AI Article Synopsis
- Single particle analysis (SPA) with high-resolution electron cryo-microscopy is a vital technique for determining the structures of membrane proteins and macromolecular assemblies, needing around 10,000 to 100,000 particle projections for a 3A resolution 3D reconstruction.
- Swarm(PS) is a user-friendly software designed to streamline the particle picking process for these projects, utilizing advanced algorithms like cross-correlation and edge detection while allowing for interactive user input to optimize performance.
- The software supports handling multiple images, offers various particle selection methods, and ensures flexibility for corrections, ultimately facilitating the exporting of data for further image processing.
Article Abstract
Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that approximately 10(4)-10(5) particle projections are required to attain a 3A resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present Swarm(PS), a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (approximately 10(2)), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. Swarm(PS) is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.jsb.2006.04.006 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Giant Thermoelectric Response of Fluxons in Superconductors.
Phys Rev Lett
December 2024
Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, USA.
We investigate the thermoelectric response of an Abrikosov vortex in type-II superconductors in the deep quantum limit. We consider two thermoelectric geometries, a type-II superconductor-insulator-normal-metal (S-I-N) junction and a local scanning tunneling microscope (STM)-tip normal metal probe over the superconductor. We exploit the strong breaking of particle-hole symmetry in vortex-bound states at subgap energies within the superconducting vortex to realize a giant thermoelectric response in the presence of fluxons.
View Article and Find Full Text PDFRealization of a Laughlin State of Two Rapidly Rotating Fermions.
Phys Rev Lett
December 2024
Physikalisches Institut der Universität Heidelberg, Im Neuenheimer Feld 226, 69120 Heidelberg, Germany.
We realize a Laughlin state of two rapidly rotating fermionic atoms in an optical tweezer. By utilizing a single atom and spin resolved imaging technique, we sample the Laughlin wave function thereby revealing its distinctive features, including a vortex distribution in the relative motion, correlations in the particles' relative angle, and suppression of the interparticle interactions. Our Letter lays the foundation for atom-by-atom assembly of fractional quantum Hall states in rotating atomic gases.
View Article and Find Full Text PDFNonreciprocal Alignment Induces Asymmetric Clustering in Active Mixtures.
Phys Rev Lett
December 2024
Institut für Theoretische Physik, Hardenbergstraße 36, Technische Universität Berlin, D-10623 Berlin, Germany.
Heterogeneity is ubiquitous in biological and synthetic active matter systems that are inherently out of equilibrium. Typically, such active mixtures involve not only conservative interactions between the constituents but also nonreciprocal couplings, whose full consequences for the collective behavior still remain elusive. Here, we study a minimal active nonreciprocal mixture with both symmetric isotropic and nonreciprocal polar interactions.
View Article and Find Full Text PDFFloquet-Driven Crossover from Density-Assisted Tunneling to Enhanced Pair Tunneling.
Phys Rev Lett
December 2024
Physikalisches Institut, University of Bonn, 53115 Bonn, Germany.
We investigate the experimental control of pair tunneling in a double-well potential using Floquet engineering. We demonstrate a crossover from a regime with density-assisted tunneling to dominant pair tunneling by tuning the effective interactions. Furthermore, we show that the pair tunneling rate can be enhanced not only compared to the Floquet-reduced single-particle tunneling but even beyond the static superexchange rate, while keeping the effective interaction in a relevant range.
View Article and Find Full Text PDFRotational Locking of Charged Microparticles in Quadrupole Ion Traps.
Phys Rev Lett
December 2024
Laboratoire De Physique de l'École Normale Supérieure, ENS, PSL, CNRS, Sorbonne Université, Université de Paris, 24 rue Lhomond, 75005 Paris, France.
Electric quadrupole traps are a leading technology for suspending charged objects ranging in size from single protons to atomic and molecular ions, and even to nano- and micron-sized bodies. If the levitated objects' charge distribution contains multipoles, the time-dependent trapping fields can significantly impact its rotational motion. Here, we experimentally observe the transition from librational motion to a regime where a microparticle rotates in sync with the trap drive.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!