Journal articles: 'Mechanically linked molecule'

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van Meurs, Matijs, Francis M. Wulfert, Rianne M. Jongman, et al. "Hemorrhagic Shock-induced Endothelial Cell Activation in a Spontaneous Breathing and a Mechanical Ventilation Hemorrhagic Shock Model Is Induced by a Proinflammatory Response and Not by Hypoxia." Anesthesiology 115, no. 3 (2011): 474–82. http://dx.doi.org/10.1097/aln.0b013e318229a640.

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Introduction The interaction between neutrophils and activated endothelium is essential for the development of multiple organ dysfunction in patients with hemorrhagic shock (HS). Mechanical ventilation frequently is used in patients with HS. The authors sought to investigate the consequences of mechanical ventilation of mice subjected to HS on microvascular endothelial activation in the lung and kidney. Methods Anesthetized wild type C57BL/6 male mice were subjected to controlled hemorrhage; subgroups of mice were mechanically ventilated during the HS insult. To study the effect of acute hypoxia on the mice, the animals were housed in hypoxic cages. Gene expression levels was assessed by quantitative real-time polymerase chain reaction. Protein expression was assessed by immunohistochemistry and enzyme-linked immunosorbent assay. Results Ninety minutes after the shock induction, a vascular bed-specific, heterogeneous proinflammatory endothelial activation represented by E-selectin, vascular cell adhesion molecule 1, and intercellular adhesion molecule 1 expression was seen in kidney and lung. No differences in adhesion molecules between the spontaneously breathing and mechanically ventilated mice were found. Concentrations of the proinflammatory cytokines chemokine (C-X-C motif) ligand 1 (11.0-fold) and interleukin-6 (21.7-fold) were increased after 90 min of HS. Two hours of 6% oxygen did not induce the expression of E-selectin, vascular cell adhesion molecule 1, and intercellular adhesion molecule 1 in the kidneys and the lung. Conclusions Hemorrhagic shock leads to an early and reversible proinflammatory endothelial activation in kidney and lung. HS-induced endothelial activation is not changed by mechanical ventilation during the shock phase. Hypoxia alone does not lead to endothelial activation. The observed proinflammatory endothelial activation is mostly ischemia- or reperfusion-dependent and not related to hypoxia.

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Zhu, Kelong, and Stephen J. Loeb. "A hydrogen-bonded polymer constructed from mechanically interlocked, suit[1]ane monomers." Canadian Journal of Chemistry 98, no. 6 (2020): 285–91. http://dx.doi.org/10.1139/cjc-2020-0002.

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A T-shaped 2,4,7-substituted benzimidazolium “axle” with two ester functionalities and a 24-membered crown ether “wheel” with appendages containing terminal olefin groups were threaded — axle through wheel — to form a [2]pseudorotaxane. Grubbs’ ring-closing metathesis (RCM) was then used to form a third loop and create a bicyclic cage that fully encapsulates the axle and permanently interlocks the two molecular components creating a suit[1]ane. There are no bulky groups on the axle to prevent unthreading, but the axle is trapped due to the cage-like nature of the newly created polyether host. After hydrolysis of the esters groups to carboxylic acids, this novel mechanically interlocked molecule (MIM) polymerizes in the solid state. The structure of the resulting supramolecular polymer was determined by single-crystal X-ray diffraction and contains linear one-dimensional tapes of suit[1]ane monomers linked by intermolecular hydrogen bonding between the carboxylic acid groups.

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Kubo, Yusuke, Kentarou Baba, Michinori Toriyama, et al. "Shootin1–cortactin interaction mediates signal–force transduction for axon outgrowth." Journal of Cell Biology 210, no. 4 (2015): 663–76. http://dx.doi.org/10.1083/jcb.201505011.

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Motile cells transduce environmental chemical signals into mechanical forces to achieve properly controlled migration. This signal–force transduction is thought to require regulated mechanical coupling between actin filaments (F-actins), which undergo retrograde flow at the cellular leading edge, and cell adhesions via linker “clutch” molecules. However, the molecular machinery mediating this regulatory coupling remains unclear. Here we show that the F-actin binding molecule cortactin directly interacts with a clutch molecule, shootin1, in axonal growth cones, thereby mediating the linkage between F-actin retrograde flow and cell adhesions through L1-CAM. Shootin1–cortactin interaction was enhanced by shootin1 phosphorylation by Pak1, which is activated by the axonal chemoattractant netrin-1. We provide evidence that shootin1–cortactin interaction participates in netrin-1–induced F-actin adhesion coupling and in the promotion of traction forces for axon outgrowth. Under cell signaling, this regulatory F-actin adhesion coupling in growth cones cooperates with actin polymerization for efficient cellular motility.

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Marin-Gonzalez, Alberto, J. G. Vilhena, Ruben Perez, and Fernando Moreno-Herrero. "Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics." Proceedings of the National Academy of Sciences 114, no. 27 (2017): 7049–54. http://dx.doi.org/10.1073/pnas.1705642114.

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Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence. The lower dsRNA stretching resistance is linked to its more open structure, whereas the opposite twist-stretch coupling of both molecules is due to the very different evolution of molecules’ interstrand distance with the stretching force. A reduction of this distance leads to overwinding in dsDNA. In contrast, dsRNA is not able to reduce its interstrand distance and can only elongate by unwinding. Interstrand distance is directly correlated with the slide base-pair parameter and its different behavior in dsDNA and dsRNA traced down to changes in the sugar pucker angle of these NAs.

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Jurásková, Alena, Stefan Møller Olsen, Kim Dam-Johansen, Michael A. Brook, and Anne Ladegaard Skov. "Reliable Condensation Curing Silicone Elastomers with Tailorable Properties." Molecules 26, no. 1 (2020): 82. http://dx.doi.org/10.3390/molecules26010082.

