes are necessarily dissipative, and continuous energy consumption is required to stabilize the adapted state. Our study reveals a general relation among energy dissipation rate, adaptation speed and the maximum adaptation accuracy. This energy-speed-accuracy relation is tested in the Escherichia coli chemosensory system, which exhibits near-perfect chemoreceptor adaptation. We identify key requirements for the underlying biochemical network to achieve accurate adaptation with a given energy budget. Moreover, direct measurements confirm the prediction that adaptation slows down as cells gradually de-energize in a nutrient-poor medium without compromising adaptation accuracy. Our work provides a general framework to study cost-performance tradeoffs for cellular regulatory functions and information processing.

Dynamic interplay between the plasma membrane and underlying cytoskeleton is essential for cellular shape change. Spatial organization of actin filaments, whose growth generates membrane deformations during motility 1, phagocytosis 2, endocytosis 3, and cytokinesis 4, is mediated by specific protein-protein interactions that branch, crosslink, and bundle filaments into networks that interact with the membrane. Although membrane curvature has been found to influence binding of proteins with curvature-sensitive domains 5, the direct effect of membrane elasticity on cytoskeletal network organization is not clear. Here we show through in vitro reconstitution and elastic modeling that a lipid bilayer can drive the emergence of bundled actin filament protrusions from branched actin filament networks, thus playing a role normally attributed to actin-binding proteins. Formation of these filopodium-like protrusions with only a minimal set of purified proteins points to an active participation of the membrane in organizing actin filaments at the plasma membrane. In this way, elastic interactions between the membrane and cytoskeleton can cooperate with accessory proteins to drive cellular shape change.

A critical need for enhancing usability and capabilities of microfluidic technologies is the development of standardized, scalable, and versatile control systems1,2. Electronically controlled valves and pumps typically used for dynamic flow regulation, although useful, can limit convenience, scalability, and robustness3-5. This shortcoming has motivated development of device-embedded non-electrical flow-control systems. Existing approaches to regulate operation timing on-chip, however, still require external signals such as timed generation of fluid flow, bubbles, liquid plugs or droplets, or an alteration of chemical compositions or temperature6-16. Here, we describe a strategy to provide device-embedded flow switching and clocking functions. Physical gaps and cavities interconnected by holes are fabricated into a three-layer elastomer structure to form networks of fluidic gates that can spontaneously generate cascading and oscillatory flow output using only a constant flow of Newtonian fluids as the device input. The resulting microfluidic substrate architecture is simple, scalable, and should be applicable to various materials. This flow-powered fluidic gating scheme brings the autonomous signal processing ability of microelectronic circuits to microfluidics where there is the added diversity in current information of having distinct chemical or particulate species and richness in current operation of having chemical reactions and physical interactions.

In physical, biological, technological and social systems, interactions between units give rise to intricate networks. These-typically non-trivial-structures, in turn, critically affect the dynamics and properties of the system. The focus of most current research on complex networks is, still, on global network properties. A caveat of this approach is that the relevance of global properties hinges on the premise that networks are homogeneous, whereas most real-world networks have a markedly modular structure. Here, we report that networks with different functions, including the Internet, metabolic, air transportation and protein interaction networks, have distinct patterns of connections among nodes with different roles, and that, as a consequence, complex networks can be classified into two distinct functional classes on the basis of their link type frequency. Importantly, we demonstrate that these structural features cannot be captured by means of often studied global properties.

During sleep, under anesthesia and in vitro, cortical neurons in sensory, motor, association and executive areas fluctuate between Up and Down states (UDS) characterized by distinct membrane potentials and spike rates [1, 2, 3, 4, 5]. Another phenomenon observed in preparations similar to those that exhibit UDS, such as anesthetized rats [6], brain slices and cultures devoid of sensory input [7], as well as awake monkey cortex [8] is self-organized criticality (SOC). This is characterized by activity “avalanches” whose size distributions obey a power law with critical exponent of about −32 and branching parameter near unity. Recent work has demonstrated SOC in conservative neuronal network models [9, 10], however critical behavior breaks down when biologically realistic non-conservatism is introduced [9]. We here report robust SOC behavior in networks of non-conservative leaky integrate-and-fire neurons with short-term synaptic depression. We show analytically and numerically that these networks typically have 2 stable activity levels corresponding to Up and Down states, that the networks switch spontaneously between them, and that Up states are critical and Down states are subcritical.

