Structure-Based Models of Biomolecules: Stretching of Proteins, Dynamics of Knots, Hydrodynamic Effects, and Indentation of Virus Capsids

Author(s):  
Marek Cieplak ◽  
Joanna I. Sułkowska
Author(s):  
U. Aebi ◽  
L.E. Buhle ◽  
W.E. Fowler

Many important supramolecular structures such as filaments, microtubules, virus capsids and certain membrane proteins and bacterial cell walls exist as ordered polymers or two-dimensional crystalline arrays in vivo. In several instances it has been possible to induce soluble proteins to form ordered polymers or two-dimensional crystalline arrays in vitro. In both cases a combination of electron microscopy of negatively stained specimens with analog or digital image processing techniques has proven extremely useful for elucidating the molecular and supramolecular organization of the constituent proteins. However from the reconstructed stain exclusion patterns it is often difficult to identify distinct stain excluding regions with specific protein subunits. To this end it has been demonstrated that in some cases this ambiguity can be resolved by a combination of stoichiometric labeling of the ordered structures with subunit-specific antibody fragments (e.g. Fab) and image processing of the electron micrographs recorded from labeled and unlabeled structures.


2016 ◽  
Vol 11 (1) ◽  
pp. 30-37 ◽  
Author(s):  
A.A. Rakhimov ◽  
A.T. Akhmetov

The paper presents results of hydrodynamic and rheological studies of the inverse water hydrocarbon emulsions. The success of the application of invert emulsions in the petroleum industry due, along with the high viscosity of the emulsion, greatly exceeding the viscosity of the carrier phase, the dynamic blocking effect, which consists in the fact that the rate of flow of emulsions in capillary structures and cracks falls with time to 3-4 orders, despite the permanent pressure drop. The reported study shows an increase in viscosity with increasing concentration or dispersion of emulsion. The increase in dispersion of w/o emulsion leads to an acceleration of the onset of dynamic blocking. The use of microfluidic devices, is made by soft photolithography, along with high-speed photography (10,000 frames/s), allowed us to see in the blocking condition the deformation of the microdroplets of water in inverse emulsion prepared from simple chemical compounds.


2021 ◽  
Vol 120 (3) ◽  
pp. 221a
Author(s):  
Mounir Fizari ◽  
Nicholas A. Keller ◽  
Douglas E. Smith

RSC Advances ◽  
2021 ◽  
Vol 11 (46) ◽  
pp. 28723-28734
Author(s):  
Amit Prabhakar ◽  
Ankur Jaiswar ◽  
Neha Mishra ◽  
Praveen Kumar ◽  
Amar Dhwaj ◽  
...  

A microfluidic device displaying multiple hydrodynamic effects was designed to separate suspended impurities (i.e. bacteria and similar length scale particles present in water in the suspension form) from water.


2012 ◽  
Vol 9 (73) ◽  
pp. 1767-1773 ◽  
Author(s):  
Tyler Skorczewski ◽  
Angela Cheer ◽  
Peter C. Wainwright

Suction feeding is the most common form of prey capture across aquatic feeding vertebrates and many adaptations that enhance efficiency and performance are expected. Many suction feeders have mechanisms that allow the mouth to form a planar and near-circular opening that is believed to have beneficial hydrodynamic effects. We explore the effects of the flattened and circular mouth opening through computational fluid dynamics simulations that allow comparisons with other mouth profiles. Compared to mouths with lateral notches, we find that the planar mouth opening results in higher flow rates into the mouth and a region of highest flow that is positioned at the centre of the mouth aperture. Planar mouths provide not only for better total fluid flow rates through the mouth but also through the centre of the mouth near where suction feeders position their prey. Circular mouths are shown to provide the quickest capture times for spherical and elliptical prey because they expose the prey item to a large region of high flow. Planar and circular mouths result in higher flow velocities with peak flow located at the centre of the mouth opening and they maximize the capacity of the suction feeders to exert hydrodynamic forces on the prey.


2018 ◽  
Vol 9 ◽  
pp. 301-310 ◽  
Author(s):  
Stefan Fringes ◽  
Felix Holzner ◽  
Armin W Knoll

The behavior of nanoparticles under nanofluidic confinement depends strongly on their distance to the confining walls; however, a measurement in which the gap distance is varied is challenging. Here, we present a versatile setup for investigating the behavior of nanoparticles as a function of the gap distance, which is controlled to the nanometer. The setup is designed as an open system that operates with a small amount of dispersion of ≈20 μL, permits the use of coated and patterned samples and allows high-numerical-aperture microscopy access. Using the tool, we measure the vertical position (termed height) and the lateral diffusion of 60 nm, charged, Au nanospheres as a function of confinement between a glass surface and a polymer surface. Interferometric scattering detection provides an effective particle illumination time of less than 30 μs, which results in lateral and vertical position detection accuracy ≈10 nm for diffusing particles. We found the height of the particles to be consistently above that of the gap center, corresponding to a higher charge on the polymer substrate. In terms of diffusion, we found a strong monotonic decay of the diffusion constant with decreasing gap distance. This result cannot be explained by hydrodynamic effects, including the asymmetric vertical position of the particles in the gap. Instead we attribute it to an electroviscous effect. For strong confinement of less than 120 nm gap distance, we detect the onset of subdiffusion, which can be correlated to the motion of the particles along high-gap-distance paths.


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