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The long-term stability of condensation curing silicone elastomers can be affected by many factors such as curing environment, cross-linker type and concentration, and catalyst concentration. Mechanically unstable silicone elastomers may lead to undesirable application failure or reduced lifetime. This study investigates the stability of different condensation curing silicone elastomer compositions. Elastomers are prepared via the reaction of telechelic silanol-terminated polydimethylsiloxane (HO-PDMS-OH) with trimethoxysilane-terminated polysiloxane ((MeO)3Si-PDMS-Si(OMe)3) and ethoxy-terminated octakis(dimethylsiloxy)-T8-silsesquioxane ((QMOEt)8), respectively. Two post-curing reactions are found to significantly affect both the stability of mechanical properties over time and final properties of the resulting elastomers: Namely, the condensation of dangling and/or unreacted polymer chains, and the reaction between cross-linker molecules. Findings from the stability study are then used to prepare reliable silicone elastomer coatings. Coating properties are tailored by varying the cross-linker molecular weight, type, and concentration. Finally, it is shown that, by proper choice of all three parameters, a coating with excellent scratch resistance and electrical breakdown strength can be produced even without an addition of fillers.

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Ahn, Seokhoon, Sriharsha V. Aradhya, Rebekka S. Klausen, et al. "Electronic transport and mechanical stability of carboxyl linked single-molecule junctions." Physical Chemistry Chemical Physics 14, no. 40 (2012): 13841. http://dx.doi.org/10.1039/c2cp41578j.

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Lepage, Mathieu L., Chakravarthi Simhadri, Chang Liu, et al. "A broadly applicable cross-linker for aliphatic polymers containing C–H bonds." Science 366, no. 6467 (2019): 875–78. http://dx.doi.org/10.1126/science.aay6230.

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Addition of molecular cross-links to polymers increases mechanical strength and improves corrosion resistance. However, it remains challenging to install cross-links in low-functionality macromolecules in a well-controlled manner. Typically, high-energy processes are required to generate highly reactive radicals in situ, allowing only limited control over the degree and type of cross-link. We rationally designed a bis-diazirine molecule whose decomposition into carbenes under mild and controllable conditions enables the cross-linking of essentially any organic polymer through double C–H activation. The utility of this molecule as a cross-linker was demonstrated for several diverse polymer substrates (including polypropylene, a low-functionality polymer of long-standing challenge to the field) and in applications including adhesion of low–surface-energy materials and the strengthening of polyethylene fabric.

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Wang, Rui-Ning, Xin-Ran Zhang, Shu-Fang Wang, Guang-Sheng Fu, and Jiang-Long Wang. "Flatbands in 2D boroxine-linked covalent organic frameworks." Physical Chemistry Chemical Physics 18, no. 2 (2016): 1258–64. http://dx.doi.org/10.1039/c5cp05313g.

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Density functional calculations have been performed to analyze the electronic and mechanical properties of a number of 2D boroxine-linked covalent organic frameworks (COFs), which are experimentally fabricated from di-borate aromatic molecules.

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Guillén, Marilia, Asiloé J. Mora, Lusbely M. Belandria, et al. "Two conformational polymorphs of 4-methylhippuric acid." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 76, no. 6 (2020): 1077–91. http://dx.doi.org/10.1107/s2052520620013773.

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4-Methylhippuric acid {systematic name: 2-[(4-methylbenzoyl)amino]ethanoic acid}, a p-xylene excreted metabolite with a backbone containing three rotatable bonds (R-bonds), is likely to produce more than one stable molecular structure in the solid state. In this work, we prepared polymorph I by slow solvent evaporation (plates with Z′ = 1) and polymorph II by mechanical grinding (plates with Z′ = 2). Potential energy surface (PES) analysis, rotating the molecule about the C—C—N—C torsion angle, shows four conformational energy basins. The second basin, with torsion angles near −73°, agree with the conformations adopted by polymorph I and molecules A of polymorph II, and the third basin at 57° matched molecules B of polymorph II. The energy barrier between these basins is 27.5 kJ mol−1. Superposition of the molecules of polymorphs I and II rendered a maximum r.m.s. deviation of 0.398 Å. Polymorphs I and II are therefore true conformational polymorphs. The crystal packing of polymorph I consists of C(5) chains linked by N—H...O interactions along the a axis and C(7) chains linked by O—H...O interactions along the b axis. In polymorph II, two molecules (A with A or B with B) are connected by two acid–amide O—H...O interactions rendering R 2 2(14) centrosymmetric dimers. These dimers alternate to pile up along the b axis linked by N—H...O interactions. A Hirshfeld surface analysis localized weaker noncovalent interactions, C—H...O and C—H...π, with contact distances close to the sum of the van der Waals radii. Electron density at a local level using the Quantum Theory of Atoms in Molecules (QTAIM) and the Electron Localization Function (ELF), or a semi-local level using noncovalent interactions, was used to rank interactions. Strong closed shell interactions in classical O—H...O and N—H...O hydrogen bonds have electron density highly localized on bond critical points. Weaker delocalized electron density is seen around the p-methylphenyl rings associated with dispersive C—H...π and H...H interactions.

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Barin, Gokhan, Ross S. Forgan, and J. Fraser Stoddart. "Mechanostereochemistry and the mechanical bond." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 468, no. 2146 (2012): 2849–80. http://dx.doi.org/10.1098/rspa.2012.0117.

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The chemistry of mechanically interlocked molecules (MIMs), in which two or more covalently linked components are held together by mechanical bonds , has led to the coining of the term mechanostereochemistry to describe a new field of chemistry that embraces many aspects of MIMs, including their syntheses, properties, topologies where relevant and functions where operative. During the rapid development and emergence of the field, the synthesis of MIMs has witnessed the forsaking of the early and grossly inefficient statistical approaches for template-directed protocols, aided and abetted by molecular recognition processes and the tenets of self-assembly. The resounding success of these synthetic protocols, based on templation, has facilitated the design and construction of artificial molecular switches and machines, resulting more and more in the creation of integrated functional systems. This review highlights (i) the range of template-directed synthetic methods being used currently in the preparation of MIMs; (ii) the syntheses of topologically complex knots and links in the form of stable molecular compounds; and (iii) the incorporation of bistable MIMs into many different device settings associated with surfaces, nanoparticles and solid-state materials in response to the needs of particular applications that are perceived to be fair game for mechanostereochemistry.

