A Concentrator of E. coli in Water Flow

2012 ◽  
Author(s):  
Mohammed S. Mayeed ◽  
Golam M. Newaz
Keyword(s):  
State Of The Art ◽  
Optimized Design ◽  
Inlet Concentration ◽  
E Coli ◽  
High Particle ◽  
Lagrangian Equations ◽  
Order Of Magnitude ◽  
Computational Research ◽  
Water Ratio ◽  
Particle Boundary

The objective of this research is to design and optimize a mini/micro-channel based concentrator of E. coli and integrate it with an acoustic wave biosensor. A computational research has been carried out using the state of the art computational software, CFD-ACE with water as bacteria bearing fluid. E. coli bacteria have been modeled as random discrete particles tracked by solving the Lagrangian equations. The design challenges are to achieve high particle to water ratio, high enough Reynolds number to avoid bacteria swimming, and various particle boundary conditions. The optimized design has achieved concentration of more than an order of magnitude higher than the inlet concentration at a flow velocity much higher than the bacteria swimming speed under various particle-boundary interactions. Bypass channels have been used to separate concentrated water-particle mixture and to put this mixture directly onto the biosensor’s bacteria detecting surface for safe and precise installation of the biosensor in the fluidic chip.

A Micro/Mini Channel Based Concentrator of E. coli in Water Flow

2007 ◽  
Author(s):  
Mohammed S. Mayeed ◽  
Abdulhakeem M. Al-Mekhnaqi ◽  
Gregory W. Auner ◽  
Golam M. Newaz
Keyword(s):  
State Of The Art ◽  
Optimized Design ◽  
Inlet Concentration ◽  
E Coli ◽  
High Particle ◽  
Lagrangian Equations ◽  
Order Of Magnitude ◽  
Computational Research ◽  
Water Ratio ◽  
Particle Boundary

The objective of this research is to design and optimize a mini/micro-channel based concentrator of E. coli and integrate it with an acoustic wave biosensor. A computational research has been carried out using the state of the art computational software, CFD-ACE with water as bacteria bearing fluid. E. coli bacteria have been modeled as random discrete particles tracked by solving the Lagrangian equations. The design challenges are to achieve high particle to water ratio, high enough Reynolds number to avoid bacteria swimming, and various particle boundary conditions. The optimized design has achieved concentration of about an order of magnitude higher than the inlet concentration at a flow velocity much higher than the bacteria swimming speed under various particle-boundary interactions. Bypass channels have been used to separate concentrated water-particle mixture and to put this mixture directly onto the biosensor’s bacteria detecting surface for safe and precise installation of the biosensor in the fluidic chip.

Surface Accumulating E. coli in Water Flow Using a Bypass Mini-Channel Based Device

2014 ◽  
Author(s):  
Mohammed S. Mayeed ◽  
Golam Newaz
Keyword(s):  
State Of The Art ◽  
Inlet Concentration ◽  
E Coli ◽  
High Particle ◽  
Lagrangian Equations ◽  
Order Of Magnitude ◽  
Computational Research ◽  
Water Ratio ◽  
Design Challenges ◽  
Particle Boundary

The objective of this research is to design and optimize a bypass mini/micro-channel based surface accumulator of E. coli which could be easily integrated with an acoustic wave biosensor. A computational research has been carried out using the state of the art computational software, CFD-ACE with water as bacteria bearing fluid. E. coli bacteria have been modeled as random discrete particles tracked by solving the Lagrangian equations. The design challenges are to achieve high particle to water ratio in a bypass channel and accumulation of particles on a surface of the channel, high enough Reynolds number to avoid bacteria swimming, and various particle boundary conditions. The optimized designs have achieved accumulation concentration of more than an order of magnitude higher than the inlet concentration at a flow velocity much higher than the bacteria swimming speed under various particle-boundary interactions. A bypass channel has been used in this design to separate concentrated water-particle mixture and accumulate particles on a surface of the channel where the biosensor can be installed safely and precisely.

