120 research outputs found
Radio-frequency dressed state potentials for neutral atoms
Potentials for atoms can be created by external fields acting on properties
like magnetic moment, charge, polarizability, or by oscillating fields which
couple internal states. The most prominent realization of the latter is the
optical dipole potential formed by coupling ground and electronically excited
states of an atom with light. Here we present an experimental investigation of
the remarkable properties of potentials derived from radio-frequency (RF)
coupling between electronic ground states. The coupling is magnetic and the
vector character allows to design state dependent potential landscapes. On atom
chips this enables robust coherent atom manipulation on much smaller spatial
scales than possible with static fields alone. We find no additional heating or
collisional loss up to densities approaching atoms / cm compared
to static magnetic traps. We demonstrate the creation of Bose-Einstein
condensates in RF potentials and investigate the difference in the interference
between two independently created and two coherently split condensates in
identical traps. All together this makes RF dressing a powerful new tool for
micro manipulation of atomic and molecular systems
Matter-wave interferometry in a double well on an atom chip
Matter-wave interference experiments enable us to study matter at its most
basic, quantum level and form the basis of high-precision sensors for
applications such as inertial and gravitational field sensing. Success in both
of these pursuits requires the development of atom-optical elements that can
manipulate matter waves at the same time as preserving their coherence and
phase. Here, we present an integrated interferometer based on a simple,
coherent matter-wave beam splitter constructed on an atom chip. Through the use
of radio-frequency-induced adiabatic double-well potentials, we demonstrate the
splitting of Bose-Einstein condensates into two clouds separated by distances
ranging from 3 to 80 microns, enabling access to both tunnelling and isolated
regimes. Moreover, by analysing the interference patterns formed by combining
two clouds of ultracold atoms originating from a single condensate, we measure
the deterministic phase evolution throughout the splitting process. We show
that we can control the relative phase between the two fully separated samples
and that our beam splitter is phase-preserving
Unconfined Aquifer Flow Theory - from Dupuit to present
Analytic and semi-analytic solution are often used by researchers and
practicioners to estimate aquifer parameters from unconfined aquifer pumping
tests. The non-linearities associated with unconfined (i.e., water table)
aquifer tests makes their analysis more complex than confined tests. Although
analytical solutions for unconfined flow began in the mid-1800s with Dupuit,
Thiem was possibly the first to use them to estimate aquifer parameters from
pumping tests in the early 1900s. In the 1950s, Boulton developed the first
transient well test solution specialized to unconfined flow. By the 1970s
Neuman had developed solutions considering both primary transient storage
mechanisms (confined storage and delayed yield) without non-physical fitting
parameters. In the last decade, research into developing unconfined aquifer
test solutions has mostly focused on explicitly coupling the aquifer with the
linearized vadose zone. Despite the many advanced solution methods available,
there still exists a need for realism to accurately simulate real-world aquifer
tests
The Biomolecular Interaction Network Database and related tools 2005 update
The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues
The neutron and its role in cosmology and particle physics
Experiments with cold and ultracold neutrons have reached a level of
precision such that problems far beyond the scale of the present Standard Model
of particle physics become accessible to experimental investigation. Due to the
close links between particle physics and cosmology, these studies also permit a
deep look into the very first instances of our universe. First addressed in
this article, both in theory and experiment, is the problem of baryogenesis ...
The question how baryogenesis could have happened is open to experimental
tests, and it turns out that this problem can be curbed by the very stringent
limits on an electric dipole moment of the neutron, a quantity that also has
deep implications for particle physics. Then we discuss the recent spectacular
observation of neutron quantization in the earth's gravitational field and of
resonance transitions between such gravitational energy states. These
measurements, together with new evaluations of neutron scattering data, set new
constraints on deviations from Newton's gravitational law at the picometer
scale. Such deviations are predicted in modern theories with extra-dimensions
that propose unification of the Planck scale with the scale of the Standard
Model ... Another main topic is the weak-interaction parameters in various
fields of physics and astrophysics that must all be derived from measured
neutron decay data. Up to now, about 10 different neutron decay observables
have been measured, much more than needed in the electroweak Standard Model.
