Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Electric-Potential Reconstructions of Single Particles Using L-Gradient Flows.

ABSTRACT: In this paper, we present a stable, reliable and robust method for reconstructing a three dimensional density function from a set of two dimensional electron microscopy images. By minimizing an energy functional consisting of a fidelity term and a regularization term, a L(2)-gradient flow is derived. The flow is integrated by a finite element method in the spatial direction and an explicit Euler scheme in temporal direction. The experimental results show that the proposed method is efficient and effective.

SUBMITTER: Li M

PROVIDER: S-EPMC3091820 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Electric-Potential Reconstructions of Single Particles Using L-Gradient Flows.

Li Ming M Xu Guoliang G Sorzano Carlos O S CO Melero Roberto R Bajaj Chandrajit C

Proceedings of the ... International Conference on Biomedical Engineering and Informatics. International Conference on Biomedical Engineering and Informatics 20101001

In this paper, we present a stable, reliable and robust method for reconstructing a three dimensional density function from a set of two dimensional electron microscopy images. By minimizing an energy functional consisting of a fidelity term and a regularization term, a L(2)-gradient flow is derived. The flow is integrated by a finite element method in the spatial direction and an explicit Euler scheme in temporal direction. The experimental results show that the proposed method is efficient and ...[more]

PMID: 21566727

Similar Datasets

Optimal noise reduction in 3D reconstructions of single particles using a volume-normalized filter.

Project description:The high noise level found in single-particle electron cryo-microscopy (cryo-EM) image data presents a special challenge for three-dimensional (3D) reconstruction of the imaged molecules. The spectral signal-to-noise ratio (SSNR) and related Fourier shell correlation (FSC) functions are commonly used to assess and mitigate the noise-generated error in the reconstruction. Calculation of the SSNR and FSC usually includes the noise in the solvent region surrounding the particle and therefore does not accurately reflect the signal in the particle density itself. Here we show that the SSNR in a reconstructed 3D particle map is linearly proportional to the fractional volume occupied by the particle. Using this relationship, we devise a novel filter (the "single-particle Wiener filter") to minimize the error in a reconstructed particle map, if the particle volume is known. Moreover, we show how to approximate this filter even when the volume of the particle is not known, by optimizing the signal within a representative interior region of the particle. We show that the new filter improves on previously proposed error-reduction schemes, including the conventional Wiener filter as well as figure-of-merit weighting, and quantify the relationship between all of these methods by theoretical analysis as well as numeric evaluation of both simulated and experimentally collected data. The single-particle Wiener filter is applicable across a broad range of existing 3D reconstruction techniques, but is particularly well suited to the Fourier inversion method, leading to an efficient and accurate implementation.

| S-EPMC3498508 | biostudies-literature

Quantifying electric field gradient fluctuations over polymers using ultrasensitive cantilevers.

Project description:An ultrasensitive cantilever, oscillating parallel to a surface in vacuum, is used to probe weak thermal electric field gradient fluctuations over thin polymer films. We measure the power spectrum of cantilever frequency fluctuations as a function of cantilever height and voltage over polymers of various compositions and thicknesses. The data are well described by a linear-response theory that calculates stochastic electric fields arising from thermally driven dielectric fluctuations.

| S-EPMC2838734 | biostudies-literature

Active particles bound by information flows.

Project description:Self-organization is the generation of order out of local interactions. It is deeply connected to many fields of science from physics, chemistry to biology, all based on physical interactions. The emergence of collective animal behavior is the result of self-organization processes as well, though they involve abstract interactions arising from sensory inputs, information processing, storage, and feedback. Resulting collective behaviors are found, for example, in crowds of people, flocks of birds, and swarms of bacteria. Here we introduce interactions between active microparticles which are based on the information about other particle positions. A real-time feedback of multiple active particle positions is the information source for the propulsion direction of these particles. The emerging structures require continuous information flows. They reveal frustrated geometries due to confinement to two dimensions and internal dynamical degrees of freedom that are reminiscent of physically bound systems, though they exist only as nonequilibrium structures.

| S-EPMC6154969 | biostudies-literature

Vortices as Brownian particles in turbulent flows.

