Academic literature on the topic 'Mechanically linked molecule'
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Journal articles on the topic "Mechanically linked molecule"
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van Meurs, Matijs, Francis M. Wulfert, Rianne M. Jongman, Martin Schipper, Martin C. Houwertjes, Michiel Vaneker, Gert Jan Scheffer, 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 (September 1, 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 (June 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, Takunori Minegishi, Tadao Sugiura, Satoshi Kozawa, Kazushi Ikeda, and Naoyuki Inagaki. "Shootin1–cortactin interaction mediates signal–force transduction for axon outgrowth." Journal of Cell Biology 210, no. 4 (August 10, 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 (June 20, 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 (December 27, 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, Brian Capozzi, Xavier Roy, Michael L. Steigerwald, Colin Nuckolls, and Latha Venkataraman. "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, Mahdi Takaffoli, Liting Bi, Bryn Crawford, Abbas S. Milani, and Jeremy E. Wulff. "A broadly applicable cross-linker for aliphatic polymers containing C–H bonds." Science 366, no. 6467 (November 14, 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, Luis E. Seijas, Jeans W. Ramírez, José L. Burgos, Luis Rincón, and Gerzon E. Delgado. "Two conformational polymorphs of 4-methylhippuric acid." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 76, no. 6 (November 16, 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 (May 9, 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.
Dissertations / Theses on the topic "Mechanically linked molecule"
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Craig, M. R. "Azo dye rotaxanes." Thesis, University of Oxford, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.365821.
Full textBook chapters on the topic "Mechanically linked molecule"
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Tuck, Adrian F. "Radiative and Chemical Kinetic Implications." In Atmospheric Turbulence. Oxford University Press, 2008. http://dx.doi.org/10.1093/oso/9780199236534.003.0009.
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The laws governing the dynamical behaviour of atoms and molecules are quantum mechanical, and specify that their internal energy states are discrete, with only definite photon energies inducing transitions between them, subject to selection rules. These energy levels appear as spectra in different regions of the electromagnetic spectrum: pure rotational lines in the microwave or far infrared, ‘rovibrational’ (rotation + vibration) lines in the middle and near infrared, while electronic transitions, sometimes with associated rotational and vibrational structure (‘rovibronic’) occur from the near infrared through the visible to the ultraviolet. An important feature of these spectra in the atmosphere is that they do not appear as single sharp lines, but are collisionally broadened about the central energy into ‘line shapes’ which frequently overlap with other transitions, both from the same molecule and from others. One of the primary dynamical quantities involved in the processes broadening these line shapes is the relative velocity of the molecules with which the photon absorbing and emitting molecules are colliding. These are primarily N2 and O2 in the atmosphere; if they have an overpopulation of fast moving molecules relative to a Maxwell–Boltzmann distribution, as we have suggested, the line shapes will be affected. Molecules such as carbon dioxide, water vapour, and ozone are all active in the infrared via rovibrational transitions, with water vapour being light enough and so having sufficiently rapid rotation that it has rotational bands appearing in the far infrared rather than the microwave. Nitrous oxide, N2O, and methane, CH4, are also active, but make smaller contributions because of their lower abundances. Molecular nitrogen and molecular oxygen, because they are homonuclear diatomic molecules, do not absorb or emit via electric dipole allowed transitions in the atmospherically important regions of the electromagnetic spectrum. Molecular oxygen, having a triplet ground state, does have weak forbidden and magnetic dipole transitions which, however, play only a very small role in the radiative balance. It should be noted that the translational energy of molecules in a large system like the atmosphere is effectively continuous rather than quantized.
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Ganghoffer, Jean-François. "Mechanical Models of Cell Adhesion Incorporating Nonlinear Behavior and Stochastic Rupture of the Bonds." In Handbook of Research on Computational and Systems Biology, 599–627. IGI Global, 2011. http://dx.doi.org/10.4018/978-1-60960-491-2.ch027.