This allows various precise tests for new physics beyond the Standard Model,
competing with or surpassing similar tests at high-energy. The review ends with
a discussion of neutron and nuclear data required in the synthesis of the
elements during the "first three minutes" and later on in stellar
nucleosynthesis.Comment: 91 pages, 30 figures, accepted by Reviews of Modern Physic
Methods for high-dimensonal analysis of cells dissociated from cyropreserved synovial tissue
Abstract Background Detailed molecular analyses of cells from rheumatoid arthritis (RA) synovium hold promise in identifying cellular phenotypes that drive tissue pathology and joint damage. The Accelerating Medicines Partnership RA/SLE Network aims to deconstruct autoimmune pathology by examining cells within target tissues through multiple high-dimensional assays. Robust standardized protocols need to be developed before cellular phenotypes at a single cell level can be effectively compared across patient samples. Methods Multiple clinical sites collected cryopreserved synovial tissue fragments from arthroplasty and synovial biopsy in a 10% DMSO solution. Mechanical and enzymatic dissociation parameters were optimized for viable cell extraction and surface protein preservation for cell sorting and mass cytometry, as well as for reproducibility in RNA sequencing (RNA-seq). Cryopreserved synovial samples were collectively analyzed at a central processing site by a custom-designed and validated 35-marker mass cytometry panel. In parallel, each sample was flow sorted into fibroblast, T-cell, B-cell, and macrophage suspensions for bulk population RNA-seq and plate-based single-cell CEL-Seq2 RNA-seq. Results Upon dissociation, cryopreserved synovial tissue fragments yielded a high frequency of viable cells, comparable to samples undergoing immediate processing. Optimization of synovial tissue dissociation across six clinical collection sites with ~ 30 arthroplasty and ~ 20 biopsy samples yielded a consensus digestion protocol using 100 μg/ml of Liberase™ TL enzyme preparation. This protocol yielded immune and stromal cell lineages with preserved surface markers and minimized variability across replicate RNA-seq transcriptomes. Mass cytometry analysis of cells from cryopreserved synovium distinguished diverse fibroblast phenotypes, distinct populations of memory B cells and antibody-secreting cells, and multiple CD4+ and CD8+ T-cell activation states. Bulk RNA-seq of sorted cell populations demonstrated robust separation of synovial lymphocytes, fibroblasts, and macrophages. Single-cell RNA-seq produced transcriptomes of over 1000 genes/cell, including transcripts encoding characteristic lineage markers identified. Conclusions We have established a robust protocol to acquire viable cells from cryopreserved synovial tissue with intact transcriptomes and cell surface phenotypes. A centralized pipeline to generate multiple high-dimensional analyses of synovial tissue samples collected across a collaborative network was developed. Integrated analysis of such datasets from large patient cohorts may help define molecular heterogeneity within RA pathology and identify new therapeutic targets and biomarkers
Methods for high-dimensonal analysis of cells dissociated from cyropreserved synovial tissue
Background: Detailed molecular analyses of cells from rheumatoid arthritis (RA) synovium hold promise in identifying cellular phenotypes that drive tissue pathology and joint damage. The Accelerating Medicines Partnership RA/SLE Network aims to deconstruct autoimmune pathology by examining cells within target tissues through multiple high-dimensional assays. Robust standardized protocols need to be developed before cellular phenotypes at a single cell level can be effectively compared across patient samples. Methods: Multiple clinical sites collected cryopreserved synovial tissue fragments from arthroplasty and synovial biopsy in a 10% DMSO solution. Mechanical and enzymatic dissociation parameters were optimized for viable cell extraction and surface protein preservation for cell sorting and mass cytometry, as well as for reproducibility in RNA sequencing (RNA-seq). Cryopreserved synovial samples were collectively analyzed at a central processing site by a custom-designed and validated 35-marker mass cytometry panel. In parallel, each sample was flow sorted into fibroblast, T-cell, B-cell, and macrophage suspensions for bulk population RNA-seq and plate-based single-cell CEL-Seq2 RNA-seq. Results: Upon dissociation, cryopreserved synovial tissue fragments yielded a high frequency of viable cells, comparable to samples undergoing immediate processing. Optimization of synovial tissue dissociation across six clinical collection sites with ~ 30 arthroplasty and ~ 20 biopsy samples yielded a consensus digestion protocol using 100 μg/ml of Liberase™ TL enzyme preparation. This protocol yielded immune and stromal cell lineages with preserved surface markers and minimized variability across replicate RNA-seq transcriptomes. Mass cytometry analysis of cells from cryopreserved synovium distinguished diverse fibroblast phenotypes, distinct populations of memory B cells and antibody-secreting cells, and multiple CD4+ and CD8+ T-cell activation states. Bulk RNA-seq of sorted cell populations demonstrated robust separation of synovial lymphocytes, fibroblasts, and macrophages. Single-cell RNA-seq produced transcriptomes of over 1000 genes/cell, including transcripts encoding characteristic lineage markers identified. Conclusions: We have established a robust protocol to acquire viable cells from cryopreserved synovial tissue with intact transcriptomes and cell surface phenotypes. A centralized pipeline to generate multiple high-dimensional analyses of synovial tissue samples collected across a collaborative network was developed. Integrated analysis of such datasets from large patient cohorts may help define molecular heterogeneity within RA pathology and identify new therapeutic targets and biomarkers
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