Project description:Brownian motion of particles in fluid is the most common form of collective behavior in physical and biological systems. Here, we demonstrate through both experiment and numerical simulation that the movement of vortices in a rotating turbulent convective flow resembles that of inertial Brownian particles, i.e., they initially move ballistically and then diffusively after certain critical time. Moreover, the transition from ballistic to diffusive behaviors is direct, as predicted by Langevin, without first going through the hydrodynamic memory regime. The transitional timescale and the diffusivity of the vortices can be collapsed excellently onto a master curve for all explored parameters. In the spatial domain, however, the vortices exhibit organized structures, as if they are performing tethered random motion. Our results imply that the convective vortices have inertia-induced memory such that their short-term movement can be predicted and their motion can be well described in the framework of Brownian motions.

| S-EPMC7438090 | biostudies-literature

Quantitative Magnetic Separation of Particles and Cells Using Gradient Magnetic Ratcheting.

Project description:Extraction of rare target cells from biosamples is enabling for life science research. Traditional rare cell separation techniques, such as magnetic activated cell sorting, are robust but perform coarse, qualitative separations based on surface antigen expression. A quantitative magnetic separation technology is reported using high-force magnetic ratcheting over arrays of magnetically soft micropillars with gradient spacing, and the system is used to separate and concentrate magnetic beads based on iron oxide content (IOC) and cells based on surface expression. The system consists of a microchip of permalloy micropillar arrays with increasing lateral pitch and a mechatronic device to generate a cycling magnetic field. Particles with higher IOC separate and equilibrate along the miropillar array at larger pitches. A semi-analytical model is developed that predicts behavior for particles and cells. Using the system, LNCaP cells are separated based on the bound quantity of 1 μm anti-epithelial cell adhesion molecule (EpCAM) particles as a metric for expression. The ratcheting cytometry system is able to resolve a ±13 bound particle differential, successfully distinguishing LNCaP from PC3 populations based on EpCAM expression, correlating with flow cytometry analysis. As a proof-of-concept, EpCAM-labeled cells from patient blood are isolated with 74% purity, demonstrating potential toward a quantitative magnetic separation instrument.

| S-EPMC4958462 | biostudies-literature

Force and torque on spherical particles in micro-channel flows using computational fluid dynamics.

Project description:To delineate the influence of hemodynamic force on cell adhesion processes, model in vitro fluidic assays that mimic physiological conditions are commonly employed. Herein, we offer a framework for solution of the three-dimensional Navier-Stokes equations using computational fluid dynamics (CFD) to estimate the forces resulting from fluid flow near a plane acting on a sphere that is either stationary or in free flow, and we compare these results to a widely used theoretical model that assumes Stokes flow with a constant shear rate. We find that while the full three-dimensional solutions using a parabolic velocity profile in CFD simulations yield similar translational velocities to those predicted by the theoretical method, the CFD approach results in approximately 50% larger rotational velocities over the wall shear stress range of 0.1-5.0?dynes?cm(-2). This leads to an approximately 25% difference in force and torque calculations between the two methods. When compared with experimental measurements of translational and rotational velocities of microspheres or cells perfused in microfluidic channels, the CFD simulations yield significantly less error. We propose that CFD modelling can provide better estimations of hemodynamic force levels acting on perfused microspheres and cells in flow fields through microfluidic devices used for cell adhesion dynamics analysis.

| S-EPMC4968475 | biostudies-other

Diffusioosmotic and convective flows induced by a nonelectrolyte concentration gradient.