Human mobility and activity patterns mediate contagion on many levels, including: spatial spread of infectious diseases, diffusion of rumors, and emergence of consensus. These patterns however are often dominated by specific locations and recurrent flows and poorly modeled by the random diffusive dynamics generally used to study them. Here we develop a theoretical framework to analyze contagion within a network of locations where individuals recall their geographic origins. We find a phase transition between a regime in which the contagion affects a large fraction of the system and one in which only a small fraction is affected. This transition cannot be uncovered by continuous models due to the stochastic features of the contagion process and defines an invasion threshold that depends on mobility parameters, providing guidance for controlling contagion spread by constraining mobility processes. We recover the threshold behavior by analyzing diffusion processes mediated by real human commuting data.

The art of network science lies in our ability to unify our understanding of structure and function. On the one hand predicting the dynamical behavior of the system from its topological structure, and on the other hand elucidating the topological structure from dynamical measurements. Here we present a formalism, which through a set of scaling laws enables us to peek into the dynamical mechanism characterizing the pairwise interactions in a network. We find that these scaling laws, described by three empirically accessible exponents, are an intrinsic property of the system's dynamics, and can thus provide insights into the type of interactions governing them - providing a theory for dynamical inference. Additionally, this formalism is useful for topological inference, translating dynamical measurements into prediction of network links. This prediction is of crucial importance in biology, as currently only a small fraction of the network links has been verified, hindering progress in drug development and mechanistic predictions.

Supercooled liquids and glasses show a range of relaxation times. Nearly all glass-forming liquids show secondary relaxations, high-frequency dynamical modes of structural reconfiguration seemingly distinct from the primary alpha relaxations. We show that accounting for driving-force fluctuations and the diversity of reconfiguring shapes in the random first-order transition theory yields a new dynamical process that shares many of the features ascribed to secondary relaxations. Whereas primary relaxation takes place through activated events involving compact regions, secondary relaxation is governed by more ramified, string-like or percolation-like clusters of particles. These secondary relaxations generate a low free-energy tail on the distribution of activation barriers, which becomes more prominent with increasing temperature. The activation barrier distributions of the two processes merge near the dynamical-crossover temperature Tc, where the secondary process ultimately becomes the dominant mode of structural relaxation. These string-like reconfigurations are seen to smooth the transition at Tc between high-temperature collisional dynamics and activated events.

The shape and differentiation of human mesenchymal stem cells is especially sensitive to the rigidity of their environment; the physical mechanisms involved are unknown. A theoretical model and experiments demonstrate here that the polarization/alignment of stress-fibers within stem cells is a non-monotonic function of matrix rigidity. We treat the cell as an active elastic inclusion in a surrounding matrix whose polarizability, unlike dead matter, depends on the feedback of cellular forces that develop in response to matrix stresses. The theory correctly predicts the monotonic increase of the cellular forces with the matrix rigidity and the alignment of stress-fibers parallel to the long axis of cells. We show that the anisotropy of this alignment depends non-monotonically on matrix rigidity and demonstrate it experimentally by quantifying the orientational distribution of stress-fibers in stem cells. These findings offer a first physical insight for the dependence of stem cell differentiation on tissue elasticity.

Scanning X-ray microscopy focuses radiation to a small spot and probes the sample by raster scanning. It allows information to be obtained from secondary signals such as X-ray fluorescence, which yields an elemental mapping of the sample not available in full-field imaging. The analysis and interpretation from these secondary signals can be considerably enhanced if these data are coupled with structural information from transmission imaging. However, absorption often is negligible and phase contrast has not been easily available. Originally introduced with visible light, Zernike phase contrast(1) is a well-established technique in full-field X-ray microscopes for visualization of weakly absorbing samples(2-7). On the basis of reciprocity, we demonstrate the implementation of Zernike phase contrast in scanning X-ray microscopy, revealing structural detail simultaneously with hard-X-ray trace-element measurements. The method is straightforward to implement without significant influence on the resolution of the fluorescence images and delivers complementary information. We show images of biological specimens that clearly demonstrate the advantage of correlating morphology with elemental information.