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Itano, Misaki, Yuichiro Kobayashi, Yoshinori Takashima, Akira Harada, and Hiroyasu Yamaguchi. "Mechanical properties of supramolecular polymeric materials cross-linked by donor–acceptor interactions." Chemical Communications 55, no. 26 (2019): 3809–12. http://dx.doi.org/10.1039/c9cc01472a.

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Jin, Eunji, In Seong Lee, Dongwook Kim, et al. "Metal-organic framework based on hinged cube tessellation as transformable mechanical metamaterial." Science Advances 5, no. 5 (2019): eaav4119. http://dx.doi.org/10.1126/sciadv.aav4119.

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Mechanical metamaterials exhibit unusual properties, such as negative Poisson’s ratio, which are difficult to achieve in conventional materials. Rational design of mechanical metamaterials at the microscale is becoming popular partly because of the advance in three-dimensional printing technologies. However, incorporating movable building blocks inside solids, thereby enabling us to manipulate mechanical movement at the molecular scale, has been a difficult task. Here, we report a metal-organic framework, self-assembled from a porphyrin linker and a new type of Zn-based secondary building unit, serving as a joint in a hinged cube tessellation. Detailed structural analysis and theoretical calculation show that this material is a mechanical metamaterial exhibiting auxetic behavior. This work demonstrates that the topology of the framework and flexible hinges inside the structure are intimately related to the mechanical properties of the material, providing a guideline for the rational design of mechanically responsive metal-organic frameworks.

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Zhang, Wei, Changchun Chai, Qingyang Fan, Yanxing Song, and Yintang Yang. "Penta-C20: A Superhard Direct Band Gap Carbon Allotrope Composed of Carbon Pentagon." Materials 13, no. 8 (2020): 1926. http://dx.doi.org/10.3390/ma13081926.

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A metastable sp3-bonded carbon allotrope, Penta-C20, consisting entirely of carbon pentagons linked through bridge-like bonds, was proposed and studied in this work for the first time. Its structure, stability, and electronic and mechanical properties were investigated based on first-principles calculations. Penta-C20 is thermodynamically and mechanically stable, with equilibrium total energy of 0.718 and 0.184 eV/atom lower than those of the synthesized T-carbon and supercubane, respectively. Penta-C20 can also maintain dynamic stability under a high pressure of 100 GPa. Ab initio molecular dynamics (AIMD) simulations indicates that this new carbon allotrope can maintain thermal stability at 800 K. Its Young’s modulus exhibits mechanical anisotropy. The calculated ideal tensile and shear strengths confirmed that Penta-C20 is a superhard material with a promising application prospect. Furthermore, Penta-C20 is a direct band gap carbon based semiconducting material with band gap of 2.89 eV.

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Nouri, Nima, and Saeed Ziaei-Rad. "A Molecular Dynamics Investigation on Mechanical Properties of Cross-Linked Polymer Networks." Macromolecules 44, no. 13 (2011): 5481–89. http://dx.doi.org/10.1021/ma2005519.

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Stewart, Daniel C., Andrés Rubiano, Monica M. Santisteban, et al. "Hypertension-linked mechanical changes of rat gut." Acta Biomaterialia 45 (November 2016): 296–302. http://dx.doi.org/10.1016/j.actbio.2016.08.045.

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Erikci, Saliha, Patricia Mundinger, and Heike Boehm. "Small Physical Cross-Linker Facilitates Hyaluronan Hydrogels." Molecules 25, no. 18 (2020): 4166. http://dx.doi.org/10.3390/molecules25184166.

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In this study, we demonstrate that small charged molecules (NH4+, GluA+, dHA+) can form physical cross-links between hyaluronan chains, facilitating polymerization reactions between synthetically introduced thiol groups (HA-DTPH). These hybrid hydrogels can be obtained under physiological conditions ideally suited for 3D cell culture systems. The type and concentration of a physical crosslinker can be adjusted to precisely tune mechanical properties as well as degradability of the desired hydrogel system. We analyze the influence of hydrogen bond formation, concentration and additional ionic interactions on the polymerization reaction of HA-DTPH hydrogels and characterize the resulting hydrogels in regard to mechanical and biocompatibility aspects.

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Quek, Su Ying, Latha Venkataraman, Hyoung Joon Choi, Steven G. Louie, Mark S. Hybertsen, and J. B. Neaton. "Amine−Gold Linked Single-Molecule Circuits: Experiment and Theory." Nano Letters 7, no. 11 (2007): 3477–82. http://dx.doi.org/10.1021/nl072058i.

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Castro, Rene Alejandro, and Evgeniy N. Lushin. "Mechanical Properties of Tetrazole Polymers." Applied Mechanics and Materials 590 (June 2014): 19–22. http://dx.doi.org/10.4028/www.scientific.net/amm.590.19.

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Low-frequency acoustic method, studies of viscoelastic properties of polymers tetrazolecontaining. It was shown that the introduction of modifiers KCl and KNO3 has a different effect on the dynamic and mechanical characteristics tetrazolecontaining polymers. It is noted that such changes are related to the restructuring of the molecular organization of cross-linked polymers.

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Li, Jin Feng, Mao Fang Huang, Jian He Liao, Pu Wang Li, and Tian Ming Gao. "The Effects of Hanging Microbe Coagulation Natural Rubber on Molecular Structures and Mechanical Properties." Advanced Materials Research 581-582 (October 2012): 715–18. http://dx.doi.org/10.4028/www.scientific.net/amr.581-582.715.

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In this study, the cross-linked network structures, dynamic mechanical properties and Po、PRI of microbe coagulated natural rubber (NR) samples were analyzed. And mechanical properties of the corresponding NR vulcanizates were further determined by universal testing machines. The results show that the NR of aging resistance increased with the cycle of hanging.When hanged 14 days,the PRI and P0 were 85 and 36.6. With the cycle of hanging rising, NR raw rubber of cross-linked density increased,and had good dynamic mechanical properties as compared with that hanged 0 days.

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Mizuse, Kenta, Kenta Kitano, Hirokazu Hasegawa, and Yasuhiro Ohshima. "Quantum unidirectional rotation directly imaged with molecules." Science Advances 1, no. 6 (2015): e1400185. http://dx.doi.org/10.1126/sciadv.1400185.

