Undulating Ribbon Research Articles

Cryo-EM structures of light-harvesting 2 complexes from Rhodopseudomonas palustris reveal the molecular origin of absorption tuning

The genomes of some purple photosynthetic bacteria contain a multigene puc family encoding a series of α- and β-polypeptides that together form a heterogeneous antenna of light-harvesting 2 (LH2) complexes. To unravel this complexity, we generated four sets of puc deletion mutants in Rhodopseudomonas palustris, each encoding a single type of pucBA gene pair and enabling the purification of complexes designated as PucA-LH2, PucB-LH2, PucD-LH2, and PucE-LH2. The structures of all four purified LH2 complexes were determined by cryogenic electron microscopy (cryo-EM) at resolutions ranging from 2.7 to 3.6 Å. Uniquely, each of these complexes contains a hitherto unknown polypeptide, γ, that forms an extended undulating ribbon that lies in the plane of the membrane and that encloses six of the nine LH2 αβ-subunits. The γ-subunit, which is located near to the cytoplasmic side of the complex, breaks the C9 symmetry of the LH2 complex and binds six extra bacteriochlorophylls (BChls) that enhance the 800-nm absorption of each complex. The structures show that all four complexes have two complete rings of BChls, conferring absorption bands centered at 800 and 850 nm on the PucA-LH2, PucB-LH2, and PucE-LH2 complexes, but, unusually, the PucD-LH2 antenna has only a single strong near-infared (NIR) absorption peak at 803 nm. Comparison of the cryo-EM structures of these LH2 complexes reveals altered patterns of hydrogen bonds between LH2 αβ-side chains and the bacteriochlorin rings, further emphasizing the major role that H bonds play in spectral tuning of bacterial antenna complexes.

Dynamic modeling of biomimetic undulatory ribbon fin underwater propulsor actuated by IPMC

Abstract In this paper, electro-mechanical dynamic modeling of a biomimetic propulsor based on undulating ribbon fin is proposed. Kinematics of the system is considered as the sinusoidal undulating motion of the ribbon fin which is guided by the actuating ionic polymer metal composite material. This is a smart material that actuates when an input voltage is applied and composed of a simple RC circuit. Elongated body theory is used to produce system dynamics considering the kinematics and also the hydrodynamic parameters like drag is undertaken as the application aspect is underwater environment. The proposed model has been used to evaluate the speed and thrust of the biomimetic system. Also, the thrust efficiency can be obtained for the different input frequencies. The proposed model may contribute to the understanding of an undulating ribbon fin inspired by IPMC for the underwater locomotion.

Shape-shifting panel from 3D printed undulated ribbon lattice

Materials that change their shape in response to external stimuli open up new prospects for efficient and versatile design and shaping of three-dimensional objects. Here, we present a novel class of micro-structures exhibiting an extension-bending coupling (EBC) effect, that can be harnessed as an elementary building block for shape-shifting panels. They are built with a single material as a network of undulated ribbons. The deformations mechanisms of both single and connected undulated ribbons are analysed using the finite element method to explain the main features of the EBC mechanism. For a particular micro-structure of the proposed class, the elastic response is investigated both under small strain assumption combining two-scale homogenization with Kirchhoff–Love plate theory, and at finite strains relying on numerical analysis. The range of achievable EBC ratio is then assessed with respect to the geometric parameters of the unit cell. Patterned specimens are manufactured using a commercial FFF Ultimaker 3D printer and are mechanically tested at finite strain up to 20%. The displacement measured by point tracking match the predictions from the finite element simulations and indicate that the structure maintain its properties at finite strain. Moreover, a tensile test load with point-like boundary is proposed to highlight exceptional out of plane displacement. The proposed ribbon based architectures can be combined with active materials for the actuation of shape shifting structures, like soft robots, control systems and power devices.