Cavity Quantum Electrodynamics (CQED) is an attractive platform for the realization of efficient light-matter quantum interfaces at the single photon level. Such interfaces are key elements for the development of quantum information and communication science due to the need for swapping information between flying and stationary qubits. Here, we report on the first CQED demonstration of collective strong coupling between atomic ions in a solid in the form of an ion Coulomb crystal and an optical field.

Atoms made of a particle and an antiparticle are unstable, usually surviving less than a microsecond. Antihydrogen, made entirely of antiparticles, is believed to be stable, and it is this longevity that holds the promise of precision studies of matter-antimatter symmetry. We have recently demonstrated trapping of antihydrogen atoms by releasing them after a confinement time of 172 ms. A critical question for future studies is: how long can anti-atoms be trapped? Here we report the observation of anti-atom confinement for 1000 s, extending our earlier results by nearly four orders of magnitude. Our calculations indicate that most of the trapped anti-atoms reach the ground state. Further, we report the first measurement of the energy distribution of trapped antihydrogen which, coupled with detailed comparisons with simulations, provides a key tool for the systematic investigation of trapping dynamics. These advances open up a range of experimental possibilities, including precision studies of CPT symmetry and cooling to temperatures where gravitational effects could become apparent.

The discovery of a new boson with a mass of approximately 125 GeV in 2012 at the LHC has heralded a new era in understanding the nature of electroweak symmetry breaking and possibly completing the standard model of particle physics. Since the first observation in decays to gamma gamma, WW, and ZZ boson pairs, an extensive set of measurements of the mass and couplings to W and Z bosons, as well as multiple tests of the spin-parity quantum numbers, have revealed that the properties of the new boson are consistent with those of the long-sought agent responsible for electroweak symmetry breaking. An important open question is whether the new particle also couples to fermions, and in particular to down-type fermions, since the current measurements mainly constrain the couplings to the up-type top quark. Determination of the couplings to down-type fermions requires direct measurement of the corresponding Higgs boson decays, as recently reported by the CMS experiment in the study of Higgs decays to bottom quarks and tau leptons. In this paper we report the combination of these two channels which results, for the first time, in strong evidence for the direct coupling of the 125 GeV Higgs boson to down-type fermions, with an observed significance of 3.8 standard deviations, when 4.4 are expected.

For coherent electron spins, hyperfine coupling to nuclei in the host material can either be a dominant source of unwanted spin decoherence or, if controlled effectively, a resource allowing storage and retrieval of quantum information. To investigate the effect of a controllable nuclear environment on the evolution of confined electron spins, we have fabricated and measured gate-defined double quantum dots with integrated charge sensors made from single-walled carbon nanotubes with a variable concentration of 13C (nuclear spin I=1/2) among the majority zero-nuclear-spin 12C atoms. Spin-sensitive transport in double-dot devices grown using methane with the natural abundance (~ 1%) of 13C is compared with similar devices grown using an enhanced (~99%) concentration of 13C. We observe strong isotope effects in spin-blockaded transport, and from the dependence on external magnetic field, estimate the hyperfine coupling in 13C nanotubes to be on the order of 100 micro-eV, two orders of magnitude larger than anticipated theoretically. 13C-enhanced nanotubes are an interesting new system for spin-based quantum information processing and memory, with nuclei that are strongly coupled to gate-controlled electrons, differ from nuclei in the substrate, are naturally confined to one dimension, lack quadrupolar coupling, and have a readily controllable concentration from less than one to 10^5 per electron.

The Landau-Zener model of a quantum mechanical two-level system driven with a linearly time dependent detuning has served over decades as a textbook paradigm of quantum dynamics. In their seminal work [L. D. Landau, Physik. Z. Sowjet. 2, 46 (1932); C. Zener, Proc. Royal Soc. London 137, 696 (1932)], Landau and Zener derived a non-perturbative prediction for the transition probability between two states, which often serves as a reference point for the analysis of more complex systems. A particularly intriguing question is whether that framework can be extended to describe many-body quantum dynamics. Here we report an experimental and theoretical study of a system of ultracold atoms, offering a direct many-body generalization of the Landau-Zener problem. In a system of pairwise tunnel-coupled 1D Bose liquids we show how tuning the correlations of the 1D gases, the tunnel coupling between the tubes and the inter-tube interactions strongly modify the original Landau-Zener picture. The results are explained using a mean-field description of the inter-tube condensate wave-function, coupled to the low-energy phonons of the 1D Bose liquid.