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A gas-phase molecular ensemble coherently excited to have an oriented rotational angular momentum has recently emerged as an appropriate microscopic system to illustrate quantum mechanical behavior directly linked to classical rotational motion, which has a definite direction. To realize an intuitive visualization of such a unidirectional molecular rotation, we report high-resolution direct imaging of direction-controlled rotational wave packets in nitrogen molecules. The rotational direction was regulated by a pair of time-delayed, polarization-skewed laser pulses, introducing the dynamic chirality to the system. The subsequent spatiotemporal propagation was tracked by a newly developed Coulomb explosion imaging setup. From the observed molecular movie, time-dependent detailed nodal structures, instantaneous alignment, angular dispersion, and fractional revivals of the wave packet are fully characterized while the ensemble keeps rotating in one direction. The present approach, providing an accurate view on unidirectional rotation in quantum regime, will guide more sophisticated molecular manipulations by utilizing its capability in capturing highly structured spatiotemporal evolution of molecular wave packets.

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Agban, Yosra, Odunayo O. Mugisho, Sachin S. Thakur, and Ilva D. Rupenthal. "Characterization of Zinc Oxide Nanoparticle Cross-Linked Collagen Hydrogels." Gels 6, no. 4 (2020): 37. http://dx.doi.org/10.3390/gels6040037.

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Collagen is the most abundant protein in mammals and possesses high biocompatibility and low antigenicity. These biological properties render it one of the most useful biomaterials for medical applications. This study investigated the mechanical and physical characteristics of collagen hydrogels cross-linked with different ratios of polyvinylpyrrolidone capped zinc oxide nanoparticles (ZPVP). Fourier transform infrared spectroscopy indicated molecular interactions between collagen fibers and ZPVP. Texture analysis revealed a significant increase in gel hardness, adhesiveness, and viscosity after cross-linking with ZPVP. Rheological measurements showed that as the ratio of ZPVP increased, stronger hydrogels were formed which in turn resulted in more sustained release of the model drug, dexamethasone sodium phosphate. We can therefore conclude that the mechanical properties of collagen hydrogels can be modified by controlling the ratio of ZPVP used for cross-linking, offering the potential to develop biocompatible sustained release drug delivery systems.

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An, Meng, Baris Demir, Xiao Wan, Han Meng, Nuo Yang, and Tiffany R. Walsh. "Predictions of Thermo-Mechanical Properties of Cross-Linked Polyacrylamide Hydrogels Using Molecular Simulations." Advanced Theory and Simulations 2, no. 3 (2019): 1800153. http://dx.doi.org/10.1002/adts.201800153.

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Luo, Zhongyi, Zichun Yang, Zhifang Fei, and Gaohui Su. "Investigating mechanical properties of cross-linked SiO2 and polyimide through molecular dynamics simulation." Polymer Bulletin 77, no. 10 (2019): 5213–25. http://dx.doi.org/10.1007/s00289-019-03014-4.

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Athir, Naveed, Ling Shi, Sayyed Asim Ali Shah, et al. "Molecular dynamics simulation of thermo-mechanical behaviour of elastomer cross-linked via multifunctional zwitterions." Physical Chemistry Chemical Physics 21, no. 38 (2019): 21615–25. http://dx.doi.org/10.1039/c9cp03221e.

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Coarse-grained (CG) molecular dynamics simulations have been employed to study the thermo-mechanical response of a physically cross-linked network composed of zwitterionic moieties and fully flexible elastomeric polymer chains.

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Wegrzynowska-Drzymalska, Katarzyna, Patrycja Grebicka, Dariusz T. Mlynarczyk, et al. "Crosslinking of Chitosan with Dialdehyde Chitosan as a New Approach for Biomedical Applications." Materials 13, no. 15 (2020): 3413. http://dx.doi.org/10.3390/ma13153413.

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Materials based on natural high molecular compounds are particularly interesting for biomedical applications. It is known that the cross-linking agent used for preparation of biomacromolecule-based materials is as important as used biopolymer. Therefore, natural cross-linkers containing reactive carbonyl groups are of great interest especially for modifying properties of natural polysaccharides. One of the most popular cross-linking agents is glutaraldehyde. Nevertheless, the unreacted particles can be released from the cross-linked material and cause cytotoxic effects. This can be eliminated when using a cross-linker based e.g., on polysaccharides. This article describes quick and efficient synthesis of dialdehyde chitosan (DACS) and its application for the preparation of chitosan films. Materials obtained with different amount of DACS were fully characterized in terms of structure and surface morphology. Thermal and mechanical properties as well as hydrophilic character were also examined. The results obtained were compared with the materials obtained by cross-linking chitosan with low molecular weight glutaraldehyde and high molecular weight cross-linking agent based on polysaccharide–dialdehyde starch. Toxicity of all obtained materials was tested using the Microtox® test. It has been shown that due to better mechanical, thermal and surface properties as well as lower toxicity, dialdehyde chitosan is a very promising crosslinking agent.

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Nikitiuk, A. S., E. A. Korznikova, S. V. Dmitriev, and O. B. Naimark. "DNA Breathers and Cell Dynamics." Mathematical Biology and Bioinformatics 14, no. 1 (2019): 137–49. http://dx.doi.org/10.17537/2019.14.137.

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Molecular-morphological signs of oncogenesis can be linked to multiscale collective effects in molecular and cell ensembles. It was shown that nonlinear behavior of biological systems can be associated with the generation of characteristic collective modes representing the open states in molecular and cell organization as the mechanism of the coherent expression dynamics. The mechanical DNA model is developed to study the nonlinear dynamics of the helicoidal geometry DNA molecule. To construct the model of DNA the Peyrard–Bishop–Barbi approach has been applied. The analytical small localized solutions as the discrete breather and the antikink have been obtained by multiple scale expansion method for multicomponent lattices. The set of collective open states (breathers) in the molecular ensembles provides the collective expression dynamics to attract cells toward a few preferred global states. This result allows the formulation of the experimental strategy to analyze the qualitative changes in cell dynamics induced by mentioned collective modes. The biomechanical changes have been shown experimentally using the original data of Coherent Phase Microscopy analyzing the time series of phase thickness fluctuations. Study of the mechanical aspects of the behavior of single cells is a prerequisite for the understanding of cell functions in the case of qualitative changes in diseases affecting the properties of cells and tissues morphology to develop diagnostic and treatment design methodology.

