The Quantum Speed Limit of Optimal Controlled Phasegates for Trapped Neutral Atoms

We study controlled phasegates for ultracold atoms in an optical potential. A shaped laser pulse drives transitions between the ground and electronically excited states where the atoms are subject to a long-range 1/R^3 interaction. We fully account for this interaction and use optimal control theory to calculate the pulse shapes. This allows us to determine the minimum pulse duration, respectively, gate time T that is required to obtain high fidelity. We accurately analyze the speed limiting factors, and we find the gate time to be limited either by the interaction strength in the excited state or by the ground state vibrational motion in the trap. The latter needs to be resolved by the pulses in order to fully restore the motional state of the atoms at the end of the gate.Comment: 11 pages, 10 figures, 1 tabl

Comparison of Alternative Meat Inspection Regimes for Pigs From Non-Controlled Housing – Considering the Cost of Error

Denmark has not had cases of bovine tuberculosis (bovTB) for more than 30 years but is obliged by trade agreements to undertake traditional meat inspection (TMI) of finisher pigs from non-controlled housing to detect bovTB. TMI is associated with higher probability of detecting bovTB but is also more costly than visual-only inspection (VOI). To identify whether VOI should replace TMI of finisher pigs from non-controlled housing, the cost of error – defined here as probability of overlooking infection and associated economic costs - should be assessed and compared with surveillance costs. First, a scenario tree model was set up to assess the ability of detecting bovTB in an infected herd (HSe) calculated for three within-herd prevalences, WHP (1, 5 and 10%), for four different surveillance scenarios (TMI and VOI with or without serological test, respectively). HSe was calculated for six consecutive 4-week surveillance periods until predicted bovTB detection (considered high-risk periods HRP). 1-HSe was probability of missing all positives by each HRP. Next, probability of spread of infection, Pspread, and number of infected animals moved were calculated for each HRP. Costs caused by overlooking bovTB were calculated taking into account Pspread, 1-HSe, eradication costs, and trade impact. Finally, the average annual costs were calculated by adding surveillance costs and assuming one incursion of bovTB in either 1, 10 or 30 years. Input parameters were based on slaughterhouse statistics, literature and expert opinion. Herd sensitivity increased by high-risk period and within-herd prevalence. Assuming WHP=5%, HSe reached median 90% by 2nd HRP for TMI, whereas for VOI this would happen after 6th HRP. Serology had limited impact on HSe. The higher the probability of infection, the higher the probability of detection and spread. TMI resulted in lowest average annual costs, if one incursion of bovTB was expected every year. However, when assuming one introduction in 10 or 30 years, VOI resulted in lowest average costs. It may be more cost-effective to focus on imported high-risk animals coming into contact with Danish livestock, instead of using TMI as surveillance on all pigs from non-controlled housing

Efficient one- and two-qubit pulsed gates for an oscillator stabilized Josephson qubit

We present theoretical schemes for performing high-fidelity one- and two-qubit pulsed gates for a superconducting flux qubit. The "IBM qubit" consists of three Josephson junctions, three loops, and a superconducting transmission line. Assuming a fixed inductive qubit-qubit coupling, we show that the effective qubit-qubit interaction is tunable by changing the applied fluxes, and can be made negligible, allowing one to perform high fidelity single qubit gates. Our schemes are tailored to alleviate errors due to 1/f noise; we find gates with only 1% loss of fidelity due to this source, for pulse times in the range of 20-30ns for one-qubit gates (Z rotations, Hadamard), and 60ns for a two-qubit gate (controlled-Z). Our relaxation and dephasing time estimates indicate a comparable loss of fidelity from this source. The control of leakage plays an important role in the design of our shaped pulses, preventing shorter pulse times. However, we have found that imprecision in the control of the quantum phase plays the major role in the limitation of the fidelity of our gates.Comment: Published version. Added references. Corrected minor typos. Added discussion on how the influence of 1/f noise is modeled. 36 pages, 11 figure

Bent surface free energy differences from simulation

We present a calculation of the change of free energy of a solid surface upon bending of the solid. It is based on extracting the surface stress through a molecular dynamics simulation of a bent slab by using a generalized stress theorem formula, and subsequent integration of the stress with respect to strain as a function of bending curvature. The method is exemplified by obtaining and comparing free energy changes with curvature of various reconstructed Au(001) surfaces.Comment: 14 pages, 2 figures, accepted for publication in Surface Science (ECOSS-19

Optimizing entangling quantum gates for physical systems

Optimal control theory is a versatile tool that presents a route to significantly improving figures of merit for quantum information tasks. We combine it here with the geometric theory for local equivalence classes of two-qubit operations to derive an optimization algorithm that determines the best entangling two-qubit gate for a given physical setting. We demonstrate the power of this approach for trapped polar molecules and neutral atoms.Comment: extended version; Phys. Rev. A (2011