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The rolling of a single biological cell is analysed using modelling of the local kinetics of successive attachment and detachment of bonds occurring at the interface between a single cell and the wall of an ECM (extracellular matrix). Those kinetics correspond to a succession of creations and ruptures of ligand-receptor molecular connections under the combined effects of mechanical, physical (both specific and non-specific), and chemical external interactions. A three-dimensional model of the interfacial molecular rupture and adhesion kinetic events is developed in the present contribution. From a mechanical point of view, this chapter works under the assumption that the cell-wall interface is composed of two elastic shells, namely the wall and the cell membrane, linked by rheological elements representing the molecular bonds. Both the time and space fluctuations of several parameters related to the mutual affinity of ligands and receptors are described by stochastic field theory; especially, the individual rupture limits of the bonds are modelled in Fourier space from the spectral distribution of power. The bonds are modelled as macromolecular chains undergoing a nonlinear elastic deformation according to the commonly used freely joined chains model, while the cell membrane facing the ECM wall is modelled as a linear elastic plate. The cell itself is represented by an equivalent constant rigidity. Numerical simulations predict the sequence of broken bonds, as well as the newly established connections on the ‘adhesive part’ of the interface. The interplay between adhesion and rupture entails a rolling phenomenon. In the last part of this chapter, a model of the deformation induced by the random fluctuation of the protrusion force resulting from the variation of affinity with chemiotactic sources is calculated, using stochastic finite element methods in combination with the theory of Gaussian random variables.
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Banerjee, Avijit, and Timothy F. Watson. "Restorative materials and their relationship to tooth structure." In Pickard's Guide to Minimally Invasive Operative Dentistry. Oxford University Press, 2015. http://dx.doi.org/10.1093/oso/9780198712091.003.0010.
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Modern restorative materials can be classified in several ways, in terms of their retention (chemically adhesive, macro-, micro- or even nanomechanical), their chemistry (e.g. resin-based vs. acid–base reaction, filler particles), or their clinical properties (e.g. aesthetics, strength, handling). It is essential that these materials are considered closely with the histological substrate to which they will adhere or with which they will interact, in order to understand the complexities of each system and their potential clinical uses. This chapter will outline and discuss aspects of dental materials science to enable the reader to understand and appreciate the links with relevant histology and relate this to the clinical aspects of minimally invasive operative dentistry. Also discussed is dental amalgam, still a popular restorative material among many dentists worldwide, although clinical indications for its use are becoming more limited as treatment rationales change and adhesive materials improve. This text will require supplementation from suitable dental histology and detailed dental material science texts. Dental resin composites are aesthetic, plastic adhesive restorative materials that consist of co-polymerized methacrylate-based resin chains embedding inert filler particles (conferring strength and wear resistance) and requiring a separate adhesive (bonding agent) to micro-/ nano-mechanically bond them to either enamel or dentine, respectively. However, not all modern dental composites are based purely on this methacrylate resin chemistry (see Section 7.2.6). Therefore the term ‘composite resin’ is inappropriate and should not be used. Resin composites have developed over the past 50 years, after the introduction of the acid-etch technique (Buonocore, 1955) and methacrylate monomers (Bowen’s resin—Bis-GMA (1971); see Section 7.2.2). The unset (or uncured) material consists of a mixture of several different types of resin methacrylate monomers, most of which are hydrophobic (water-hating) in nature (see Figure 7.1). The monomer chain length affects certain properties of the resin composite:… • Viscosity (or flowability) of the material. This is important in order to minimize voids trapped within the uncured composite during placement and packing within the depths of a cavity (the stiffer the consistency, the greater the risk of trapping air voids). The shorter the uncured monomer length (and therefore the lower the molecular weight), the lower is its viscosity. Often shorter-length, lower-molecular- weight methacrylate monomers form the basis of the resin chemistry of flowable resin composites, and other diluent molecules may be added.
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Lambourne, Jonathan, and Ruaridh Buchanan. "Basic Immunology." In Tutorial Topics in Infection for the Combined Infection Training Programme. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198801740.003.0012.
