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- Collins, D., et al.
(author)
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Lord Kelvin's isotropic helicoid
- 2021
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In: Physical Review Fluids. - 2469-990X. ; 6:7
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Journal article (peer-reviewed)abstract
- Nearly 150 years ago, Lord Kelvin proposed the isotropic helicoid, a particle with isotropic yet chiral interactions with a fluid so that translation couples to rotation. An implementation of his design fabricated with a three-dimensional printer is found experimentally to have no detectable translation-rotation coupling, although the particle point-group symmetry allows this coupling. We explain these results by demonstrating that in Stokes flow, the chiral coupling of such isotropic helicoids made out of nonchiral vanes is due only to hydrodynamic interactions between these vanes. Therefore it is small. In summary, Kelvin's predicted isotropic helicoid exists, but only as a weak breaking of a symmetry of noninteracting vanes in Stokes flow.
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- Hejazi, B., et al.
(author)
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Emergent scar lines in chaotic advection of passive directors
- 2017
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In: Physical Review Fluids. - 2469-990X. ; 2:12
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Journal article (peer-reviewed)abstract
- We examine the spatial field of orientations of slender fibers that are advected by a two-dimensional fluid flow. The orientation field of these passive directors are important in a wide range of industrial and geophysical flows. We introduce emergent scar lines as the dominant coherent structures in the orientation field of passive directors in chaotic flows. Previous work has identified the existence of scar lines where the orientation rotates by p over short distances, but the lines that were identified disappeared as time progressed. As a result, earlier work focused on topological singularities in the orientation field, which we find to play a negligible role at long times. We use the standard map as a simple time-periodic two-dimensional flow that produces Lagrangian chaos. This class of flows produces persistent patterns in passive scalar advection and we find that a different kind of persistent pattern develops in the passive director orientation field. We identify the mechanism by which emergent scar lines grow to dominate these patterns at long times in complex flows. Emergent scar lines form where the recent stretching of the fluid element is perpendicular to earlier stretching. Thus these scar lines can be labeled by their age, defined as the time since their stretching reached a maximum.
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- Lee, Hyun Ju, et al.
(author)
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Intricate role of water in proton transport through cytochrome c oxidase
- 2010
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In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 132:45, s. 16225-16239
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Journal article (peer-reviewed)abstract
- Cytochrome c oxidase (CytcO), the final electron acceptor in the respiratory chain, catalyzes the reduction of O2 to H2O while simultaneously pumping protons across the inner mitochondrial or bacterial membrane to maintain a transmembrane electrochemical gradient that drives, for example, ATP synthesis. In this work mutations that were predicted to alter proton translocation and enzyme activity in preliminary computational studies are characterized with extensive experimental and computational analysis. The mutations were introduced in the D pathway, one of two proton-uptake pathways, in CytcO from Rhodobacter sphaeroides. Serine residues 200 and 201, which are hydrogen-bonded to crystallographically resolved water molecules halfway up the D pathway, were replaced by more bulky hydrophobic residues (Ser200Ile, Ser200Val/Ser201Val, and Ser200Val/Ser201Tyr) to query the effects of changing the local structure on enzyme activity as well as proton uptake, release, and intermediate transitions. In addition, the effects of these mutations on internal proton transfer were investigated by blocking proton uptake at the pathway entrance (Asp132Asn replacement in addition to the above-mentioned mutations). Even though the overall activities of all mutant CytcO's were lowered, both the Ser200Ile and Ser200Val/Ser201Val variants maintained the ability to pump protons. The lowered activities were shown to be due to slowed oxidation kinetics during the PR → F and F → O transitions (PR is the "peroxy" intermediate formed at the catalytic site upon reaction of the four-electron-reduced CytcO with O2, F is the oxoferryl intermediate, and O is the fully oxidized CytcO). Furthermore, the PR → F transition is shown to be essentially pH independent up to pH 12 (i.e., the apparent pKa of Glu286 is increased from 9.4 by at least 3 pKa units) in the Ser200Val/Ser201Val mutant. Explicit simulations of proton transport in the mutated enzymes revealed that the solvation dynamics can cause intriguing energetic consequences and hence provide mechanistic insights that would never be detected in static structures or simulations of the system with fixed protonation states (i.e., lacking explicit proton transport). The results are discussed in terms of the proton-pumping mechanism of CytcO.
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- Zhao, L., et al.
(author)
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Passive directors in turbulence
- 2019
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In: Physical Review Fluids. - 2469-990X. ; 4:5
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Journal article (peer-reviewed)abstract
- In experiments and numerical simulations we measure angles between the symmetry axes of small spheroids advected in turbulence (passive directors). Since turbulent strains tend to align nearby spheroids, one might think that their relative angles are quite small. We show that this intuition fails in general because angles between the symmetry axes of nearby particles are anomalously large. We identify two mechanisms that cause this phenomenon. First, the dynamics evolves to a fractal attractor despite the fact that the fluid velocity is spatially smooth at small scales. Second, this fractal forms steps akin to scar lines observed in the director patterns for random or chaotic two-dimensional maps.
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