Accumulation of E. Coli Bacteria in Mini-Channel Flow

2005 ◽  
Vol 128 (3) ◽  
pp. 458-461 ◽  
Author(s):  
M. S. Mayeed ◽  
A. Mian ◽  
G. W. Auner ◽  
G. M. Newaz
Keyword(s):  
Reynolds Number ◽  
Shear Force ◽  
State Of The Art ◽  
Inlet Concentration ◽  
High Concentration ◽  
E Coli ◽  
Lower Shear ◽  
Lagrangian Equations ◽  
Particle Boundary ◽  
Low Shear

The objective of this research is to design and optimize a mini/micro-channel based surface-accumulator of E. coli bacteria to be detected by acoustic wave biosensors. A computational approach has been carried out using the state of the art software, CFD-ACE with water as bacteria bearing fluid. E. coli bacteria have been modeled as random discrete particles tracked by solving the Lagrangian equations. The design challenges are to achieve low shear force (pico-N), high concentration at accumulation, and high enough Reynolds number to avoid bacteria swimming. A range of low Reynolds number (Re) has been considered along with the effects of particle boundary interactions, gravity, Saffman lift, etc. More than two orders of magnitude higher concentration at the accumulation than the inlet concentration, and lower shear force of less than pico-N have been achieved in the optimized designs.

scholarly journals Passively parallel regularized stokeslets

2020 ◽  
Vol 378 (2179) ◽  
pp. 20190528
Author(s):  
Meurig T. Gallagher ◽  
David J. Smith
Keyword(s):  
Gpu Computing ◽  
State Of The Art ◽  
Computer Code ◽  
Flagellar Motility ◽  
The Past ◽  
Recent Modification ◽  
Flow Phenomena ◽  
Order Of Magnitude ◽  
Computational Research ◽  
Magnitude Improvement

Stokes flow, discussed by G.G. Stokes in 1851, describes many microscopic biological flow phenomena, including cilia-driven transport and flagellar motility; the need to quantify and understand these flows has motivated decades of mathematical and computational research. Regularized stokeslet methods, which have been used and refined over the past 20 years, offer significant advantages in simplicity of implementation, with a recent modification based on nearest-neighbour interpolation providing significant improvements in efficiency and accuracy. Moreover this method can be implemented with the majority of the computation taking place through built-in linear algebra, entailing that state-of-the-art hardware and software developments in the latter, in particular multicore and GPU computing, can be exploited through minimal modifications (‘passive parallelism’) to existing Matlab computer code. Hence, and with widely available GPU hardware, significant improvements in the efficiency of the regularized stokeslet method can be obtained. The approach is demonstrated through computational experiments on three model biological flows: undulatory propulsion of multiple Caenorhabditis elegans , simulation of progression and transport by multiple sperm in a geometrically confined region, and left–right symmetry breaking particle transport in the ventral node of the mouse embryo. In general an order-of-magnitude improvement in efficiency is observed. This development further widens the complexity of biological flow systems that are accessible without the need for extensive code development or specialist facilities. This article is part of the theme issue ‘Stokes at 200 (part 2)’.

scholarly journals Small footprint optoelectrodes using ring resonators for passive light localization

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Vittorino Lanzio ◽  
Gregory Telian ◽  
Alexander Koshelev ◽  
Paolo Micheletti ◽  
Gianni Presti ◽  
...  
Keyword(s):  
State Of The Art ◽  
Three Dimensional ◽  
Network Activity ◽  
Ring Resonators ◽  
Spatiotemporal Resolution ◽  
Optical Ring Resonators ◽  
Light Localization ◽  
Order Of Magnitude ◽  
Small Footprint

AbstractThe combination of electrophysiology and optogenetics enables the exploration of how the brain operates down to a single neuron and its network activity. Neural probes are in vivo invasive devices that integrate sensors and stimulation sites to record and manipulate neuronal activity with high spatiotemporal resolution. State-of-the-art probes are limited by tradeoffs involving their lateral dimension, number of sensors, and ability to access independent stimulation sites. Here, we realize a highly scalable probe that features three-dimensional integration of small-footprint arrays of sensors and nanophotonic circuits to scale the density of sensors per cross-section by one order of magnitude with respect to state-of-the-art devices. For the first time, we overcome the spatial limit of the nanophotonic circuit by coupling only one waveguide to numerous optical ring resonators as passive nanophotonic switches. With this strategy, we achieve accurate on-demand light localization while avoiding spatially demanding bundles of waveguides and demonstrate the feasibility with a proof-of-concept device and its scalability towards high-resolution and low-damage neural optoelectrodes.

