Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Stokes trap for multiplexed particle manipulation and assembly using fluidics.

ABSTRACT: The ability to confine and manipulate single particles and molecules has revolutionized several fields of science. Hydrodynamic trapping offers an attractive method for particle manipulation in free solution without the need for optical, electric, acoustic, or magnetic fields. Here, we develop and demonstrate the Stokes trap, which is a new method for trapping multiple particles using only fluid flow. We demonstrate simultaneous manipulation of two particles in a simple microfluidic device using model predictive control. We further show that this approach can be used for fluidic-directed assembly of multiple particles in solution. Overall, this technique opens new vistas for fundamental studies of particle-particle interactions and provides a new method for the directed assembly of colloidal particles.

SUBMITTER: Shenoy A

PROVIDER: S-EPMC4839392 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Stokes trap for multiplexed particle manipulation and assembly using fluidics.

Shenoy Anish A Rao Christopher V CV Schroeder Charles M CM

Proceedings of the National Academy of Sciences of the United States of America 20160328 15

The ability to confine and manipulate single particles and molecules has revolutionized several fields of science. Hydrodynamic trapping offers an attractive method for particle manipulation in free solution without the need for optical, electric, acoustic, or magnetic fields. Here, we develop and demonstrate the Stokes trap, which is a new method for trapping multiple particles using only fluid flow. We demonstrate simultaneous manipulation of two particles in a simple microfluidic device using ...[more]

PMID: 27035979

Similar Datasets

Particle manipulation in a microfluidic channel using acoustic trap.

Project description:A high frequency sound beam was employed to explore an experimental method that could control particle motions in a microfluidic device. A 24 MHz single element lead zirconate titanate (PZT) transducer was built to transmit a focused ultrasound of variable duty factors (pulse duration/pulse repetition time), and its 1-3 piezocomposite structure established a tight focusing with f-number (focal depth/aperture size) of one. The transducer was excited by the Chebyshev windowed chirp signal sweeping from 18 MHz to 30 MHz with a 50% of duty factor, in order to ensure that enough sound beams were penetrated into the microfluidic device. The device was fabricated from a polydimethylsiloxane (PDMS) mold, and had a main channel composed of three subchannels among which particles flowed in the middle. A 60~70 ?m diameter single droplet in the flow could be trapped near the channel bifurcation, and subsequently diverted into the sheath flow by releasing or shifting the acoustic trap. Hence, the results showed the potential use of a focused sound beam in microfluidic devices, and further suggested that this method could be exploited in the development of ultrasound-based flow cytometry and cell sorting devices.

| S-EPMC3217264 | biostudies-literature

DNA Assembly in 3D Printed Fluidics.

Project description:The process of connecting genetic parts-DNA assembly-is a foundational technology for synthetic biology. Microfluidics present an attractive solution for minimizing use of costly reagents, enabling multiplexed reactions, and automating protocols by integrating multiple protocol steps. However, microfluidics fabrication and operation can be expensive and requires expertise, limiting access to the technology. With advances in commodity digital fabrication tools, it is now possible to directly print fluidic devices and supporting hardware. 3D printed micro- and millifluidic devices are inexpensive, easy to make and quick to produce. We demonstrate Golden Gate DNA assembly in 3D-printed fluidics with reaction volumes as small as 490 nL, channel widths as fine as 220 microns, and per unit part costs ranging from $0.61 to $5.71. A 3D-printed syringe pump with an accompanying programmable software interface was designed and fabricated to operate the devices. Quick turnaround and inexpensive materials allowed for rapid exploration of device parameters, demonstrating a manufacturing paradigm for designing and fabricating hardware for synthetic biology.

| S-EPMC4699221 | biostudies-literature

In-fibre particle manipulation and device assembly via laser induced thermocapillary convection.

Project description:The ability to manipulate in-fibre particles is of technological and scientific significance, yet particle manipulation inside solid environment remains fundamentally challenging. Here we show an accurately controlled, non-contact, size- and material-independent method for manipulating in-fibre particles based on laser-induced thermocapillary convection. The laser liquefaction process transforms the fibre from a solid media into an ideal fluid environment and triggers the in-fibre thermocapillary convection. In-fibre particles, with diameter from submicron to hundreds of microns, can be migrated toward the designated position. The number of particles being migrated, the particle migration velocity and direction can be precisely controlled. As a proof-of-concept, the laser-induced flow currents lead to the migration-to-contact of dislocated in-fibre p- and n-type semiconductor particles and the forming of dual-particle p-n homo- and heterojunction directly in a fibre. This approach not only enables in-fibre device assembly to achieve multi-component fibre devices, but also provide fundamental insight for in-solid particle manipulation.

| S-EPMC6858441 | biostudies-literature

Accelerating Enzymatic Catalysis Using Vortex Fluidics.

Project description:Enzymes catalyze chemical transformations with outstanding stereo- and regio-specificities, but many enzymes are limited by their long reaction times. A general method to accelerate enzymes using pressure waves contained within thin films is described. Each enzyme responds best to specific frequencies of pressure waves, and an acceleration landscape for each protein is reported. A vortex fluidic device introduces pressure waves that drive increased rate constants (kcat ) and enzymatic efficiency (kcat /Km ). Four enzymes displayed an average seven-fold acceleration, with deoxyribose-5-phosphate aldolase (DERA) achieving an average 15-fold enhancement using this approach. In solving a common problem in enzyme catalysis, a powerful, generalizable tool for enzyme acceleration has been uncovered. This research provides new insights into previously uncontrolled factors affecting enzyme function.

| S-EPMC5524626 | biostudies-literature

Particle manipulation beyond the diffraction limit using structured super-oscillating light beams.