The Impact of Vegetation on Archaeological Sites in the Low Arctic in Light of Climate Change

Vegetation is changing across the Arctic in response to increasing temperatures, which may influence archaeological sites in the region. At the moment, very little is known about how different plant species influence archaeological remains. In this study we visited 14 archaeological sites stretching across a climatic gradient from the outer coast to the inner fjords in the Nuuk Fjord area of West Greenland to assess the impact of vegetation growth on archaeological preservation. Examination of the physical disturbance of archaeological layers and materials by roots from different plant species showed that horsetail (Equisetum arvense) was particularly destructive because of its deep penetrating rhizomes and ubiquity across the study area. Willow (Salix glauca) also caused physical disturbance due to a dense root network, but its roots were mainly found in the upper 30 cm of the soil. Focus was also given to the impact from vegetation on the visibility of sites, where growth of willow was found be the main problem, especially in the inner fjords. Historic descriptions and aerial photographs from the sites show that shrub growth was already widespread in the region by the 1930s, but photos of some of the sites investigated show that the willow shrubs are significantly taller today, which has decreased the visibility of site features. The impact from horsetail and willow on archaeological sites may be mitigated using geotextiles and grazing by livestock, but both methods require further studies before being implemented in the study area.À la grandeur de l’Arctique, la végétation change en réaction aux températures à la hausse, ce qui peut exercer une influence sur les sites archéologiques de la région. En ce moment, on en sait peu sur la manière dont les différentes espèces végétales influencent les restes archéologiques. Dans le cadre de cette étude, nous avons visité 14 sites archéologiques répartis sur un gradient climatique allant de la zone côtière extérieure aux fjords intérieurs de la région du fjord de Nuuk, dans l’ouest du Groenland, afin d’évaluer l’incidence de la croissance de la végétation sur la préservation archéologique. L’examen de la perturbation physique des couches et du matériel archéologiques au moyen des racines de différentes espèces végétales a permis de constater que la prêle (Equisetum arvense) jouait un rôle particulièrement destructeur en raison de ses rhizomes profonds et omniprésents dans toute la zone étudiée. Le saule (Salix glauca) entraîne aussi des perturbations physiques en raison de son réseau de racines denses, bien que ses racines se trouvent principalement dans la couche supérieure de sol de 30 cm. Nous avons aussi accordé de l’importance à l’incidence de la végétation sur la visibilité des sites, ce qui a permis de conclure que la croissance du saule constituait le problème principal, surtout dans la zone intérieure des fjords. Les descriptions historiques et les photographies aériennes des sites montrent que la croissance d’arbustes était déjà répandue dans la région dans les années 1930, bien que certaines photos des sites étudiés permettent de comprendre que les saules arbustifs sont beaucoup plus grands aujourd’hui, ce qui diminue la visibilité des caractéristiques des sites. L’incidence de la prêle et du saule sur les sites archéologiques pourrait être atténuée par l’utilisation de géotextiles et le broutage du bétail. Il y a toutefois lieu de se pencher de plus près sur ces deux méthodes avant de les adopter dans la zone étudiée

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

Motivation: Many biological processes are guided by receptor interactions with linear ligands of variable length. One such receptor is the MHC class I molecule. The length preferences vary depending on the MHC allele, but are generally limited to peptides of length 8–11 amino acids. On this relatively simple system, we developed a sequence alignment method based on artificial neural networks that allows insertions and deletions in the alignment. Results: We show that prediction methods based on alignments that include insertions and deletions have significantly higher performance than methods trained on peptides of single lengths. Also, we illustrate how the location of deletions can aid the interpretation of the modes of binding of the peptide-MHC, as in the case of long peptides bulging out of the MHC groove or protruding at either terminus. Finally, we demonstrate that the method can learn the length profile of different MHC molecules, and quantified the reduction of the experimental effort required to identify potential epitopes using our prediction algorithm. Availability and implementation: The NetMHC-4.0 method for the prediction of peptide-MHC class I binding affinity using gapped sequence alignment is publicly available at: http://www.cbs.dtu.dk/ services/NetMHC-4.0.Fil: Andreatta, Massimo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentin

A Sparse Reformulation of the Green's Function Formalism Allows Efficient Simulations of Morphological Neuron Models

We prove that when a class of partial differential equations, generalized from the cable equation, is defined on tree graphs and the inputs are restricted to a spatially discrete, well chosen set of points, the Green's function (GF) formalism can be rewritten to scale as O (n) with the number n of inputs locations, contrary to the previously reported O (n(2)) scaling. We show that the linear scaling can be combined with an expansion of the remaining kernels as sums of exponentials to allow efficient simulations of equations from the aforementioned class. We furthermore validate this simulation paradigm on models of nerve cells and explore its relation with more traditional finite difference approaches. Situations in which a gain in computational performance is expected are discussed.Peer reviewedFinal Accepted Versio