Problems Affecting Labor

Much experimental work has been devoted in comparing the folding behavior of proteins sharing the same fold but different sequence. The recent design of proteins displaying very high sequence identities but different 3D structure allows the unique opportunity to address the protein-folding problem from a complementary perspective. Here we explored by ℙ-value analysis the pathways of folding of three different heteromorphic pairs, displaying increasingly high-sequence identity (namely, 30%, 77%, and 88%), but different structures called G A (a 3-α helix fold) and G B (an α/β fold). The analysis, based on 132 site-directed mutants, is fully consistent with the idea that protein topology is committed very early along the pathway of folding. Furthermore, data reveals that when folding approaches a perfect two-state scenario, as in the case of the G A domains, the structural features of the transition state appear very robust to changes in sequence composition. On the other hand, when folding is more complex and multistate, as for the G Bs, there are alternative nuclei or accessible pathways that can be alternatively stabilized by altering the primary structure. The implications of our results in the light of previous work on the folding of different members belonging to the same protein family are discussed

Low-temperature nucleation in a kinetic Ising model under different stochastic dynamics with local energy barriers

Using both analytical and simulational methods, we study low-temperature nucleation rates in kinetic Ising lattice-gas models that evolve under two different Arrhenius dynamics that interpose between the Ising states a transition state representing a local energy barrier. The two dynamics are the transition-state approximation [T. Ala-Nissila, J. Kjoll, and S. C. Ying, Phys. Rev. B 46, 846 (1992)] and the one-step dynamic [H. C. Kang and W. H. Weinberg, J. Chem. Phys. 90, 2824 (1989)]. Even though they both obey detailed balance and are here applied to a situation that does not conserve the order parameter, we find significant differences between the nucleation rates observed with the two dynamics, and between them and the standard Glauber dynamic [R. J. Glauber, J. Math. Phys. 4, 294 (1963)], which does not contain transition states. Our results show that great care must be exercised when devising kinetic Monte Carlo transition rates for specific physical or chemical systems.Comment: 14 pages RevTex, 6 embedded figures. Minor revisions. J. Chem. Phys., in pres

The Single-Photon Router

We have embedded an artificial atom, a superconducting "transmon" qubit, in an open transmission line and investigated the strong scattering of incident microwave photons ($\sim6$ GHz). When an input coherent state, with an average photon number $N\ll1$ is on resonance with the artificial atom, we observe extinction of up to 90% in the forward propagating field. We use two-tone spectroscopy to study scattering from excited states and we observe electromagnetically induced transparency (EIT). We then use EIT to make a single-photon router, where we can control to what output port an incoming signal is delivered. The maximum on-off ratio is around 90% with a rise and fall time on the order of nanoseconds, consistent with theoretical expectations. The router can easily be extended to have multiple output ports and it can be viewed as a rudimentary quantum node, an important step towards building quantum information networks.Comment: 5 pages, 3 figure

Philosophy and updating of the asteroid photometric catalogue

The Asteroid Photometric Catalogue now contains photometric lightcurves for 584 asteroids. We discuss some of the guiding principles behind it. This concerns both observers who offer input to it and users of the product

Are pinholes the cause of excess current in superconducting tunnel junctions? A study of Andreev current in highly resistive junctions

In highly resistive superconducting tunnel junctions, excess subgap current is usually observed and is often attributed to microscopic "pinholes" in the tunnel barrier. We have studied the subgap current in superconductor-insulator-superconductor (SIS) and superconductor-insulator-normal-metal (SIN) junctions. In Al/AlOx/Al junctions, we observed a decrease of 2 orders of magnitude in the current upon the transition from the SIS to the SIN regime, where it then matched theory. In Al/AlOx/Cu junctions, we also observed generic features of coherent diffusive Andreev transport in a junction with a homogenous barrier. We use the quasiclassical Keldysh-Green function theory to quantify single- and two-particle tunneling and find good agreement over 2 orders of magnitude in transparency. We argue that our observations rule out pinholes as the origin of the excess current.Comment: 4 pages, 4 figure

Energy bursts in fiber bundle models of composite materials

As a model of composite materials, a bundle of many fibers with stochastically distributed breaking thresholds for the individual fibers is considered. The bundle is loaded until complete failure to capture the failure scenario of composite materials under external load. The fibers are assumed to share the load equally, and to obey Hookean elasticity right up to the breaking point. We determine the distribution of bursts in which an amount of energy $E$ is released. The energy distribution follows asymptotically a universal power law $E^{-5/2}$, for any statistical distribution of fiber strengths. A similar power law dependence is found in some experimental acoustic emission studies of loaded composite materials.Comment: 5 pages, 4 fig

Effects of demographic stochasticity on biological community assembly on evolutionary time scales

We study the effects of demographic stochasticity on the long-term dynamics of biological coevolution models of community assembly. The noise is induced in order to check the validity of deterministic population dynamics. While mutualistic communities show little dependence on the stochastic population fluctuations, predator-prey models show strong dependence on the stochasticity, indicating the relevance of the finiteness of the populations. For a predator-prey model, the noise causes drastic decreases in diversity and total population size. The communities that emerge under influence of the noise consist of species strongly coupled with each other and have stronger linear stability around the fixed-point populations than the corresponding noiseless model. The dynamics on evolutionary time scales for the predator-prey model are also altered by the noise. Approximate $1/f$ fluctuations are observed with noise, while $1/f^{2}$ fluctuations are found for the model without demographic noise

Mechanics of universal horizons

Modified gravity models such as Ho\v{r}ava-Lifshitz gravity or Einstein-{\ae}ther theory violate local Lorentz invariance and therefore destroy the notion of a universal light cone. Despite this, in the infrared limit both models above possess static, spherically symmetric solutions with "universal horizons" - hypersurfaces that are causal boundaries between an interior region and asymptotic spatial infinity. In other words, there still exist black hole solutions. We construct a Smarr formula (the relationship between the total energy of the spacetime and the area of the horizon) for such a horizon in Einstein-{\ae}ther theory. We further show that a slightly modified first law of black hole mechanics still holds with the relevant area now a cross-section of the universal horizon. We construct new analytic solutions for certain Einstein-{\ae}ther Lagrangians and illustrate how our results work in these exact cases. Our results suggest that holography may be extended to these theories despite the very different causal structure as long as the universal horizon remains the unique causal boundary when matter fields are added.Comment: Minor clarifications. References update

Single-shot Readout of a Superconducting Qubit using a Josephson Parametric Oscillator

We propose and demonstrate a new read-out technique for a superconducting qubit by dispersively coupling it to a Josephson parametric oscillator. We employ a tunable quarter-wavelength superconducting resonator and modulate its resonant frequency at twice its value with an amplitude surpassing the threshold for parametric instability. We map the qubit states onto two distinct states of classical parametric oscillation: one oscillating state, with $185\pm15$ photons in the resonator, and one with zero oscillation amplitude. This high contrast obviates a following quantum-limited amplifier. We demonstrate proof-of-principle, single-shot readout performance, and present an error budget indicating that this method can surpass the fidelity threshold required for quantum computing.Comment: 11 pages, 5 figure

Evaluation of New Density Functional with Account of van der Waals Forces by Use of Experimental H2 Physisorption Data on Cu(111)

Detailed experimental data for physisorption potential-energy curves of H2 on low-indexed faces of Cu challenge theory. Recently, density-functional theory has been developed to also account for nonlocal correlation effects, including van der Waals forces. We show that one functional, denoted vdW-DF2, gives a potential-energy curve promisingly close to the experiment-derived physisorptionenergy curve. The comparison also gives indications for further improvements of the functionals