5-(3-Hydroxyphenyl)-1,3,4-oxadiazole-2(3H)-thione hemihydrate

The title 1,3,4-oxadiazole derivative crystallizes as a hemihydrate, C8H6N2O2S·0.5H2O, with the water molecule located on a twofold rotation axis. The 1,3,4-oxadiazole molecule is essentially planar, the r.m.s. deviation of the non-H atoms being 0.0443 Å. The dihedral angle between the mean planes of the phenyl and oxadiazole rings is 6.101 (17)°. In the crystal, molecules are linked via O—H...S and N—H...O hydrogen bonds involving the water molecule, the N—H group and the thione S atom into undulating ribbons. Additional π–π interactions generate a two-dimensional supramolecular framework extending parallel to (001).

An antibacterial silver(I) supramolecular network assembled from thiophene-2,5-dicarboxylate and benzimidazole

A silver(I) supramolecular network Ag(BIm)2(HTDC) (1) was assembled from thiophene-2,5-dicarboxylic acid (H2TDC) and benzimidazole (BIm) ligands and characterized by single-crystal X-ray diffraction, elemental analysis, FT-IR, and thermal gravimetric analysis. Complex 1 possesses a two-dimensional structure with a hydrogen-bonded grid network, in which the adjacent [Ag(BIm)2]+ cations and (HTDC)– are bridged via N–H···O hydrogen bonds forming undulating ribbons. The antibacterial properties of 1 were investigated by determining the minimal inhibitory concentration (MIC), the growth curve of bacteria and zone inhibition value assays against Gram-negative bacterium, Escherichia coli, and Gram-positive bacterium, Staphylococcus aureus. The MIC of 1 against E. coli and S. aureus are 15-20 ppm and 20-30 ppm which showed that 1 has higher antibacterial activity than commercial silver nanoparticles. The mechanism of antibacterial activity of 1 was also discussed.

Crystal structure and Hirshfeld surface analysis of 1-(4-chloro-phen-yl)-2-{[5-(4-chloro-phen-yl)-1,3,4-oxa-diazol-2-yl]sulfan-yl}ethanone.

In the title compound, C16H10Cl2N2O2S, the dihedral angles formed by the chloro-substituted benzene rings with the central oxa-diazole ring are 6.54 (9) and 6.94 (8)°. In the crystal, C-H⋯N hydrogen bonding links the mol-ecules into undulating ribbons running parallel to the b axis. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are the H⋯C (18%), H⋯H (17%), H⋯Cl (16.6%), H⋯O (10.4%), H⋯N (8.9%) and H⋯S (5.9%) inter-actions.

(5Z)-5-(4-Chlorobenzylidene)-1,3-thiazolidine-2,4-dione

In the title compound, C10H6ClNO2S, the dihedral angle between the planes of the 4-chlorophenyl and thiazolidine rings is 8.62 (9)°. In the crystal, molecules form undulating ribbons running approximately parallel to (101) through N—H...O hydrogen bonds.

1-Ethyl-3-nitroquinolin-4(1H)-one

The title compound, C11H10N2O3, was obtained as side-product in a project focussing on the synthesis of carbolines. It was prepared from nitroquinolinone, ethanol and phosphoryl chloride. With the exception of the methyl group [C—N—C—Cmethyltorsion angle = −96.4 (2)°], the molecule is essentially planar (r.m.s. deviation = 0.033 Å). In the molecular packing, undulating ribbons along thebaxis are connectedviaC—H...O hydrogen bonds; an intramolecular C—H...O interaction is also noted.

Self-Assembly of Amphiphilic Triblock Terpolymers Mediated by Multifunctional Organic Acids: Vesicles, Toroids, and (Undulated) Ribbons

The self-assembly of block copolymers in the presence of additives represents an elegant strategy to adjust micellar morphologies in solution and to design complex structures that are not accessible otherwise. Herein, we use linear ABC triblock terpolymers comprising a polyamine block: polybutadiene-block-poly(tert-butyl methacrylate)-block-poly(2-(dimethylamino)ethyl methacrylate) (PB-b-PtBMA-b-PDMAEMA) terpolymers coassembled with organic di- or triacids in mixtures of THF and water. The interactions between the organic multiacids and the hydrophilic PDMAEMA block can be adjusted via the chain architecture, amount, and functionality of added acid, the solvent quality, and the PDMAEMA block length. Consequently, these parameters allow a certain level of control over the resulting micellar morphology. Characterization by (cryogenic) transmission electron microscopy and atomic force microscopy revealed the formation of spherical, disk-shaped, and toroidal structures, alongside ribbons featuring enlarged end-caps. In the latter case, changing the solvent composition or the amount/type of organic diacid induced the formation of undulated ribbons and, eventually, partition into spherical particles.