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There are four major components of the immune system. These include: 1. mechanical barriers to pathogen entry. 2. the innate immune system. 3. the adaptive immune system. 4. the lymphoid organs. Mechanical barriers include skin and mucous membranes and tight junctions between epithelial cells prevent pathogen entry. Breaches can be iatrogenic, for example, IV lines, surgical wounds, and mucositis, and are a large source of healthcare- associated infections. The innate immune system provides the first internal line of defence, as well as initiating and shaping the adaptive immune response. The innate system comprises a range of responses: phagocytosis by neutrophils and macrophages (guided in part by the adaptive immune system), the complement cascade, and the release of antimicrobial peptides by epithelial cells (e.g. defensins, cathelicidin). The adaptive immune system includes both humoral (antibody- mediated) and cell-mediated responses. It is capable of greater diversity and specificity than the innate immune system, and can develop memory to pathogens and provide increased protection on re-exposure. Immune cells are divided into myeloid cells (neutrophils, eosinophils, basophils, mast cells, and monocytes/macrophages) and lymphoid cells (B, T, and NK cells). These all originate in the bone marrow from pluripotent haematopoietic stem cells. The lymphoid organs include the spleen, the lymph nodes, and mucosal-associated lymphoid tissues—which respond to antigens in the blood, tissues, and epithelial surfaces respectively. The three main ‘professional’ phagocytes are macrophages, dendritic cells, and neutrophils. They are similar with respect to how they recognize pathogens, but differ in their principal location and effector functions. Phagocytes express an array of Pattern Recognition Receptors (PRRs) e.g. Toll-like receptors and lectins (proteins that bind carbohydrates). PRRs recognize Pathogen- Associated Molecular Patterns (PAMPs)— elements which are conserved across species, such as cell-surface glycoproteins and nucleic acid sequences. Though limited in number, PRRs have evolved to recognize a huge array of pathogens. Binding of PRRs to PAMPs enhances phagocytosis. Macrophages are tissue-resident phagocytes, initiating and co-ordinating the local immune response. The cytokines and chemokines they produce cause vasodilation and alter the expression of endothelial cell adhesion factors, recruiting circulating immune cells.
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Dyall, Kenneth G., and Knut Faegri. "Relativistic Electromagnetic Interactions." In Introduction to Relativistic Quantum Chemistry. Oxford University Press, 2007. http://dx.doi.org/10.1093/oso/9780195140866.003.0007.
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Chemical concepts are conveniently formulated in terms of molecules—aggregates of atoms linked by electromagnetic interactions. The proper relativistic description of these interactions is a prerequisite for the development of a theory of relativistic quantum chemistry. As a simple starting point we will consider classical systems made up of point charges, postponing the transition to a quantum mechanical description until later. From the previous chapter we know something about how an electron’s particle properties might be affected by relativity. In this chapter we describe the effects of relativity on the interaction with the electromagnetic field. Again, we adopt a minimalist approach. Electromagnetism and electrodynamics are subjects covered in numerous textbooks for a wide variety of target audiences. To develop the necessary theory from first principles is far beyond the scope of this book. We will only highlight those parts necessary for the later development and understanding of a theory of relativistic quantum chemistry. This means that some of the fundamental equations must be presented without derivation, requiring that the reader either knows these from before or that they must be taken on faith. In particular, in this chapter we make use of the Maxwell equations, the Lorentz force equation, and the generalized potential. The reader will be able to find descriptions or derivations of these in Jackson (1975), for example. We will also need to use a number of relations from vector calculus, and these will normally be introduced in the general form when required. In dealing with fields that vary over time and space, we will need various differential operators. In the nonrelativistic theory of electrodynamics the gradient operator, ∇, and the time derivative, d/dt , are used. From our experience in the previous chapter with mixing of space and time coordinates under Lorentz transformations, we might expect these to combine in a four-space differential operator also.
Conference papers on the topic "Mechanically linked molecule"
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Manion, Charles A., Ryan Arlitt, Irem Tumer, Matthew I. Campbell, and P. Alex Greaney. "Towards Automated Design of Mechanically Functional Molecules." In ASME 2015 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/detc2015-46078.