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Lerner, Aaron, and Torsten Matthias. "Processed Food Additive Microbial Transglutaminase and Its Cross-Linked Gliadin Complexes Are Potential Public Health Concerns in Celiac Disease." International Journal of Molecular Sciences 21, no. 3 (2020): 1127. http://dx.doi.org/10.3390/ijms21031127.

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Microbial transglutaminase (mTG) is a survival factor for microbes, but yeasts, fungi, and plants also produce transglutaminase. mTG is a cross-linker that is heavily consumed as a protein glue in multiple processed food industries. According to the manufacturers’ claims, microbial transglutaminase and its cross-linked products are safe, i.e., nonallergenic, nonimmunogenic, and nonpathogenic. The regulatory authorities declare it as “generally recognized as safe” for public users. However, scientific observations are accumulating concerning its undesirable effects on human health. Functionally, mTG imitates its family member, tissue transglutaminase, which is the autoantigen of celiac disease. Both these transglutaminases mediate cross-linked complexes, which are immunogenic in celiac patients. The enzyme enhances intestinal permeability, suppresses mechanical (mucus) and immunological (anti phagocytic) enteric protective barriers, stimulates luminal bacterial growth, and augments the uptake of gliadin peptide. mTG and gliadin molecules are cotranscytosed through the enterocytes and deposited subepithelially. Moreover, mucosal dendritic cell surface transglutaminase induces gliadin endocytosis, and the enzyme-treated wheat products are immunoreactive in CD patients. The present review summarizes and updates the potentially detrimental effects of mTG, aiming to stimulate scientific and regulatory debates on its safety, to protect the public from the enzyme’s unwanted effects.

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Yount, Wayne C., David M. Loveless, and Stephen L. Craig. "Small-Molecule Dynamics and Mechanisms Underlying the Macroscopic Mechanical Properties of Coordinatively Cross-Linked Polymer Networks." Journal of the American Chemical Society 127, no. 41 (2005): 14488–96. http://dx.doi.org/10.1021/ja054298a.

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Cossio, Pilar, Gerhard Hummer, and Attila Szabo. "On artifacts in single-molecule force spectroscopy." Proceedings of the National Academy of Sciences 112, no. 46 (2015): 14248–53. http://dx.doi.org/10.1073/pnas.1519633112.

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In typical force spectroscopy experiments, a small biomolecule is attached to a soft polymer linker that is pulled with a relatively large bead or cantilever. At constant force, the total extension stochastically changes between two (or more) values, indicating that the biomolecule undergoes transitions between two (or several) conformational states. In this paper, we consider the influence of the dynamics of the linker and mesoscopic pulling device on the force-dependent rate of the conformational transition extracted from the time dependence of the total extension, and the distribution of rupture forces in force-clamp and force-ramp experiments, respectively. For these different experiments, we derive analytic expressions for the observables that account for the mechanical response and dynamics of the pulling device and linker. Possible artifacts arise when the characteristic times of the pulling device and linker become comparable to, or slower than, the lifetimes of the metastable conformational states, and when the highly anharmonic regime of stretched linkers is probed at high forces. We also revisit the problem of relating force-clamp and force-ramp experiments, and identify a linker and loading rate-dependent correction to the rates extracted from the latter. The theory provides a framework for both the design and the quantitative analysis of force spectroscopy experiments by highlighting, and correcting for, factors that complicate their interpretation.

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Yanagisawa, Yu, Yiling Nan, Kou Okuro, and Takuzo Aida. "Mechanically robust, readily repairable polymers via tailored noncovalent cross-linking." Science 359, no. 6371 (2017): 72–76. http://dx.doi.org/10.1126/science.aam7588.

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Expanding the range of healable materials is an important challenge for sustainable societies. Noncrystalline, high-molecular-weight polymers generally form mechanically robust materials, which, however, are difficult to repair once they are fractured. This is because their polymer chains are heavily entangled and diffuse too sluggishly to unite fractured surfaces within reasonable time scales. Here we report that low-molecular-weight polymers, when cross-linked by dense hydrogen bonds, yield mechanically robust yet readily repairable materials, despite their extremely slow diffusion dynamics. A key was to use thiourea, which anomalously forms a zigzag hydrogen-bonded array that does not induce unfavorable crystallization. Another key was to incorporate a structural element for activating the exchange of hydrogen-bonded pairs, which enables the fractured portions to rejoin readily upon compression.

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Parrella, Giuseppe, André Moretti, Patrick Gognalons, et al. "The Am Gene Controlling Resistance to Alfalfa mosaic virus in Tomato Is Located in the Cluster of Dominant Resistance Genes on Chromosome 6." Phytopathology® 94, no. 4 (2004): 345–50. http://dx.doi.org/10.1094/phyto.2004.94.4.345.

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The dominant gene Am from Lycopersicon hirsutum f. sp. glabratum PI134417 confers resistance to most strains of Alfalfa mosaic virus, including the recently identified necrotic strains. The phenotypic response includes a lack of symptom development following mechanical inoculation of leaves. To study the resistance mechanism controlled by Am, biological (back-inoculation to susceptible hosts), serological (double-antibody sandwich, enzyme-linked immunosorbent assay), and molecular (reverse transcription-polymerase chain reaction and hybridization with specific riboprobes) methods of virus detection have been conducted on mechanically inoculated PI134417 leaves. The virus was never recovered, indicating that Am acts by an inhibition of viral accumulation during the early events of the virus life cycle. Am has been mapped genetically to the short arm of tomato chromosome 6 in the resistance hotspot, which includes the R-genes Mi and Cf-2/Cf-5 and the quantitative resistance factors Ty-1, Ol-1, and Bw-5.

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Elerman, Yalçün, Mehmet Kabak, and Ayhan Elmali. "Crystal Structure and Conformation of N-(5-Chlorosalicylidene)- 2-hydroxy-5-chloroaniline." Zeitschrift für Naturforschung B 57, no. 6 (2002): 651–56. http://dx.doi.org/10.1515/znb-2002-0610.