Project description:The diffraction-limited resolution of light focused by a lens was derived in 1873 by Ernst Abbe. Later in 1952, a method to reach sub-diffraction light spots was proposed by modulating the wavefront of the focused beam. In a related development, super-oscillating functions, that is, band-limited functions that locally oscillate faster than their highest Fourier component, were introduced and experimentally applied for super-resolution microscopy. Up till now, only simple Gaussian-like sub-diffraction spots were used. Here we show that the amplitude and phase profile of these sub-diffraction spots can be arbitrarily controlled. In particular, we utilize Hermite-Gauss, Laguerre-Gauss and Airy functions to structure super-oscillating beams with sub-diffraction lobes. These structured beams are then used for high-resolution trapping and manipulation of nanometer-sized particles. The trapping potential provides unprecedented localization accuracy and stiffness, significantly exceeding those provided by standard diffraction-limited beams.

| S-EPMC6062334 | biostudies-literature

Spectrally reconfigurable integrated multi-spot particle trap.

Project description:Optical manipulation of small particles in the form of trapping, pushing, or sorting has developed into a vast field with applications in the life sciences, biophysics, and atomic physics. Recently, there has been increasing effort toward integration of particle manipulation techniques with integrated photonic structures on self-contained optofluidic chips. Here, we use the wavelength dependence of multi-spot pattern formation in multimode interference (MMI) waveguides to create a new type of reconfigurable, integrated optical particle trap. Interfering lateral MMI modes create multiple trapping spots in an intersecting fluidic channel. The number of trapping spots can be dynamically controlled by altering the trapping wavelength. This novel, spectral reconfigurability is utilized to deterministically move single and multiple particles between different trapping locations along the channel. This fully integrated multi-particle trap can form the basis of high throughput biophotonic assays on a chip.

| S-EPMC4833011 | biostudies-literature

A Temperature-Jump Optical Trap for Single-Molecule Manipulation.

Project description:To our knowledge, we have developed a novel temperature-jump optical tweezers setup that changes the temperature locally and rapidly. It uses a heating laser with a wavelength that is highly absorbed by water so it can cover a broad range of temperatures. This instrument can record several force-distance curves for one individual molecule at various temperatures with good thermal and mechanical stability. Our design has features to reduce convection and baseline shifts, which have troubled previous heating-laser instruments. As proof of accuracy, we used the instrument to carry out DNA unzipping experiments in which we derived the average basepair free energy, entropy, and enthalpy of formation of the DNA duplex in a range of temperatures between 5°C and 50°C. We also used the instrument to characterize the temperature-dependent elasticity of single-stranded DNA (ssDNA), where we find a significant condensation plateau at low force and low temperature. Oddly, the persistence length of ssDNA measured at high force seems to increase with temperature, contrary to simple entropic models.

| S-EPMC4472040 | biostudies-literature

Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs.

Project description:MotivationWith the current pace at which reference genomes are being produced, the availability of tools that can reliably and efficiently generate genome assembly summary statistics has become critical. Additionally, with the emergence of new algorithms and data types, tools that can improve the quality of existing assemblies through automated and manual curation are required.ResultsWe sought to address both these needs by developing gfastats, as part of the Vertebrate Genomes Project (VGP) effort to generate high-quality reference genomes at scale. Gfastats is a standalone tool to compute assembly summary statistics and manipulate assembly sequences in FASTA, FASTQ or GFA [.gz] format. Gfastats stores assembly sequences internally in a GFA-like format. This feature allows gfastats to seamlessly convert FAST* to and from GFA [.gz] files. Gfastats can also build an assembly graph that can in turn be used to manipulate the underlying sequences following instructions provided by the user, while simultaneously generating key metrics for the new sequences.Availability and implementationGfastats is implemented in C++. Precompiled releases (Linux, MacOS, Windows) and commented source code for gfastats are available under MIT licence at https://github.com/vgl-hub/gfastats. Examples of how to run gfastats are provided in the GitHub. Gfastats is also available in Bioconda, in Galaxy (https://assembly.usegalaxy.eu) and as a MultiQC module (https://github.com/ewels/MultiQC). An automated test workflow is available to ensure consistency of software updates.Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC9438950 | biostudies-literature

A Plasmonic Spanner for Metal Particle Manipulation.

Project description:Typically, metal particles are difficult to manipulate with conventional optical vortex (OV) tweezers, because of their strong absorption and scattering. However, it has been shown that the vortex field of surface plasmonic polaritons, called plasmonic vortex (PV), is capable of stable trapping and dynamic rotation of metal particles, especially those of mesoscopic and Mie size. To uncover the different physical mechanisms of OV and PV tweezers, we investigated the force distribution and trapping potential of metal particles. In OV tweezers the stronger scattering force causes a positive potential barrier that repels particles, whereas in PV tweezers the dominant gradient force contributes to a negative potential well, resulting in stably trapped particles. Compared with OV, the orbital angular momentum of PV produces an azimuthal scattering force that rotates the trapped particles with more precise radius and position. Our results demonstrate that PV tweezers are superior in manipulation of metal particles.

| S-EPMC4612544 | biostudies-literature

Serial dilution via surface energy trap-assisted magnetic droplet manipulation.

Project description:This paper demonstrates a facile method of generating precise serial dilutions in the form of droplets on an open surface platform. The method relies on the use of surface energy traps (SETs), etched areas of high surface energy on a Teflon coated glass substrate, to assist in the magnetic manipulation of droplets to meter and dispense liquid of defined volumes for the preparation of serial dilutions. The volume of the dispensed liquid can be precisely controlled by the size of the SETs, facilitating generation of concentration profiles of high linearity. We have applied this approach to the generation of serial dilutions of antibiotics for anti-microbial susceptibility testing (AST).

| S-EPMC3963271 | 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