2,2-Dibenzylhydrazin-1-ium chloride

In the title salt, C14H17N2 +·Cl−, the central N atom is pyramidal (sum of bond angles = 330.9°) and there is a near orthogonal relationship between the benzene rings [dihedral angle = 89.95 (10)°]. The crystal packing features N—H⋯Cl hydrogen bonds, which lead to a supra­molecular undulating ribbon along the a axis comprising edge-shared eight-membered {⋯HNH⋯Cl}2 synthons. The chains are connected into layers in the ab plane by C—H⋯π inter­actions.

Self-organization of the vesicular stomatitis virus nucleocapsid into a bullet shape

The typical bullet shape of Rhabdoviruses is thought to rely on the matrix protein for stabilizing the nucleocapsid coil. Here we scrutinize the morphology of purified and recombinant nucleocapsids of vesicular stomatitis virus in vitro. We elucidate pH and ionic strength conditions for their folding into conical tips and further growth into whole bullets, and provide cryo-electron microscopy reconstructions of the bullet tip and the helical trunk. We address conformational variability of the reconstituted nucleocapsids and the issue of constraints imposed by the binding of matrix protein. Our findings bridge the gap between the isolated nucleoprotein-RNA string in its form of an undulating ribbon, and the tight bullet-shaped virion skeleton.

Ordered to Isotropic Morphology Transition in Pattern-Directed Dewetting of Polymer Thin Films on Substrates with Different Feature Heights

Controlled dewetting of a thin polymer film on a topographically patterned substrate is an interesting approach for aligning isotropic dewetted structures. In this article, we investigate the influence of substrate feature height (H(S)) on the dewetting pathway and final pattern morphology by studying the dewetting of polystyrene (PS) thin films on grating substrates with identical periodicity (λ(P) = 1.5 μm), but H(S) varying between 10 nm and 120 nm. We identify four distinct categories of final dewetted morphology, with different extent of ordering: (1) array of aligned droplets (H(S) ≈ 120 nm); (2) aligned undulating ribbons (H(S) ≈ 70-100 nm); (3) multilength scale structures with coexisting large droplets uncorrelated to the substrate and smaller droplets/ribbons aligned along the stripes (H(S) ≈ 40-60 nm); and (4) large droplets completely uncorrelated to the substrate (H(S) < 25 nm). The distinct morphologies across the categories are attributed to two major factors: (a) whether the as-cast film is continuous (H(S)≤ 80 nm) or discontinuous (H(S)≥ 100 nm) and (b) in case of a continuous film, whether the film ruptures along each substrate stripe (H(S)≥ 70 nm) or with nucleation of random holes that are not correlated to the substrate features (H(S)≤ 60 nm). While the ranges of H(S) values indicated in the parentheses are valid for PS films with an equivalent thickness (h(E)) ≈ 50.3 nm on a flat substrate, a change in h(E) merely alters the cut-off values of H(S), as the final dewetted morphologies and transition across categories remain generically unaltered. We finally show that the structures obtained by dewetting on different H(S) substrates exhibits different levels of hydrophobicity because of combined spatial variation of chemical and topographic contrast along the surface. Thus, the work reported in this article can find potential application in fabricating surfaces with controlled wettability.

2,3-Dimethoxy-10-oxostrychnidinium 2-(2,4,6-trinitroanilino)benzoate monohydrate: a 1:1 proton-transfer salt of brucine witho-picraminobenzoic acid

