关键词： amphetamine   free energy for the binding   gut microbiota   molecular dynamics simulation  

摘要： The human gut harbors diverse bacterial species in the gut, which play an important role in the metabolism of foodand host *** studies have also revealed their role in altering the pharmacological propertiesand efficacy of oral drugs through promiscuous metabolism. However, the atomistic details of the enzyme-drug interactions of gut bacterial enzymes which can potentially carry out the metabolism of drug molecules are still scarce. A well-known example is the FDA drug amphetamine (a central nervous system stimulant), which has been predicted to undergo promiscuous metabolism by gut bacteria. Therefore, to understand the atomistic details and energy landscape of the gut microbial enzyme-mediated metabolism of this drug, molecular dynamics studies were performed. It was observed that amphetamine binds to tyramine oxidase from the Escherichia coli strain present in the human gut microbiota at the binding site harboring polar and nonpolar amino acids. The stability analysis of amphetamine at the binding site showed that the binding is stable and the free energy for the binding of amphetamine was found to be similar to -51.71kJ/mol. The insights provided by this study on promiscuous metabolism of amphetamine by a gut enzyme will be very useful to improve the efficacy of the drug.

关键词： TiO2@In2O3 heteroarchitecture photoelectrodes   Photoelectrochemical hydrogen generation   BPA degradation   Charge transfer mechanism  

摘要： In this study, we have synthesized hierarchical TiO2@In2O3 heteroarchitecture photoanodes via a hydrothermal method and studied their interfacial charge carrier dynamics through water splitting and organic decomposition. Photoelectrochemical measurements show that the IN-0.4 exhibits an obvious enhancement in photocurrent density compared to the pristine TiO2. Electrochemical impendence spectroscopy (EIS) and Time-resolved photoluminescence (PL) have been employed to study the charge recombination in TiO2@In2O3 nanostructure. The surface passivation of TiO2 nanorods (NRs) with In2O3 nanostructures helps to the suppression of the surface defects. The surface-passivated photoanode (IN-0.4) has demonstrated the improved hydrogen generation activity (125 mu mol.h(-1)) of TiO2 nanorods (NRs) with In2O3 nanostructures during water splitting and organic decomposition. The probable causes of the enhancement in hydrogen evolution could be due to (i) enhanced photogenerated electron transport (ii) increased active surface area with In2O3 and/or (iii) catalytic activity of In2O3. Moreover, the photoelectrocatalytic activities of IN-0.4 were slight affect during degradation of Bisphenol A and methyl orange dye, which might be due to the lower hole mobility in TiO2@In2O3 heteroarchitecture photoelectrodes. These sightings and proposed schematic model can help to understand the charge transfer dynamics in hierarchical TiO2@In2O3 heteroarchitecture photoelectrodes as well as designing multifaceted photoelectrodes for solar energy conversion.

关键词： Density-matrix   Adsorption   Vibrational states   Phonons   Chemical reaction dynamics  

摘要： We present a quantum-mechanical tier model for vibrational relaxation of low-lying excited states of an adsorbate vibrational mode (system), coupled to surface phonons (bath), at zero temperature. The tier model, widely used in studies of intramolecular vibrational energy redistribution in polyatomics, is adapted here to adsorbate-surface systems with the help of an embedded cluster approach, using orthogonal coordinates for the system and bath modes, and a phononic expansion of their interaction. The key idea of the model is to organize the system-bath zeroth-order vibrational space into a hierarchical structure of vibrational tiers and keep therein only vibrational states that are sequentially generated from the system-bath initial vibrational state. Each tier is generated from the previous one by means of a successor operator, derived from the system-bath interaction Hamiltonian. This sequential procedure leads to a drastic reduction of the dimension of the system-bath vibrational space. We notably show that for harmonic vibrational motion of the system and linear system-bath couplings in the system coordinate, the dimension of the tier-model vibrational basis scales as similar to N-lxv. Here, N is the number of bath modes, l is the highest-order of the phononic expansion, and l is the size of the system vibrational basis. This polynomial scaling is computationally far superior to the exponential scaling of the original zeroth-order vibrational basis, similar to M-N, with M being the number of basis functions per bath mode. In addition, since each tier is coupled only to its adjacent neighbors, the matrix representation of the system-bath Hamiltonian in this new vibrational basis has a symmetric block-tridiagonal form, with each block being very sparse. This favors the combination of the tier-model with iterative Krylov techniques, such as the Lanczos algorithm, to solve the time-dependent Schrodinger equation for the full Hamiltonian. To illustrate the method, w