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Abstract N-(5-Chlorosalicylidene)-2-hydroxy-5-chloroaniline was synthesized and its crystal structure determined. It crystallizes in the orthorhombic space group Pna21 with a = 14.668(4), b = 6.084(3), c = 27.980(4) Å , R = 0.051 for 4788 independent reflections). There are two independent nearly planar molecules in the asymmetric unit. The intramolecular hydrogen bonds occur between the pairs of atoms N1 and O1 [2.553(6) Å], N1 and O2 [2.585(5) Å], N2 and O3 [2.567(6) Å], N2 and O4 [2.620(5) Å], the hydrogen atoms essentially being bonded to the nitrogen atoms. The neighboring molecules are linked via an intermolecular O-H···O hydrogen bond [2.557(5) Å ]. Conformations of the title compound were investigated by semi-empirical quantum mechanical AM1 calculations. The optimized geometry of the molecular structure corresponding to the nearly planar conformation is the most stable conformation in the calculations. The results strongly indicate that the minimum energy conformation is primarily determined by non-bonded steric interactions.

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Zidek, Jan, Josef Jancar, Andrey Milchev, and Thomas A. Vilgis. "Mechanical Response of Hybrid Cross-Linked Networks to Uniaxial Deformation: A Molecular Dynamics Model." Macromolecules 47, no. 24 (2014): 8795–807. http://dx.doi.org/10.1021/ma501504z.

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Abdullah, Mohamed, F. Gholamian, and A. R. Zarei. "Noncrystalline Binder Based Composite Propellant." ISRN Aerospace Engineering 2013 (September 24, 2013): 1–6. http://dx.doi.org/10.1155/2013/679710.

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This study reports on propellants based on cross-linked HTPE binder plasticized with butyl nitroxyethylnitramine (BuNENA) as energetic material and HP 4000D as noncrystalline prepolymer. This binder was conducted with solid loading in the 85%. The results showed an improvement in processability, mechanical properties and burning rate. In addition, its propellant delivers (about 6 seconds) higher performance (specific impulse) than the best existing composite solid rocket propellant. Thermal analyses have performed by (DSC, TGA). The thermal curves have showed a low glass transition temperature () of propellant samples, and there was no sign of binder polymer crystallization at low temperatures (−50°C). Due to its high molecular weight and unsymmetrical or random molecule distributions, the polyether (HP 4000D) has been enhanced the mechanical properties of propellants binder polymer over a large range of temperatures [−50, 50°C]. The propellants described in this paper have presented high volumetric specific impulse (>500 s·gr·cc−1). These factors combined make BuNENA based composite propellant a potentially attractive alternative for a number of missions demanding composite solid propellants.

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Wioland, Hugo, Antoine Jegou, and Guillaume Romet-Lemonne. "Torsional stress generated by ADF/cofilin on cross-linked actin filaments boosts their severing." Proceedings of the National Academy of Sciences 116, no. 7 (2019): 2595–602. http://dx.doi.org/10.1073/pnas.1812053116.

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Proteins of the actin depolymerizing factor (ADF)/cofilin family are the central regulators of actin filament disassembly. A key function of ADF/cofilin is to sever actin filaments. However, how it does so in a physiological context, where filaments are interconnected and under mechanical stress, remains unclear. Here, we monitor and quantify the action of ADF/cofilin in different mechanical situations by using single-molecule, single-filament, and filament network techniques, coupled to microfluidics. We find that local curvature favors severing, while tension surprisingly has no effect on cofilin binding and weakly enhances severing. Remarkably, we observe that filament segments that are held between two anchoring points, thereby constraining their twist, experience a mechanical torque upon cofilin binding. We find that this ADF/cofilin-induced torque does not hinder ADF/cofilin binding, but dramatically enhances severing. A simple model, which faithfully recapitulates our experimental observations, indicates that the ADF/cofilin-induced torque increases the severing rate constant 100-fold. A consequence of this mechanism, which we verify experimentally, is that cross-linked filament networks are severed by cofilin far more efficiently than nonconnected filaments. We propose that this mechanochemical mechanism is critical to boost ADF/cofilin’s ability to sever highly connected filament networks in cells.

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Banerjee, Souradeep, Soham Chakraborty, Abhijit Sreepada, et al. "Cutting-Edge Single-Molecule Technologies Unveil New Mechanics in Cellular Biochemistry." Annual Review of Biophysics 50, no. 1 (2021): 419–45. http://dx.doi.org/10.1146/annurev-biophys-090420-083836.

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Single-molecule technologies have expanded our ability to detect biological events individually, in contrast to ensemble biophysical technologies, where the result provides averaged information. Recent developments in atomic force microscopy have not only enabled us to distinguish the heterogeneous phenomena of individual molecules, but also allowed us to view up to the resolution of a single covalent bond. Similarly, optical tweezers, due to their versatility and precision, have emerged as a potent technique to dissect a diverse range of complex biological processes, from the nanomechanics of ClpXP protease–dependent degradation to force-dependent processivity of motor proteins. Despite the advantages of optical tweezers, the time scales used in this technology were inconsistent with physiological scenarios, which led to the development of magnetic tweezers, where proteins are covalently linked with the glass surface, which in turn increases the observation window of a single biomolecule from minutes to weeks. Unlike optical tweezers, magnetic tweezers use magnetic fields to impose torque, which makes them convenient for studying DNA topology and topoisomerase functioning. Using modified magnetic tweezers, researchers were able to discover the mechanical role of chaperones, which support their substrate proteinsby pulling them during translocation and assist their native folding as a mechanical foldase. In this article, we provide a focused review of many of these new roles of single-molecule technologies, ranging from single bond breaking to complex chaperone machinery, along with the potential to design mechanomedicine, which would be a breakthrough in pharmacological interventions against many diseases.

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van der Sleen, Lyan M., and Katarzyna M. Tych. "Bioconjugation Strategies for Connecting Proteins to DNA-Linkers for Single-Molecule Force-Based Experiments." Nanomaterials 11, no. 9 (2021): 2424. http://dx.doi.org/10.3390/nano11092424.