In the structure of the title 1:1 proton-transfer compound of brucine with 2-(2,4,6-trinitroanilino)benzoic acid, C(23)H(27)N(2)O(4)(+)·C(13)H(7)N(4)O(8)(-)·H(2)O, the brucinium cations form classic undulating ribbon substructures through overlapping head-to-tail interactions, while the anions and the three related partial solvent water molecules (having occupancies of 0.73, 0.17 and 0.10) occupy the interstitial regions of the structure. The cations are linked to the anions directly through N-H...O(COO(-)) hydrogen bonds and indirectly by the three water molecules, which form similar conjoint cyclic bridging units [graph set R(2)(4)(8)] through O-H...O(C=O) and O-H...O(COO(-)) hydrogen bonds, giving a two-dimensional layered structure. Within the anion, intramolecular N-H...O(COO(-)) and N-H...O(nitro) hydrogen bonds result in the benzoate and picrate rings being rotated slightly out of coplanarity [inter-ring dihedral angle = 32.50 (14)°]. This work provides another example of the molecular selectivity of brucine in forming stable crystal structures, and also represents the first reported structure of any form of the guest compound 2-(2,4,6-trinitroanilino)benzoic acid.

Computational Hydrodynamics and Statistical Modeling on Biologically Inspired Undulating Robotic Fins: A Two-Dimensional Study

Undulation fishes, whose propulsion is mainly achieved by undulating ribbon fins, are good at maneuvering or stabilizing at low speeds. This paper suggests and proposes a two-dimensional approximate computational model, which is used to conduct an initial analysis on undulation propulsion scheme. It is believed that this undulating mode has a better potential for exploitation in artificial underwater systems. Hydrodynamics of two-dimensional undulating fins under a series of kinematical parameter sets is explored via numerical simulation. The periodicity of undulation forces and moments is studied. The effects of inlet velocity, wavelength, undulation frequency, and undulation amplitude are investigated. Furthermore, a dimensionless two-parameter model for undulation surge force is established with a given wavelength (in terms of, a single wavelength or a dual wavelength) using statistical method. The work in this paper is able to provide studies on bionic undulation mode. It has also formed a meaningful basis for three-dimensional (3D) hydrodynamics and corresponding control methods in bionic undulation robots.

Structural Investigations and Thermal Behaviour of Mercury(II) Sulfito Complexes

AbstractThe crystal structures of (NH4)[HgSO3Cl] (1) and of (NH4)2[Hg(SO3)2] (2) were determined from single crystal diffractometer data sets. 1: 22 °C, Pnma, Z = 4, a = 15.430(3), b = 5.525(1), c = 6.679(1) Å, R(F) = 0.0256, Rw(F2) = 0.0642 (all 1056 unique reflections). 2: −108 °C, P212121, Z = 4, a = 6.2240(4), b = 9.3908(6), c = 13.6110(8) Å, R(F) = 0.0179, Rw(F2) = 0.0493 (all 2699 unique reflections). The structure of 1 contains bent Cl‐Hg‐SO3 entities (site symmetry m; d(Hg‐Cl) = 2.3403(13) Å, d(Hg‐S) = 2.3636(12) Å, ∠(Cl‐Hg‐S) = 164.51(5)°, d(S‐O) 2×1.458(3) Å, 1.468(4) Å, ${\bar d}\rm (S-O)$= 1.461Å) linked to undulated ribbons parallel to the b‐axis by intermolecular secondary bonds SO···Hg (d(O···Hg) = 2×2.595(3) Å). These ribbons in turn aggregate to layers around the bc‐plane. The layers are stacked along the a‐axis with interlayer distances of a/2. The structure of 2 is made up of O3S‐Hg‐SO3 moieties (d(Hg‐S) = 2.3935(7), 2.3935(8) Å; ∠(Hg‐S‐Hg) = 174.41(3)°; ${\bar d}\rm (S-O)$ = 1.474Å), that are linked to ribbons parallel to the a axis by coordination of Hg to three remote O atoms (2.801(4) &lt; d(Hg‐O) &lt; 2.844(3) Å). Adjacent ribbons are joined together by an additional Hg‐O contact of 2.733(3) Å, leading to a three‐dimensional anionic framework. Both crystal structures are stabilised by disordered NH4+ cations, placed between the anionic layers or in the vacancies of the framework, via moderate hydrogen bonding interactions N‐H···O with donor‐acceptor distances ranging from 2.8 to 3.2Å. 1 and 2 were further characterised by thermal analysis (TG, DSC). They start to decompose at temperatures above 130 °C.