关键词： Genetics   Conformation   Noncovalent interactions   Cluster chemistry   Stability  

摘要： Intrinsically disordered proteins (IDPs) form a special category because they lack a unique well-folded 3D structure under physiological conditions. They play crucial role in cell signaling and regulatory functions and are responsible for several diseases. Although they are abundant in nature, only a small fraction of them have been characterized until date. Such proteins adopt a range of conformations and can undergo transformation from disordered-to-ordered state or vice versa upon binding to ligand. Insights of such conformational transition is perplexing in several cases. In the present study, we characterized disordered as well as ordered states and the interactions contributing the transitions through a mutational study by employing replica exchange molecular dynamics simulation with generalized Born implicit solvent model on a protein from the beta gamma-crystallin superfamily. Most of the proteins within this superfamily are inherently ordered and highly stable. However, Hahellin, although a member of the beta gamma-crystallin family, is intrinsically disordered in its apo-form which takes a well-ordered beta gamma-crystallin fold upon binding to Ca2+. It is intriguing that the mutation at the fifth position of the canonical motif to Arg increases the domain stability in several ordered microbial beta gamma-crystallins with concomitant loss in Ca2+ binding affinity. We carried out similar Ser to Arg mutations at fifth position of the canonical motif for the first time in an intrinsically disordered protein to understand the mechanistic insights of conformational transition. Our study revealed that newly formed ionic and hydrogen bonding interactions at the canonical Ca2+ binding sites play a crucial role in transforming the disordered conformation into ordered beta gamma-crystallin.

关键词： Cement - fly ash pastes   Fly ash   Activation   Polynaphthalene sulfonate superplasticizer (PNS)   Rheology   Hydration  

摘要： In this study fly ash was milled in three types of mills up to the same median particle size similar to 6 mu m. The milling was performed in presence of polynaphthalene sulfonate (PNS) superplasticizer and apart of it. It is shown that the introduction of PNS during the milling allows to prevent adverse agglomeration of the particles, while increment of the specific surface area is independent of the presence of PNS. Cement - fly ash pastes prepared with PNS introduced during the fly ash activation exhibit a reduction of the yield stress by 35%, plastic viscosity by 25% and the induction period of hydration by 30% in comparison to the paste prepared with PNS introduced with the mixing water. (C) 2019 Elsevier Ltd. All rights reserved.

关键词： Orthogonal cutting   Carbon fibre reinforced plastic composites (CFRP)   Bouncing back   Smoothed particle hydrodynamics (SPH)   Finite element method (FEM)  

摘要： FE models of orthogonal cutting of FRP composites are usually used implementing element deletion when the failure condition has been reached. This typically results in loss of contact between tool and workpiece during cutting leading to very poor thrust force prediction. In this study, a comprehensive three-dimensional numerical model of orthogonal cutting of UD-CFRP employing the SPH method at the micro-scale level is developed for different fibre orientations (theta = 0 degrees, 45 degrees, 90 degrees, 135 degrees). Results are compared with those obtained by a FEM model and against experimental findings. Results show that the SPH method is able to improve prediction of cutting force (similar to 30% at theta = 0 degrees) and thrust force (similar to 30% at theta = 90 degrees, 135 degrees), showing also a chip formation mechanism closer to that experimentally observed. In addition, the developed approach allows simulating the bouncing back, that for theta = 0 degrees results equal to the cutting edge radius (similar to 5 mu m), as expected from the literature, and calculating the actual depth of cut.

关键词： Polymer-matrix composites (PMCs)   Interface/interphase   Mechanical properties   Thermal properties   Computational modelling  

摘要： In this study, the effects of nitrogen-doped carbon nanotubes (CNTs) on the interphase characteristics of epoxy matrix nanocomposites were investigated using molecular dynamics (MD) simulations. CNTs including the three different nitrogen doping groups (quaternary, pyridinic, and pyrrolic) were modeled to verify their effect on the nanocomposites. Pull-out and heat-flow simulations were performed to analyze the interphase characteristics of the nanocomposites. The influence of each doping group on the elastic moduli and thermal conductivities of the nanocomposites was analyzed by performing additional MD simulations. The trend of interphase characteristics obtained from the MD simulations was compared to that of the tensile strengths and thermal conductivities of the nanocomposites obtained from experimental studies. The results reveal that their interphase characteristics changed by the nitrogen-doped CNTs can significantly affect both mechanical and thermal properties of its nanocomposites.