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Metal Organic Responsive Frameworks (MORFs) are a proposed new class of smart materials consisting of a Metal Organic Framework (MOF) with photoisomerizing beams (also known as linkers) that fold in response to light. Within a device these new light responsive materials could provide the capabilities such as photo-actuation, photo-tunable rigidity, and photo-tunable porosity. However, conventional MOF architectures are too rigid to allow isomerization of photoactive sub-molecules. We propose a new computational approach for designing MOF linkers to have the required mechanical properties to allow the photoisomer to fold by borrowing concepts from de novo molecular design and graph synthesis. Here we show how this approach can be used to design compliant linkers with the necessary flexibility to be actuated by photoisomerization and used to design MORFs with desired functionality.
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Dhilna, C. R., S. M. Gopinath, B. Savitha, D. Parthasarathi, M. Surya, and Muthipeedika Nibin Joy. "Molecular docking studies of some urea derivatives linked with imidazolyl benzamides." In PROCEEDINGS OF INTERNATIONAL CONFERENCE ON RECENT TRENDS IN MECHANICAL AND MATERIALS ENGINEERING: ICRTMME 2019. AIP Publishing, 2020. http://dx.doi.org/10.1063/5.0018040.
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Liu, Jun, Mohamed Alhashme, and Ronggui Yang. "Thermal Transport Across Carbon Nanotube Connected by Molecular Linkers." In ASME 2011 International Mechanical Engineering Congress and Exposition. ASMEDC, 2011. http://dx.doi.org/10.1115/imece2011-64931.
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Carbon nanotubes (CNTs) have been reported to have excellent thermal and mechanical properties over the past two decades. However, the practical application of CNT-based technologies has been limited, due to the inability to transform the excellent properties of single CNTs into macroscopic applications. CNT network structure connects CNTs and can be possibly scaled up to macro-scale CNT-based application. In this paper, nonequilibrium molecular dynamics is applied to investigate thermal transport across two CNTs connected longitudinally by molecular linkers. We show the effect of different types and lengths of molecular linkers on interfacial thermal conductance. We also analyze the density of vibrational normal modes to further understand the interfacial thermal conductance between different molecular linkers and CNTs. These results provide guidance for choosing molecular linkers to build up large-scale CNT-based network structures.
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Aouf, Rashad, and Vojislav Ilic. "Microscopic Observation of Energy Propagation in Polymeric Fluids Crossing a Barrier." In ASME 2008 International Mechanical Engineering Congress and Exposition. ASMEDC, 2008. http://dx.doi.org/10.1115/imece2008-66752.
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A major challenge facing tumour treatment procedures, including hyperthermia, is the inadequate modelling of the bio-heat transfer process. Therefore, an accurate mathematical bio-heat transfer model has to precisely quantify the temperature distribution within a complex geometry of a tumour tissue, in order to help optimize unwanted side effects for patients and minimize (avoid) collateral tissue damage. This study examines the three-dimensional molecular dynamics (MDs) simulation of a Lennard-Jones fluid in the hope of contributing to the understanding of the propagation of a thermal wave in fluids causing phase change i.e. irreversible gelation. It is intended to establish, from such information, a useful benchmark for application to large scale phenomena involving macro scale heat transfer. Specifically, this study examines assemblies of N particles (N = 500 atoms) and analyses the microscopic simulation of double well interaction with permanent molecular bond formation at various temperatures within the range 1–2.5Kb/εT. The dynamics of the fluid is also being studied under the influence of a temperature gradient, dt/dx, where neighbouring particles (i.e. atoms/molecules) are randomly linked by permanent bonds to form clusters of different sizes. The atomic/molecular model consist of an isothermal source and sink whose particles are linked by springs to lattice sites to avoid melting, and a bulk of 500 atoms/molecules in the middle representing the Lennard-Jones fluid. Then, this study simulates the energy propagation following the temperature gradient between the heat source and heat sink at T1 = 2.5 and T2 = 1.5 respectively. The potential equation involved in this study is given by the Finitely Extensible Non Elastic (FENE) and Lennard-Jones (LJ) interaction potential. It is observed that the atoms of the bulk start to form a large cluster (∼ 300 atoms) with long time of simulation estimated by 106 time steps where τ = SQRT(ε/mσ2) and Δt = 10−3. It is also obtained that the potential energy of 13.65KbT across a barrier to establish permanent bonds giving rise to irreversible gel formation. All the parameters used in this study are expressed in Lennard-Jones units.