Characterization of chloroplast division using the Arabidopsis mutant arc5.

arc5 is a chloroplast division mutant of Arabidopsis thaliana. To identify the role of ARC5 in the chloroplast replication process we have followed the changes in arc5 chloroplasts during their perturbed division. ARC5 does not affect proplastid division but functions at a later stage in chloroplast development. Chloroplasts in developing mesophyll cells of arc5 leaves do not increase in number and all of the chloroplasts in mature leaf cells show a central constriction. Young arc5 chloroplasts are capable of initiating the division process but fail to complete daughter-plastid separation. Wild-type plastids increase in number to a mean of 121 after completing the division process, but in the mutant arc5 the approximately 13 plastids per cell are still centrally constricted but much enlarged. As the arc5 chloroplasts expand and elongate without dividing, the internal thylakoid membrane structure becomes flexed into an undulating ribbon. We conclude that the ARC5 gene is necessary for the completion of the last stage of chloroplast division when the narrow isthmus breaks, causing the separation of the daughter plastids.

Intercellular junctions in myriapods

Tissue from the intestinal tract of myriapods, including millipedes, centipedes and pauropods were examined in tracer-impregnated sections and freeze-fracture replicas. The foregut and hindgut of all three classes exhibit pleated septate junctions; these display undulating intercellular ribbons in thin sections. In replicas they show discrete intramembranous particle (IMP) arrays aligned in rows in parallel; with one another. The tissues of the hindgut also possess scalariform junctions, characterized by cross-striated intercellular clefts in sections and IMP-enriched membranes in replicas. Gap junctions occur in all groups, but they are atypical in replicas in that their component IMPs do not always fracture onto the E face, as is characteristic of other arthropods; some IMPs cleave to the P face and others to the E face. The midgut of these organisms exhibits smooth septate junctions with conventional straight septal ribbons and occasional interseptal columns. However the intramembranous appearance in replicas is variable, particularly in centipedes, in that the rows of IMPs in chemically-unfixed propanecryofixed tissues, are prominent and adhere preferentially to the E face, with complementary P face grooves, while in fixed tissues the IMPs are much less distinct and fracture to either P face or E face. They tend not to protrude far beyond the mid-plane of the membrane bilayer and lie in rows which commonly take on the form of a network. Individual rows of the network sometimes curve to run beside a second row, over a short distance, before bending away into another part of the network. The aligned particle rows, which are much more prominent in millipedes, where they frequently lie in close parallel appositions, do not fuse into ridges as often occurs in insect tissues. The myriapod junctions, therefore, are of the same general kind as are found in the gut tract of other arthropod groups, but differ with respect to the subtleties of their intramembranous organization and disposition.

Flagellar cells and ciliary cells in the renal tubule of elasmobranchs.

Flagella or cilia are present on most epithelial cells in the renal tubule of elasmobranch fishes (little skate, spiny dogfish, smooth dogfish, Atlantic sharpnose, scalloped hammerhead, cow-nosed ray). Flagellar cells, those with numerous flagella ordered in one, two, or more rows on the luminal surface, are shown here for the first time in a vertebrate. The flagellar cells are intercalated among other epithelial cells, each bearing a single cilium, from Bowman's capsule to the third subdivision of the intermediate segment of the nephron. The flagella form undulated ribbons up to 55 microns long. In every ribbon the axis of the central pair of microtubules in the axoneme is oriented parallel to the long axis of the flagellar row. This suggests a beat perpendicular to these two axes. The arrangement of the flagella in ribbons most likely promotes movement of glomerular filtrate down the renal tubule. Cells bearing numerous cilia occur in the large collecting ducts of spiny dogfish but without apparent preferential orientation of the cilia.

Dynamic mechanical properties of carbon fibers

We have determined the dynamic mechanical properties in a low frequency range (0.01–10 Hz) of carbon and graphite fibers at different temperatures and evaluated the influence of fiber stretching. The results, showing frequency and extension dependent losses and changes in Young's moduli, indicate the presence of relatively large, independently mobile fiber constituents, which appear to correspond to the slowly undulating ribbons recognized earlier as the basic carbon fiber components.