Internal decoherence in nano-object interferometry due to phonons

We discuss the coherent splitting and recombining of a nanoparticle in a mesoscopic "closed-loop" Stern-Gerlach interferometer in which the observable is the spin of a single impurity embedded in the particle. This spin, when interacting with a pulsed magnetic gradient, generates the force on the particle. We calculate the internal decoherence which arises as the displaced impurity excites internal degrees of freedom (phonons) that may provide Welcher Weg information and preclude interference. We estimate the constraints this decoherence channel puts on future interference experiments with massive objects. We find that for a wide range of masses, forces and temperatures, phonons do not inhibit Stern-Gerlach interferometry with micro-scale objects. However, phonons do constitute a fundamental limit on the splitting of larger macroscopic objects if the applied force induces phonons.Comment: 10 pages, 6 figures, submitted to Festschrift in honor of Nobel prize awarded to R. Penros

Fundamental Limits for Coherent Manipulation on Atom Chips

The limitations for the coherent manipulation of neutral atoms with fabricated solid state devices, so-called `atom chips', are addressed. Specifically, we examine the dominant decoherence mechanism, which is due to the magnetic noise originating from the surface of the atom chip. It is shown that the contribution of fluctuations in the chip wires at the shot noise level is not negligible. We estimate the coherence times and discuss ways to increase them. Our main conclusion is that future advances should allow for coherence times as long as one second, a few micrometers away from the surface.Comment: selected papers of the DPG spring meeting `Quantum Optics' (Osnabrueck, Germany, 4-8 march 2002), submitted to Applied Physics

Superconducting atom chips: advantages and challenges

Superconductors are considered in view of applications to atom chip devices. The main features of magnetic traps based on superconducting wires in the Meissner and mixed states are discussed. The former state may mainly be interesting for improved atom optics, while in the latter, cold atoms may provide a probe of superconductor phenomena. The properties of a magnetic side guide based on a single superconducting strip wire placed in an external magnetic field are calculated analytically and numerically. In the mixed state of type II superconductors, inhomogeneous trapped magnetic flux, relaxation processes and noise caused by vortex motion are posing specific challenges for atom trapping.Comment: submitted to Eur. Phys. J. D, latex article class (27 pages, 20 .eps figure files

Annotation-based feature extraction from sets of SBML models

Background: Model repositories such as BioModels Database provide computational models of biological systems for the scientific community. These models contain rich semantic annotations that link model entities to concepts in well-established bio-ontologies such as Gene Ontology. Consequently, thematically similar models are likely to share similar annotations. Based on this assumption, we argue that semantic annotations are a suitable tool to characterize sets of models. These characteristics improve model classification, allow to identify additional features for model retrieval tasks, and enable the comparison of sets of models. Results: In this paper we discuss four methods for annotation-based feature extraction from model sets. We tested all methods on sets of models in SBML format which were composed from BioModels Database. To characterize each of these sets, we analyzed and extracted concepts from three frequently used ontologies, namely Gene Ontology, ChEBI and SBO. We find that three out of the methods are suitable to determine characteristic features for arbitrary sets of models: The selected features vary depending on the underlying model set, and they are also specific to the chosen model set. We show that the identified features map on concepts that are higher up in the hierarchy of the ontologies than the concepts used for model annotations. Our analysis also reveals that the information content of concepts in ontologies and their usage for model annotation do not correlate. Conclusions: Annotation-based feature extraction enables the comparison of model sets, as opposed to existing methods for model-to-keyword comparison, or model-to-model comparison

Contributions to the reuse and reproducibility of computational biology models

Diese Arbeit befasst sich mit der Reproduzierbarkeit und Wiederverwendbarkeit von systembiologischen Modellen, wobei die FAIR-Prinzipien (findable, accessible, interoperable, reusable) im Vordergrund stehen. Sie konzentriert sich auf 5 zentrale Forschungsfragen: Schaffung einer Grundlage für die Modellverwaltung, Auffinden heterogener, halbstrukturierter Modelldaten, Nachverfolgung der Modellentwicklung im Laufe der Zeit, Speicherung von Modellen und ihren Metadaten, Definition der wichtigsten Modellkomponenten für die Ähnlichkeitsanalyse.This thesis addresses systems biology model reproducibility and reusability, emphasizing FAIR (findable, accessible, interoperable, reusable) principles. It focuses on 5 core research queries: establishing a baseline for model management, retrieving and ranking heterogeneous, semi-structured model data, tracing model evolution over time, storing models and their metadata, defining crucial model components for similarity analysis

Combining computational models, semantic annotations, and 1 associated simulation experiments in a graph database PrePrints

Abstract 13 Model repositories such as the BioModels Database or the CellML Model Repository are 14 frequently accessed to retrieve computational models describing biological systems. However, 15 the current designs of these databases limit the types of supported queries, and many data 16 in these repositories cannot easily be accessed. Computational methods for model retrieval 17 cannot be applied. In this paper we present a storage concept that meets this challenge. It 18 grounds on a graph database, reects the models' structure, incorporates semantic annotations 19 and experiment descriptions, and ultimately connects dierent types of model-related data. 20 The connections between heterogeneous model-related data and bio-ontologies enable ecient 21 search via biological facts and grant access to new model features such as network structure. 22 The introduced concept notably improves the access of computational models and associate

Realization of a complete Stern-Gerlach interferometer: Towards a test of quantum gravity

The Stern-Gerlach effect, discovered a century ago, has become a paradigm of quantum mechanics. Surprisingly there has been little evidence that the original scheme with freely propagating atoms exposed to gradients from macroscopic magnets is a fully coherent quantum process. Specifically, no full-loop Stern-Gerlach interferometer has been realized with the scheme as envisioned decades ago. Furthermore, several theoretical studies have explained why such an interferometer is a formidable challenge. Here we provide a detailed account of the first full-loop Stern-Gerlach interferometer realization, based on highly accurate magnetic fields, originating from an atom chip, that ensure coherent operation within strict constraints described by previous theoretical analyses. Achieving this high level of control over magnetic gradients is expected to facilitate technological as well as fundamental applications, such as probing the interface of quantum mechanics and gravity. While the experimental realization described here is for a single atom, future challenges would benefit from utilizing macroscopic objects doped with a single spin. Specifically, we show that such an experiment is in principle feasible, opening the door to a new era of fundamental probes