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Liang, Zhi, Hai-Lung Tsai, and Lan Jiang. "Determination of Laser Absorption Coefficients of Gas Mixtures Using an Ab Initio MD Model." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-41449.
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In an effort to study the laser induced dissociation of gas mixtures for an ongoing research project on diamond thin film coating using multiple lasers, it is necessary to determine the absorption coefficient of laser energy by CO2 gas. An ab initio molecular dynamics (AIMD) model is used to determine the laser absorption coefficient of CO2 gas as a function of laser wavelength and gas temperature. The translational, rotational, and vibration motions of molecules are all taken into account in our model. The intra-molecular potential energy is obtained by solving the Kohn-Sham equation. The Projector-Augmented Wave (PAW) exchange-correlation potential function is used in the ab initio calculation. Specific heat of the CO2 gas is also calculated. The calculated thermal properties of CO2 gas and the vibration spectrum of molecules are in good agreement with the experimental results. The calculated normalized absorption line shape CO2 gas is close to the experimental results.
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Liang, Zhi, and Hai-Lung Tsai. "Ab Initio Calculations of Infrared Absorption Cross Sections of CO2 Gas." In ASME 2008 International Mechanical Engineering Congress and Exposition. ASMEDC, 2008. http://dx.doi.org/10.1115/imece2008-67776.
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An ab initio model is used to determine the infrared absorption cross sections of CO2 gas as a function of laser wavelength. The intra-molecular potential energy and electric dipole moment of the CO2 molecule as a function of molecular nuclear configurations are obtained by solving the Kohn-Sham (KS) equation. The rotational constants at different vibrational levels, the vibrational energy eigen values and transition dipole moments are determined by solving the pure vibrational Schro¨dinger equation. Using the Fermi’s Golden Rule and all the calculated ab initio results, the absorption cross sections of CO2 gas at room temperature and one atmosphere pressure are obtained. The calculated results have a good agreement with experimental results. Based on the calculated ab initio results, the infrared absorption cross sections of CO2 gas at higher pressures are calculated. The absorption spectra at high pressures are found to be much smoother due to the overlaps between neighboring absorption line shapes.
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Yang, Xiaofan, and Z. Charlie Zheng. "Continuum/Nano-Scale Simulation of Surface Diffusion Process in Flow." In ASME 2011 International Mechanical Engineering Congress and Exposition. ASMEDC, 2011. http://dx.doi.org/10.1115/imece2011-62960.
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Fluid transport with diffusion through micro-/nano-channels is found in many natural phenomena and industrial processes, including fluid transport or diffusion through nano-materials, molecular/atomistic transfer across nuclear pores or in the MEMS devices among other applications. Those nano-pores can be treated as nano-channels in the thin layers of the membranes. The transport phenomena of fluid in such small confined channels, usually in the size of ten molecular diameters or less, differs significantly from its bulk behaviors and cannot be described with continuum theory. In this case, molecular dynamics (MD) simulation, rather than continuum methods, is better suited to study the phenomena. The surface diffusion, related to both the fluid and solid material properties and the flow rate, can be used as a parameter for estimating the adsorbing capacity of a porous nano-material. The transport of fluids through porous materials occurs mainly by diffusion. In this study, a molecular-continuum hybrid scheme is used for the study of the diffusion in a representative Couette flow problem. By varying the velocity of the moving-solid wall, we investigated the effect of the shearing condition on the mass flux going through the pores. The relationship of the physical mechanisms and the transport phenomena (e.g. Fick’s law) were then linked among the different length scales. Activated carbon with its high surface area has been emerging as a promising candidate for an adsorbent due to not only its stable thermodynamic and mechanical properties but also its homogenous and isotropic porous distribution and relatively even pore size. In this study, we focus on the characteristics of the permeation and the adsorption process between different gases and the carbon substrate under various shearing conditions. The investigation of the diffusion process of fluids through the pores of the nano-materials has become an interesting topic in recent decades. This investigation has been divided into two major areas: 1) the