Two Orders of Magnitude Improvement in the Detection Limit of Droplet-Based Micro-Magnetofluidics with Planar Hall Effect Sensors

2021 ◽  
Vol 6 (1) ◽  
pp. 47
Author(s):  
Julian Schütt ◽  
Rico Illing ◽  
Oleksii Volkov ◽  
Tobias Kosub ◽  
Pablo Nicolás Granell ◽  
...  
Keyword(s):  
Detection Limit ◽  
Hall Effect ◽  
State Of The Art ◽  
Limit Of Detection ◽  
Research Field ◽  
High Throughput Analysis ◽  
Planar Hall Effect ◽  
Biologically Relevant ◽  
Sensing Platform ◽  
Order Of Magnitude

The detection, manipulation, and tracking of magnetic nanoparticles is of major importance in the fields of biology, biotechnology, and biomedical applications as labels as well as in drug delivery, (bio-)detection, and tissue engineering. In this regard, the trend goes towards improvements of existing state-of-the-art methodologies in the spirit of timesaving, high-throughput analysis at ultra-low volumes. Here, microfluidics offers vast advantages to address these requirements, as it deals with the control and manipulation of liquids in confined microchannels. This conjunction of microfluidics and magnetism, namely micro-magnetofluidics, is a dynamic research field, which requires novel sensor solutions to boost the detection limit of tiny quantities of magnetized objects. We present a sensing strategy relying on planar Hall effect (PHE) sensors in droplet-based micro-magnetofluidics for the detection of a multiphase liquid flow, i.e., superparamagnetic aqueous droplets in an oil carrier phase. The high resolution of the sensor allows the detection of nanoliter-sized superparamagnetic droplets with a concentration of 0.58 mg cm−3, even when they are only biased in a geomagnetic field. The limit of detection can be boosted another order of magnitude, reaching 0.04 mg cm−³ (1.4 million particles in a single 100 nL droplet) when a magnetic field of 5 mT is applied to bias the droplets. With this performance, our sensing platform outperforms the state-of-the-art solutions in droplet-based micro-magnetofluidics by a factor of 100. This allows us to detect ferrofluid droplets in clinically and biologically relevant concentrations, and even in lower concentrations, without the need of externally applied magnetic fields.

scholarly journals STUDIES ON HEMAGGLUTINATION AND HEMOLYSIS BY ESCHERICHIA COLI ANTISERA

1952 ◽  
Vol 96 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Erwin Neter ◽  
Lee F. Bertram ◽  
Dorothy A. Zak ◽  
Miriam R. Murdock ◽  
Carl E. Arbesman
Keyword(s):  
Escherichia Coli ◽  
Guinea Pig ◽  
Red Blood Cells ◽  
Blood Cells ◽  
Homologous Blood ◽  
E Coli ◽  
Blood Group A ◽  
Human Red Blood Cells ◽  
Order Of Magnitude ◽  
Group A

A study on hemagglutination and hemolysis by Escherichia coli O111 and O55 (rabbit) antisera and on hemagglutination and hemolysis inhibition by E. coli O111 and O55 antigens revealed the following facts. 1. Red blood cells of man, dog, rabbit, guinea pig, sheep, rat, and chicken adsorb E. coli O111 and O55 antigens and thus become specifically agglutinable by the homologous E. coli antisera. 2. The adsorption of these E. coli antigens is a function of the concentration of the antigen, the time (from 5 minutes to 2 hours) of treatment of the red blood cells with the antigen, and the concentration of the red blood cells used. 3. Red blood cells of man and sheep adsorb simultaneously both antigens, as indicated by the fact that both antisera give agglutination of all red blood cells. Complete agglutination does not occur when a mixture of red blood cells treated separately with the two antigens is added to one or the other of the two antisera. 4. Treatment of red blood cells of man with one of the antigens does not block the adsorption of the second antigen. Human cells treated with either or both antigens are still agglutinated by the homologous blood group (A, B, and Rh)-specific antibodies. 5. In the presence of guinea pig complement, E. coli O111 and O55 antisera produce hemolysis of modified human red blood cells in titers of the same order of magnitude as those giving hemagglutination and bacterial agglutination. The same antisera produce hemolysis of sheep cells treated with the identical antigens in titers exceeding by far those giving agglutination of modified human or sheep red blood cells. 6. Both sediment and supernate of a boiled E. coli suspension are capable of modifying red blood cells for E. coli hemagglutination; in contrast, the supernate obtained from an unboiled suspension and then heated does not modify red blood cells for hemagglutination, although it contains the antigen which can specifically adsorb E. coli antibodies, as shown by means of the hemagglutination and hemolysis inhibition tests. 7. Both the unheated and the boiled suspensions of E. coli O111 and O55 inhibit hemagglutination and hemolysis specifically. 8. Rabbit red blood cells modified by either E. coli O111 or 055 antigens, upon intravenous injection into rabbits, engender specific E. coli antibodies. The significance of the results is discussed.