关键词： Hydrogen bonds  

摘要： Ultraconfined interlayer water within the tobermorite molecular structure is responsible for changes in the uniaxial tensile and compressive response of the family of tobermorites: 9, 11 and 14 A. These confined interlayer water molecules are engaged in solvation of cations and anions within the tobermorite structure, which has been demonstrated through the intermolecular vibrational spectra and hydrogen bond lifetime of the water molecules. This study demonstrates that instead of ionization of water molecules (as proposed in an earlier study), breaking of hydrogen bonds of water is more plausible leading to solvation of ions within the molecular structure of tobermorite. A schematic of the coordinate covalent bonds between the water molecules and the cations and anions of the tobermorite structure has been proposed in this study.

关键词： Anions   Ligands   Nanoparticles   Nanoparticle formation   Kinetics  

摘要： Ligands are known to affect the formation, stabilization, size, and size-dispersion control of transition-metal and other nanoparticles, yet the kinetic and mechanistic basis for such ligand effects remains to be elucidated and then coupled to predictions for improved particle size and narrower particle size distribution syntheses. Toward this broad goal, the effect of the added excess ligand (L) and the stabilizer, L = POM9- (= the polyoxometalate, P2W15Nb3O629-) is studied for the formation of POM9--stabilized Ir(0)(n) nanoparticles, {Ir(0)(n)center dot(POM9-)(m)}(9m-), synthesized from an atomically characterized precatalyst (COD)Ir center dot POM8- under H-2. First, the balanced reaction stoichiometry and characterization of the nanoparticle products are established. Next, the kinetics of nanoparticle formation is analyzed initially by the FW 2-step minimum mechanism consisting of slow, continuous nucleation, A -> B (rate constant k(1obs)), and autocatalytic surface growth, A + B -> 2B (rate constant k(2obs)) where A is nominally (COD)Ir center dot POM8- and B is nominally the growing, average {Ir(0)(n)center dot(POM9-)(m)}(9m-) nanoparticle. The autocatalytic surface growth rate constant, k(2obs), was then studied as a function of the amount of added POW9-. An inverse, quadratic-root-type dependence of k(2obs), on the concentration of L = POM9- is observed, which was then analyzed in terms of two main mechanisms. Specifically, the dependence of k(2obs), on the [POM9-] was analyzed in terms of (i) an A center dot L (sic) A + L dissociative equilibrium, (COD)Ir-I center dot POM8- + 2 solvent (sic) (COD)Ir-I(solv)(2)(+) + POM9-, and then (ii) this same A center dot L (sic) A + L plus also a B + L (sic) B center dot L nanoparticle-surface capping equilibrium, where B represents the average Ir(0)(n) nanoparticle. Three other mechanisms were also considered. The high-resolution transmission electron microscopy of the parent nanoparticles when no excess POM9- has been

关键词： Nanocrystalline platinum   Grain-size effect   Temperature effect   Mechanical properties   Molecular dynamics  

摘要： A series of molecular dynamics simulations has been carried out to study the mechanical properties of nanocrystalline platinum. The effects of average grain size and temperature on mechanical behaviors are discussed. The simulated uniaxial tensile results indicate the presence of a critical average grain size about 14.1 nm, for which there is an inversion of the conventional Hall-Petch relation at temperature of 300 K. The transition can be explained by a change of dominant deformation mechanism from dislocation motion for average grain size above 14.1 nm to grain boundary sliding for smaller grain size. The Young's modulus shows a linear relationship with the reciprocal of grain size, and the modulus of the grain boundary is about 42% of that of the grain core at 300 K. The parameters of mechanical properties, including Young's modulus, ultimate strength, yield stress and flow stress, decrease with the increase of temperature. It is noteworthy that the critical average grain size for the inversion of the Hall-Petch relation is sensitive to temperature and the Young's modulus has an approximate linear relation with the temperature. The results will accelerate its functional applications of nanocrystalline materials. (C) 2019 Elsevier B.V. All rights reserved.