diffusivity estimation and 2) the transient diffusion rate. We apply a continuum/MD hybrid scheme to a model problem of various gases transport through a carbon substrate with several pores in a channel flow under different shear rates. Instead of inserting and deleting particles from the control volumes used in the DCV-GCMD method, we keep the number of particles in the simulation system constant. The interactions between fluid/fluid, fluid/solid and solid/solid are all assumed to be under Lennard-Jones potentials. In the modeled Couette flow, the two solid walls are constructed with nano-pores that allow fluids to go through the substrate to study the transient diffusion rate (flux). Before simulating the fluid transport through the nano-pores, we need to validate the natural diffusion properties of the bulk fluid. To do this, a system (as a cube) consisting of pure liquid argon molecules is used to perform the pure MD simulation. The radial distribution function (RDF) is used as the parameter to verify the natural diffusion of the liquid argon fluid in the bulk flow, which is a structural correlation. It describes the spherically averaged local organization around any given molecule. Figure 1 shows a good comparison of the radial distribution functions between the MD prediction and the experimental measurement of Eisenstein and Gingrich (1942). By comparing our calculation to Wu et al. (2008) under similar circumstances, we found that the average (from 8 pores) and corrected mass flux J · (RTh) is linearly proportional to the average pressure gradient along the pore. And the slope of this relationship is the transport diffusivity, which is 4.6 × 10−7m2/s under 273K and 4.9 × 10−7m2/s under 300K. This indicates that the current simulation follows the Fick’s law exactly. Similarly, for other gases, the same linear relationships can also be obtained. These calculations are listed in Table 1 that shows the transport diffusivity increases with temperature. The mass fluxes of three gases at various pore widths are calculated as shown in Fig. 2. Generally, with larger pores, the mass fluxes increase. However, among three gases, the increase of H2 is much faster than the other two gases because of hydrogen’s smaller molecular size. In another word, smaller molecules as H2 have faster diffusion rates during the adsorption process.
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Hay, Akara, and Shanzhong (Shawn) Duan. "Implementation of an Integrated Sequential Procedure for Computer Simulation of Dynamics of Multibody Molecular Structures in Polymers and Biopolymers." In ASME 2019 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2019. http://dx.doi.org/10.1115/imece2019-11752.
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Abstract This paper presents the implementation results of an integrated sequential algorithm, which the second author developed mathematically in a pseudo code format previously to improve computational efficiency of computer simulation of the dynamical behaviors of multibody molecular structures in polymers and biopolymers. This new algorithm is a seamless integration between multibody molecular algorithm (MMA: a multibody-dynamics-based procedure for motion simulation of molecular structure) and fast multipole method (FMM). The fast multipole method is used to calculate interatomic forces from potentials, and the multibody molecular algorithm is used to generate equations of motion associated with molecular structures. The algorithm improves computational efficiency when comparing with its counterpart procedures. A study case of an opened-chain molecular structure was used to demonstrate the algorithm works and to study improvement of computing efficiency of the algorithm. The algorithm is coded in MATLAB and run on both laptop and workstations computers with various numbers of molecules along the chain. FMM started with scaling all atoms into a box with coordinate ranges to ensure numerical stability of subsequent operations. The flow of calculations in FMM was carried out along the chain structure with five computational passes. MMA began with numbering subsets, forming bond graph, and developing three computing passes along the chain structure. Flows of both calculations and data in FMM and MMA were lined up recursively along the chain structure to obtain an O(N)1 computational efficiency. Simulation results were compared with results produced by MMA and traditional methods of FMM for interatomic force calculation procedure. Implementation presented in this paper first proves that the integration between FMM and MMA works and the integrated algorithm improves computing efficiency associated with both calculation of interatomic forces from potentials and formation/solution of equations of motion. Implementation results also indicates that the integrated algorithm works more efficiently for a large-sized molecular chain than a small-sized molecular chain. Further work is needed to optimize the related FMM codes.