Topological quantum computation provides an elegant way around decoherence, as one encodes quantum information in a non-local fashion that the environment finds difficult to corrupt. Here we establish that one of the key operations---braiding of non-Abelian anyons---can be implemented in one-dimensional semiconductor wire networks. Previous work [Lutchyn et al., arXiv:1002.4033 and Oreg et al., arXiv:1003.1145] provided a recipe for driving semiconducting wires into a topological phase supporting long-sought particles known as Majorana fermions that can store topologically protected quantum information. Majorana fermions in this setting can be transported, created, and fused by applying locally tunable gates to the wire. More importantly, we show that networks of such wires allow braiding of Majorana fermions and that they exhibit non-Abelian statistics like vortices in a p+ip superconductor. We propose experimental setups that enable the Majorana fusion rules to be probed, along with networks that allow for efficient exchange of arbitrary numbers of Majorana fermions. This work paves a new path forward in topological quantum computation that benefits from physical transparency and experimental realism.

Computing ground states of local Hamiltonians is a fundamental problem in condensed matter physics. We give the first randomized polynomial-time algorithm for finding ground states of gapped one-dimensional Hamiltonians: it outputs an (inverse-polynomial) approximation, expressed as a matrix product state (MPS) of polynomial bond dimension. The algorithm combines many ingredients, including recently discovered structural features of gapped 1D systems, convex programming, insights from classical algorithms for 1D satisfiability, and new techniques for manipulating and bounding the complexity of MPS. Our result provides one of the first major classes of Hamiltonians for which computing ground states is provably tractable despite the exponential nature of the objects involved.

The problem of how complex quantum systems eventually come to rest lies at the heart of statistical mechanics. The maximum entropy principle put forward in 1957 by E. T. Jaynes suggests what quantum states one should expect in equilibrium but does not hint as to how closed quantum many-body systems dynamically equilibrate. A number of theoretical and numerical studies accumulate evidence that under specific conditions quantum many-body models can relax to a situation that locally or with respect to certain observables appears as if the entire system had relaxed to a maximum entropy state. In this work, we report the experimental observation of the non-equilibrium dynamics of a density wave of ultracold bosonic atoms in an optical lattice in the regime of strong correlations. Using an optical superlattice, we are able to prepare the system in a well-known initial state with high fidelity. We then follow the dynamical evolution of the system in terms of quasi-local densities, currents, and coherences. Numerical studies based on the time-dependent density-matrix renormalization group method are in an excellent quantitative agreement with the experimental data. For very long times, all three local observables show a fast relaxation to equilibrium values compatible with those expected for a global maximum entropy state. We find this relaxation of the quasi-local densities and currents to initially follow a power-law with an exponent being significantly larger than for free or hardcore bosons. For intermediate times the system fulfills the promise of being a dynamical quantum simulator, in that the controlled dynamics runs for longer times than present classical algorithms based on matrix product states can efficiently keep track of.

Long range correlations in two-dimensional (2D) systems are significantly altered by disorder potentials. Theory has predicted the existence of disorder induced phenomena such as Anderson localization and the emergence of novel glass and insulating phases as the Bose glass. More recently, it has been shown that disorder breaking the 2D continuous symmetry, such as a one dimensional (1D) modulation, can enhance long range correlations. Experimentally, developments in quantum gases have allowed the observation of a wealth of phenomena induced by the competition between interaction and disorder. However, there are no experiments exploring the effect of symmetry-breaking disorder. Here, we create a 2D vortex lattice at 0.1 K in a superconducting thin film with a well-defined 1D thickness modulation and track the field induced modification using scanning tunneling microscopy. We find that the 1D modulation becomes incommensurate to the vortex lattice and drives an order-disorder transition, behaving as a scale-invariant disorder potential. We show that the transition occurs in two steps and is mediated by the proliferation of topological defects. We find that critical exponents determining the loss of positional and orientational order are far above theoretical expectations for scale-invariant disorder and follow instead the critical behaviour which describes dislocation unbinding melting. Our data show for the first time that randomness disorders a 2D crystal, and evidence enhanced long range correlations in presence of a 1D modulation demonstrating the transformation induced by symmetry breaking disorder in interactions and the critical behaviour of the transition.