Project description:Glucose is an important energy source in our bodies, and its consumption results in gradients over length scales ranging from the subcellular to entire organs. Concentration gradients can drive material transport through both diffusioosmosis and convection. Convection arises because concentration gradients are mass density gradients. Diffusioosmosis is fluid flow induced by the interaction between a solute and a solid surface. A concentration gradient parallel to a surface creates an osmotic pressure gradient near the surface, resulting in flow. Diffusioosmosis is well understood for electrolyte solutes, but is more poorly characterized for nonelectrolytes such as glucose. We measure fluid flow in glucose gradients formed in a millimeter-long thin channel and find that increasing the gradient causes a crossover from diffusioosmosis-dominated to convection-dominated flow. We cannot explain this with established theories of these phenomena which predict that both scale linearly. In our system, the convection speed is linear in the gradient, but the diffusioosmotic speed has a much weaker concentration dependence and is large even for dilute solutions. We develop existing models and show that a strong surface-solute interaction, a heterogeneous surface, and accounting for a concentration-dependent solution viscosity can explain our data. This demonstrates how sensitive nonelectrolyte diffusioosmosis is to surface and solution properties and to surface-solute interactions. A comprehensive understanding of this sensitivity is required to understand transport in biological systems on length scales from micrometers to millimeters where surfaces are invariably complex and heterogeneous.

| S-EPMC7568292 | biostudies-literature

Optical gradient force on chiral particles.

Project description:When a chiral nanoparticle is optically trapped using a circularly polarized laser beam, a circular polarization (CP)-dependent gradient force can be induced on the particle. We investigated the CP-dependent gradient force exerted on three-dimensional chiral nanoparticles. The experimental results showed that the gradient force depended on the handedness of the CP of the trapping light and the particle chirality. The analysis revealed that the spectral features of the CP handedness-dependent gradient force are influenced not only by the real part of the refractive index but also by the electromagnetic field perturbed by the chiral particle resonant with the incident light. This is in sharp contrast to the well-known behavior of the gradient force, which is governed by the real part of the refractive index. The extended aspect of the chiral optical force obtained here can provide novel methodologies on chirality sensing, manipulation, separation, enantioselective biological reactions, and other fields.

| S-EPMC9491721 | biostudies-literature

Density functional theory-based electric field gradient database.

Project description:The deviation of the electron density around the nuclei from spherical symmetry determines the electric field gradient (EFG), which can be measured by various types of spectroscopy. Nuclear Quadrupole Resonance (NQR) is particularly sensitive to the EFG. The EFGs, and by implication NQR frequencies, vary dramatically across materials. Consequently, searching for NQR spectral lines in previously uninvestigated materials represents a major challenge. Calculated EFGs can significantly aid at the search's inception. To facilitate this task, we have applied high-throughput density functional theory calculations to predict EFGs for 15187 materials in the JARVIS-DFT database. This database, which will include EFG as a standard entry, is continuously increasing. Given the large scope of the database, it is impractical to verify each calculation. However, we assess accuracy by singling out cases for which reliable experimental information is readily available and compare them to the calculations. We further present a statistical analysis of the results. The database and tools associated with our work are made publicly available by JARVIS-DFT ( https://www.ctcms.nist.gov/~knc6/JVASP.html ) and NIST-JARVIS API ( http://jarvis.nist.gov/ ).

| S-EPMC7578653 | biostudies-literature

Elongation and migration of single DNA molecules in microchannels using oscillatory shear flows.

Project description:Much of modern biology relies on the strategic manipulation of molecules for creating ordered arrays prior to high throughput molecular analysis. Normally, DNA arrays involve deposition on surfaces, or confinement in nanochannels; however, we show that microfluidic devices can present stretched molecules within a controlled flow in ways complementing surface modalities, or extreme confinement conditions. Here we utilize pressure-driven oscillatory shear flows generated in microchannels as a new way of stretching DNA molecules for imaging "arrays" of individual DNA molecules. Fluid shear effects both stretch DNA molecules and cause them to migrate away from the walls becoming focused in the centerline of a channel. We show experimental findings confirming simulations using Brownian dynamics accounting for hydrodynamic interactions between molecules and channel-flow boundary conditions. Our findings characterize DNA elongation and migration phenomena as a function of molecular size, shear rate, oscillatory frequency with comparisons to computer simulation studies.

| S-EPMC2768593 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data