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Hargude, N. V., and S. M. Sawant. "Experimental Investigation of a Spark Ignited Engine Using Magnetic Air Conditioner (MAC) for Improved Performance and Reduced Emissions." In ASME 2016 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/imece2016-66521.
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In 21st century, to cope up with exponential technological development, use of eco-friendly conventional energy system is a critical issue. Saving of energy is nothing but production of energy. Conventional fuel used in stationary power plant an IC engine is bulk in quantity, which will not be last longer and will exhaust very soon. Stationary power plants and Automobile propelled by I.C. engines have a problem of pollutant emission in environment which mainly depends on combustion process occurs in power plant and I.C. engines. Incomplete combustion of hydro-carbon fuel/s produce very large amount of harmful emission gases resulting into smog in cities & reduces performance of the system. These systems, equipped with Internal Combustion or External combustion produces large amount of exhaust gases CO, HC and NOx like monoxides etc. Since hazardous emissions which are harmful to human life and ecosystem resulting in many types of diseases of human especially in urban areas where automobile vehicle equipped with IC engine density is very high. These emissions have effect on result in environmental cycles also. In today’s globalised world, many attempts are made to reduce intensity of hazardous emissions of an IC engine through pre processing of fuels and post processing combustion exhaust gases in IC engine by many means like MPFI, PCV, EGR, catalytic converter, supercharger, turbocharger, etc. In order to handle, these issues, additional attempt is made. This attempt uses Air conditioner/Energizer for Pre-processing air and unit developed called as Magnetic air Conditioner (MAC). A permanent magnet, magnetic air conditioner (MAC) is mounted in path of air lines. Mounting MAC in air line enhances quality of air and air molecules properties like it aligns and orientations, especially in an oxygen molecule. Better atomization of an oxygen molecule which further enters into combustion chambers of SI engine along with air. In a conventional four stroke spark Ignited engine, oxygen molecules reacts with hydro -carbon, which assist for complete combustion of hydro-carbon. Use of such Magnetic air conditioners improves performance of SI engine. The specific fuel consumption also decreases, resulting in to decrease in BSFC with increase in load. Use of MAC in engine also reduces emissions like CO, HC, ultimately resulting into reduction in smog in urban areas. The present article describes the mechanism of MAC, objectives and its effect on SI engine, such as enhanced performance parameter, various efficiencies like mechanical, brake thermal, volumetric saving in fuel, and reduced emission. One case study is presented in which ferrite magnets are used as MAC which improves performance and reduces emissions.
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Bidone, Tamara Carla, Haosu Tang, and Dimitrios Vavylonis. "Insights Into the Mechanics of Cytokinetic Ring Assembly Using 3D Modeling." In ASME 2014 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/imece2014-39006.
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During fission yeast cytokinesis, actin filaments nucleated by cortical formin Cdc12 are captured by myosin motors bound to a band of cortical nodes. The myosin motors exert forces that pull nodes together into a contractile ring. Cross-linking interactions help align actin filaments and nodes into a single bundle. Mutations in the myosin motor domain and changes in the concentration of cross-linkers alpha-actinin and fimbrin alter the morphology of the condensing network, leading to clumps, rings or extended meshworks. How the contractile tension developing during ring formation depends on the interplay between network morphology, myosin motor activity, cross-linking and actin filament turnover remains to be elucidated. We addressed this question using a 3D computational model in which semiflexible actin filaments (represented as beads connected by springs) grow from formins, can be captured by myosin in neighboring nodes, and get cross-linked with one another through an attractive interaction. We identify regimes of tension generation between connected nodes under a wide set of conditions regarding myosin dynamics and strength of cross-linking between actin filaments. We find conditions that maximize circumferential tension, correlate them with network morphology and propose experiments to test these predictions. This work addresses “Morphogenesis of soft and living matter” using computational modeling to simulate cytokinetic ring assembly from the key molecular mechanisms of viscoelastic cross-linked actin networks that include active molecular motors.