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The mechanical properties of proteins can be studied with single molecule force spectroscopy (SMFS) using optical tweezers, atomic force microscopy and magnetic tweezers. It is common to utilize a flexible linker between the protein and trapped probe to exclude short-range interactions in SMFS experiments. One of the most prevalent linkers is DNA due to its well-defined properties, although attachment strategies between the DNA linker and protein or probe may vary. We will therefore provide a general overview of the currently existing non-covalent and covalent bioconjugation strategies to site-specifically conjugate DNA-linkers to the protein of interest. In the search for a standardized conjugation strategy, considerations include their mechanical properties in the context of SMFS, feasibility of site-directed labeling, labeling efficiency, and costs.

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Dell’Angela, M., G. Kladnik, A. Cossaro, et al. "Relating Energy Level Alignment and Amine-Linked Single Molecule Junction Conductance." Nano Letters 10, no. 7 (2010): 2470–74. http://dx.doi.org/10.1021/nl100817h.

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Tang, Yujing, Chao Tang, Dong Hu, and Yingang Gui. "Effect of Aminosilane Coupling Agents with Different Chain Lengths on Thermo-Mechanical Properties of Cross-Linked Epoxy Resin." Nanomaterials 8, no. 11 (2018): 951. http://dx.doi.org/10.3390/nano8110951.

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In this paper, a molecular dynamics simulation method was used to study the thermo-mechanical properties of cross-linked epoxy resins doped with nano silica particles that were grafted with 3-aminopropyltriethoxysilane, N-(2-aminoethyl)-3-aminopropyltrimethoxysilane, and 3-[2-(2-aminoethylamino)ethylamino]-propyl-trimethoxysilane with different chain lengths. Firstly, a set of pure epoxy resin models, and four sets of SiO2/EP composite models were established. Then, a reasonable structure was obtained through a series of optimizations using molecular dynamics calculations. Next, the mechanical properties, hydrogen bond statistics, glass transition temperature, free volume fraction, and chain spacing of the five models were studied comparatively. The results show that doped nano silica particles of surfaces grafted with 3-aminopropyltriethoxysilane, N-(2-aminoethyl)-3-aminopropyltrimethoxysilane, and 3-[2-(2-aminoethylamino)ethylamino]-propyl-trimethoxysilane with different chain lengths enhanced mechanical properties such as elastic modulus, shear modulus, and volume modulus obviously. The glass transition temperature increased by 15–16 K, 40–41 K, and 24–27 K, respectively. Finally, the data show that the cross-linked epoxy resin modified by nanoparticles grafted with N-(2-aminoethyl)-3-aminopropyl trimethoxysilane had better effects for improving thermo-mechanical properties by the comparatively studying the five groups of parameter models under the same conditions.

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Budy, S. M., T. Hawkins, P. Foy, M. J. Matthewson, D. W. Smith, and J. Ballato. "Thermal and Mechanical Analysis of Cross-Linked Optical Fiber Coatings." Journal of Lightwave Technology 27, no. 24 (2009): 5626–30. http://dx.doi.org/10.1109/jlt.2009.2032368.

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Jiang, Yan, Zulin Da, Fengxian Qiu, Yijun Guan, and Guorong Cao. "Fabrication of chromophore molecule-linked azo polymer as waveguide material of polymeric thermo-optic digital optical switch." Journal of Nonlinear Optical Physics & Materials 26, no. 03 (2017): 1750032. http://dx.doi.org/10.1142/s0218863517500321.

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A chromophore molecule-linked azo polymer as waveguide material (MCAP) of polymeric thermo-optic digital optical switch (DOS) was prepared with a chromophore molecule (ABFA), a polyether polyol and isophorone diisocyanate (IPDI). The chemical structures of ABFA monomer and azo polymer MCAP were characterized by FT-IR and UV–Visible spectroscopy. The thermal and mechanical properties of the MCAP film were investigated. The refractive index and transmission loss of MCAP film were measured at different temperatures and different laser wavelengths by an attenuated total reflection (ATR) technique and CCD digital imaging devices. A polymeric thermo-optic DOS based on the thermo-optic effect of the MCAP was designed and the performance of the switch was simulated by using the finite difference beam propagation method (FD-BPM). The experimental results showed that the power consumption of the polymeric thermo-optic switch could be only 0.64[Formula: see text]mW, while the response time of the switch could be as short as 3.0[Formula: see text]ms.

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Saito, Keisuke, Naoki Sakashita, and Hiroshi Ishikita. "Energetics of the Proton Transfer Pathway for Tyrosine D in Photosystem II." Australian Journal of Chemistry 69, no. 9 (2016): 991. http://dx.doi.org/10.1071/ch16248.

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The proton transfer pathway for redox active tyrosine D (TyrD) in photosystem II is a hydrogen-bond network that involves D2-Arg180 and a series of water molecules. Using quantum mechanical/molecular mechanical calculations, the detailed properties of the energetics and structural geometries were investigated. The potential-energy profile of all hydrogen bonds along the proton transfer pathway indicates that the overall proton transfer from TyrD is energetically downhill. D2-Arg180 plays a key role in the proton transfer pathway, providing a driving force for proton transfer, maintaining the hydrogen-bond network structure, stabilising P680•+, and thus deprotonating TyrD-OH to TyrD-O•. A hydrophobic environment near TyrD enhances the electrostatic interactions between TyrD and redox active groups, e.g. P680 and the catalytic Mn4CaO5 cluster: the redox states of those groups are linked with the protonation state of TyrD, i.e. release of the proton from TyrD. Thus, the proton transfer pathway from TyrD may ultimately contribute to the conversion of S0 into S1 in the dark in order to stabilise the Mn4CaO5 cluster when the photocycle is interrupted in S0.

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Mayumi, Koichi, Chang Liu, and Kohzo Ito. "Mechanical and Fracture Properties of Dynamically Cross-Linked Polymer Gels and Elastomers with Molecular Necklaces." Nihon Reoroji Gakkaishi 47, no. 2 (2019): 43–49. http://dx.doi.org/10.1678/rheology.47.43.