New Instrumentation in Argonne's Hvem-Tandem Facility: Expanded Capability for in Situ Ion Beam Studies+

1995 ◽  
Vol 396 ◽  
Author(s):  
Charles W. Allen ◽  
Loren L. Funk ◽  
Edward A. Ryan
Keyword(s):  
Scientific Community ◽  
State Of The Art ◽  
Ion Irradiation ◽  
Ion Beam ◽  
Voltage Electron ◽  
User Facility ◽  
Order Of Magnitude ◽  
New Instrumentation ◽  
Better Than

AbstractDuring 1995, a state-of-the-art intermediate voltage electron microscope (IVEM) has been installed in the HVEM-Tandem Facility with in situ ion irradiation capabilities similar to those of the HVEM. A 300 kV Hitachi H-9000NAR has been interfaced to the two ion accelerators of the Facility, with a spatial resolution for imaging which is nearly an order of magnitude better than that for the 1.2 MV HVEM which dates from the early 1970s. The HVEM remains heavily utilized for electron- and ion irradiation-related materials studies, nevertheless, especially those for which less demanding microscopy is adequate. The capabilities and limitations of this IVEM and HVEM are compared. Both the HVEM and IVEM are part of the DOE funded User Facility and therefore are available to the scientific community for materials studies, free of charge for non-proprietary research.

scholarly journals Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation

2019 ◽  
Vol 21 (1) ◽  
pp. 1-31 ◽  
Author(s):  
Lindong Weng ◽  
Shannon L. Stott ◽  
Mehmet Toner
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Motion ◽  
State Of The Art ◽  
Level Structure ◽  
Cost Effective ◽  
Atomic Level ◽  
Computational Research ◽  
Dynamics Simulations ◽  
Biological Entities

Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.

scholarly journals Increased Mutation Frequency in Redox-Impaired Escherichia coli Due to RelA- and RpoS-Mediated Repression of DNA Repair

2010 ◽  
Vol 76 (16) ◽  
pp. 5463-5470 ◽  
Author(s):  
Amarjeet Singh ◽  
Anis Karimpour-Fard ◽  
Ryan T. Gill
Keyword(s):  
Escherichia Coli ◽  
Dna Repair ◽  
Mutation Frequency ◽  
Spontaneous Mutation ◽  
Regulatory Gene ◽  
Stringent Response ◽  
Anaerobic Growth ◽  
E Coli ◽  
Direct Measurements ◽  
Order Of Magnitude

ABSTRACT Balancing of reducing equivalents is a fundamental issue in bacterial metabolism and metabolic engineering. Mutations in the key metabolic genes ldhA and pflB of Escherichia coli are known to stall anaerobic growth and fermentation due to a buildup of intracellular NADH. We observed that the rate of spontaneous mutation in E. coli BW25113 (ΔldhA ΔpflB) was an order of magnitude higher than that in wild-type (WT) E. coli BW25113. We hypothesized that the increased mutation frequency was due to an increased NADH/NAD+ ratio in this strain. Using several redox-impaired strains of E. coli and different redox conditions, we confirmed a significant correlation (P < 0.01) between intracellular-NADH/NAD+ ratio and mutation frequency. To identify the genetic basis for this relationship, whole-genome transcriptional profiles were compared between BW25113 WT and BW25113 (ΔldhA ΔpflB). This analysis revealed that the genes involved in DNA repair were expressed at significantly lower levels in BW25113 (ΔldhA ΔpflB). Direct measurements of the extent of DNA repair in BW25113 (ΔldhA ΔpflB) subjected to UV exposure confirmed that DNA repair was inhibited. To identify a direct link between DNA repair and intracellular-redox ratio, the stringent-response-regulatory gene relA and the global-stress-response-regulatory gene rpoS were deleted. In both cases, the mutation frequencies were restored to BW25113 WT levels.

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