Chemical bonding in molecules and solids arises from the overlap of valence electron wave functions, forming extended molecular orbitals and dispersing Bloch states, respectively. Core electrons with high binding energies, on the other hand, are localized to their respective atoms and their wave functions do not overlap significantly. Here we report the observation of band formation and considerable dispersion (up to 60 meV) in the $1s$ core level of the carbon atoms forming graphene, despite the high C $1s$ binding energy of $\approx$ 284 eV. Due to a Young's double slit-like interference effect, a situation arises in which only the bonding or only the anti-bonding states is observed for a given photoemission geometry. Comment: 12 pages, 3 figures, including supplementary material

Superconductivity (SC) in so-called "unconventional superconductors" is nearly always found in the vicinity of another ordered state, such as antiferromagnetism, charge density wave (CDW), or stripe order. This suggests a fundamental connection between SC and fluctuations in some other order parameter. To better understand this connection, we used high-pressure x-ray scattering to directly study the CDW order in the layered dichalcogenide TiSe2, which was previously shown to exhibit SC when the CDW is suppressed by pressure [1] or intercalation of Cu atoms [2]. We succeeded in suppressing the CDW fully to zero temperature, establishing for the first time the existence of a quantum critical point (QCP) at Pc = 5.1 +/- 0.2 GPa, which is more than 1 GPa beyond the end of the SC region. Unexpectedly, at P = 3 GPa we observed a reentrant, weakly first order, incommensurate phase, indicating the presence of a Lifshitz tricritical point somewhere above the superconducting dome. Our study suggests that SC in TiSe2 may not be connected to the QCP itself, but to the formation of CDW domain walls.

Iron-based high temperature superconductivity develops when the `parent' antiferromagnetic/orthorhombic phase is suppressed, typically by introduction of dopant atoms. But their impact on atomic-scale electronic structure, while in theory quite complex, is unknown experimentally. What is known is that a strong transport anisotropy with its resistivity maximum along the crystal b-axis, develops with increasing concentration of dopant atoms; this `nematicity' vanishes when the `parent' phase disappears near the maximum superconducting Tc. The interplay between the electronic structure surrounding each dopant atom, quasiparticle scattering therefrom, and the transport nematicity has therefore become a pivotal focus of research into these materials. Here, by directly visualizing the atomic-scale electronic structure, we show that substituting Co for Fe atoms in underdoped Ca(Fe1-xCox)2As2 generates a dense population of identical anisotropic impurity states. Each is ~8 Fe-Fe unit cells in length, and all are distributed randomly but aligned with the antiferromagnetic a-axis. By imaging their surrounding interference patterns, we further demonstrate that these impurity states scatter quasiparticles in a highly anisotropic manner, with the maximum scattering rate concentrated along the b-axis. These data provide direct support for the recent proposals that it is primarily anisotropic scattering by dopant-induced impurity states that generates the transport nematicity; they also yield simple explanations for the enhancement of the nematicity proportional to the dopant density and for the occurrence of the highest resistivity along the b-axis.

The melting temperature ($T_m$) of a solid is generally determined by the pressure applied to it, or indirectly by its density ($n$) through the equation of state. This remains true even for helium solids\cite{wilk:67}, where quantum effects often lead to unusual properties\cite{ekim:04}. In this letter we present experimental evidence to show that for a two dimensional (2D) solid formed by electrons in a semiconductor sample under a strong perpendicular magnetic field\cite{shay:97} ($B$), the $T_m$ is not controlled by $n$, but effectively by the \textit{quantum correlation} between the electrons through the Landau level filling factor $\nu$=$nh/eB$. Such melting behavior, different from that of all other known solids (including a classical 2D electron solid at zero magnetic field\cite{grim:79}), attests to the quantum nature of the magnetic field induced electron solid. Moreover, we found the $T_m$ to increase with the strength of the sample-dependent disorder that pins the electron solid.