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Yang, Jun, Dongshuai Hou, and Qingjun Ding. "Structure, Dynamics, and Mechanical Properties of Cross-Linked Calcium Aluminosilicate Hydrate: A Molecular Dynamics Study." ACS Sustainable Chemistry & Engineering 6, no. 7 (2018): 9403–17. http://dx.doi.org/10.1021/acssuschemeng.8b01749.

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Shukla, Manoj Kumar, Amit Kumar, Anurag Yadav, and Kamal Sharma. "Improved Mechanical Properties of Graphene Oxide Reinforced Cross-linked Epoxy Nanocomposites: A Molecular Dynamics Approach." Materials Today: Proceedings 11 (2019): 679–85. http://dx.doi.org/10.1016/j.matpr.2019.03.027.

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Duan, Weipeng, Meiping Wu, and Jitai Han. "Correction: Research into the thermal stability and mechanical properties of vitamin E diffusion modified irradiation cross-linked graphene oxide/ultra-high molecular weight polyethylene composites." RSC Advances 10, no. 38 (2020): 22491. http://dx.doi.org/10.1039/d0ra90064h.

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Correction for ‘Research into the thermal stability and mechanical properties of vitamin E diffusion modified irradiation cross-linked graphene oxide/ultra-high molecular weight polyethylene composites’ by Weipeng Duan et al., RSC Adv., 2020, 10, 4175–4188, DOI: 10.1039/C9RA09893C.

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Klomp, L. W. J., L. van Rens, and G. J. Strous. "Identification of a human gastric mucin precursor: N-linked glycosylation and oligomerization." Biochemical Journal 304, no. 3 (1994): 693–98. http://dx.doi.org/10.1042/bj3040693.

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Gastric mucin plays an important role in the protection of the stomach wall from chemical, microbiological and mechanical damage. We have previously isolated human gastric mucus glycoproteins and raised a polyclonal antiserum against these macromolecules. This antiserum specifically reacted with gastric mucins in immunoblotting experiments and stained mucous granules at the apical side of gastric surface epithelial cells. A similar staining pattern was obtained after incubation with an antiserum against rat gastric mucin. Next we used the antiserum in pulse-chase experiments of human stomach tissue explants. After short labelling periods with [35S]methionine and [35S]cysteine, the antiserum reacted with a polypeptide with an apparent molecular mass of approx. 500 kDa as determined by SDS/PAGE, which was converted after 90 min into a heterogeneous high-molecular-mass glycoprotein. This high-molecular-mass form, but not the 500 kDa polypeptide, was detectable in the culture medium after 2 h. This strongly suggests that the 500 kDa polypeptide is the precursor of the purified gastric mucin. Analysis of pulse-chase experiments by non-reducing SDS/PAGE revealed that the precursors form disulphide-linked oligomers early in biosynthesis, before the addition of O-linked sugars. After preincubation with the N-glycosylation inhibitor, tunicamycin, the apparent molecular mass of the precursor decreased marginally but consistently, indicating that N-linked glycan chains are present on the mucin precursor.

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Gossett, J. Jared, and Stephen C. Harvey. "Computational Screening and Design of DNA-Linked Molecular Nanowires." Nano Letters 11, no. 2 (2011): 604–8. http://dx.doi.org/10.1021/nl103665z.

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Millereau, Pierre, Etienne Ducrot, Jess M. Clough, et al. "Mechanics of elastomeric molecular composites." Proceedings of the National Academy of Sciences 115, no. 37 (2018): 9110–15. http://dx.doi.org/10.1073/pnas.1807750115.

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A classic paradigm of soft and extensible polymer materials is the difficulty of combining reversible elasticity with high fracture toughness, in particular for moduli above 1 MPa. Our recent discovery of multiple network acrylic elastomers opened a pathway to obtain precisely such a combination. We show here that they can be seen as true molecular composites with a well–cross-linked network acting as a percolating filler embedded in an extensible matrix, so that the stress–strain curves of a family of molecular composite materials made with different volume fractions of the same cross-linked network can be renormalized into a master curve. For low volume fractions (<3%) of cross-linked network, we demonstrate with mechanoluminescence experiments that the elastomer undergoes a strong localized softening due to scission of covalent bonds followed by a stable necking process, a phenomenon never observed before in elastomers. The quantification of the emitted luminescence shows that the damage in the material occurs in two steps, with a first step where random bond breakage occurs in the material accompanied by a moderate level of dissipated energy and a second step where a moderate level of more localized bond scission leads to a much larger level of dissipated energy. This combined use of mechanical macroscopic testing and molecular bond scission data provides unprecedented insight on how tough soft materials can damage and fail.

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Hirata, Hiroaki, Keng-Hwee Chiam, Chwee Teck Lim, and Masahiro Sokabe. "Actin flow and talin dynamics govern rigidity sensing in actin–integrin linkage through talin extension." Journal of The Royal Society Interface 11, no. 99 (2014): 20140734. http://dx.doi.org/10.1098/rsif.2014.0734.

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At cell–substrate adhesion sites, the linkage between actin filaments and integrin is regulated by mechanical stiffness of the substrate. Of potential molecular regulators, the linker proteins talin and vinculin are of particular interest because mechanical extension of talin induces vinculin binding with talin, which reinforces the actin–integrin linkage. For understanding the molecular and biophysical mechanism of rigidity sensing at cell–substrate adhesion sites, we constructed a simple physical model to examine a role of talin extension in the stiffness-dependent regulation of actin–integrin linkage. We show that talin molecules linking between retrograding actin filaments and substrate-bound integrin are extended in a manner dependent on substrate stiffness. The model predicts that, in adhesion complexes containing ≈30 talin links, talin is extended enough for vinculin binding when the substrate is stiffer than 1 kPa. The lifetime of talin links needs to be 2–5 s to achieve an appropriate response of talin extension against substrate stiffness. Furthermore, changes in actin velocity drastically shift the range of substrate stiffness that induces talin–vinculin binding. Our results suggest that talin extension is a key step in sensing and responding to substrate stiffness at cell adhesion sites.

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Journal articles on the topic 'Mechanically linked molecule'

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