关键词： Deformation physics   Molecular dynamics   Bio-inspired   Nanocomposite   Mechanical properties  

摘要： Nanoscale composites inspired from biological materials such as nacre and bone are excellent candidates for improving the mechanical properties of ceramic matrix composites (CMC) or in general any brittle-matrix composites. These composites are based on the regularly staggered model (RSM) and on the stair-wise staggered model (SSM), and consist of stiffer platelets embedded in a compliant matrix. The interface between the platelets and the matrix plays a key role as an enormous amount of interfacial area exists in the nanocomposite materials. We investigate the influence of interface strength on the overall mechanical properties and deformation mechanisms of bio-inspired brittle-matrix nanocomposites. Atomistic simulations are used for this purpose and the interface strength is controlled by varying the binding energy between the platelet atoms and the matrix atoms. We found that the mechanical properties of both models initially increase with the interface strength. However, above a critical value, the trend changes drastically between the two models. The RSM model continues to maintain the flow stress and toughness at higher interface strengths, due to the persistence of deformation mechanisms such as bulk matrix plasticity and platelet pullout. In contrast, in the SSM model the flow stress and toughness are deteriorated as softening of stress and fracturing of platelets occur at higher interface strengths. The knowledge gained from this study paves new way for the development of bio-inspired ceramic-matrix composites with improved mechanical properties.

关键词： Stiffness  

摘要： The effects of clustered line patterns of hydroxyl functionalization and percent surface coverage along the armchair and zigzag directions of the graphene lattice on the mechanical response of graphene sheets (GS) under tension loading, in zigzag and armchair directions, and under shear loading in the zigzag direction were studied. The initial, functionalization induced bending deformation, caused by clustered line pattern arrangements, led to strong elastic anisotropy of graphene with an increased linear compressibility in the direction perpendicular to the line patterns and increased stiffness in the direction parallel to the line patterns. The line pattern functionalized graphene acted similar to a nanoscale mechanical spring. It is shown that clustered line pattern functionalization along the zigzag direction can increase the stiffness of the GS along the zigzag direction and stretchability along the armchair direction without significantly stretching the carbon bonds and can enhance the toughness of the GS relative to random functionalization. It was also found that the Poisson's ratio can be tuned from positive to negative through line pattern arrangements, reaching a minimum of -0.287 at an -OH percentage of 75% for stretching along the zigzag direction, thus indicating auxetic behavior. (c) 2019 Elsevier Ltd. All rights reserved.

关键词： Butachlor   Bioremediation   Environmental pollution   Immobilization   Metabolites  

摘要： The present study reports a new bacterial isolate identified as Pseudomonas putida strain G3 that can be used for the efficient biodegradation of butachlor, a systemic selective herbicide. Reports suggests butachlor to be a persistent pollutant, a suspected carcinogen and mutagen which poses threat to the environment. Batch biodegradation of the herbicides over a concentration ranging from 100 to 1000 mg/L by the bacterial strain has been studied after process parameter optimization. The bacterial strain is able to degrade up to 700 mg/L of butachlor completely within 360 h. However, increasing the concentration of the herbicide resulted in substrate inhibition in the efficiency of the microbial strain G3. Thus, to determine the bio-kinetic parameters, various inhibition models were fitted to the results obtained during batch biodegradation study. The maximum estimated specific degradation rate was found to be 2.74 mg/L/h. To enhance the bioremediation efficiency of the bacterial strain in presence of higher concentration of the herbicide, the microbial cells were immobilized on Ca-alginate beads and the efficiencies of free and immobilized bacterial cultures were evaluated. The ESI-MS analysis indicated that butachlor biodegradation took place with 2-chloro-N-(2,6-diethylphenyl)-N-hydroxymethylacetamide, 2-chloro-N-(2,6-diethylphenyl) acetamide and 2,6-diethylaniline as intermediate metabolites and a degradation pathway has been proposed. The bacterial strain is able to degrade up to 500 mg/L and 1000 mg/L of other herbicides such as Alachlor and Glyphosate efficiently proposing its wide substrate specificity. The study serves as an important basis that should help to design future bioremediation technology that would be expedient for the treatment of various herbicides. (C) 2019 Published by Elsevier B.V. on behalf of Institution of Chemical Engineers.

关键词： 1,3-Thiazole   1,2,4-Triazole   Acetamides   Elastase   Kinetics   Molecular docking  

摘要： Keeping in mind the pharmacological importance of 2-aminothiazole and 1,2,4-triazole heterocyclic moieties, a series of novel ethylated bi-heterocyclic acetamide hybrids, 9a-p, was synthesized in a multi-step protocol. The structures of newly synthesized compounds were characterized by H-1 NMR, C-13 NMR, IR and EI-MS spectral studies. The inhibitory effects of these bi-heterocyclic acetamides (9a-n) were evaluated against elastase and all these molecules were identified as potent inhibitors relative to the standard used. The Kinetics mechanism was analyzed by Lineweaver-Burk plots which revealed that, 9h, inhibited elastase competitively by forming an enzyme-inhibitor complex. The inhibition constants K-i calculated from Dixon plots for this compound was 0.9 mu M. The computational study was articulate with the experimental results and these ligands unveiled good binding energy values (kcal/mol). So, these molecules can be considered as promising medicinal scaffolds for the treatment of skin melanoma, wrinkle formation, uneven pigmentation, and solar elastosis.

关键词： Molecular Dynamics Simulation   Carboxylic Acids   Acetic Acids   molecular model   Molecular Conformation   Carboxyl Group   Molecular Dynamics   chemical group  

摘要： Accurate hydrogen placement in molecular modeling is crucial for studying the interactions and dynamics of biomolecular systems. The carboxyl functional group is a prototypical example of a functional group that requires protonation during structure preparation. To our knowledge, when in their neutral form, carboxylic acids are typically protonated in the syn conformation by default in classical molecular modeling packages, with no consideration of alternative conformations, though we are not aware of any careful examination of this topic. Here, we investigate the general belief that carboxylic acids should always be protonated in the syn conformation. We calculate and compare the relative energetic stabilities of syn and anti acetic acid using ab initio quantum mechanical calculations and atomistic molecular dynamics simulations. We focus on the carboxyl torsional potential and configurations of microhydrated acetic acid from molecular dynamics simulations, probing the effects of solvent, force field (GAFF vs GAFF2), and partial charge assignment of acetic acid. We show that while the syn conformation is the preferred state, the anti state may in some cases also be present under normal NPT conditions in solution.

关键词： MD simulation   Nano-indentation   Zirconium   Dislocations  

摘要： In the present study, the plastic flow behavior of Zr at 300 K in the presence of defects i.e. self-interstitials, vacancies and voids, which generally form during irradiation, has been investigated by molecular dynamics (MD) simulation of nano-indentation. For the purpose of comparison, a perfect defect-free domain was also probed under similar loading conditions. During nano-indentation various dislocation activities, i.e. nucleation, interactions, locking etc., involved during a typical loading cycle, were distinctly captured. This study has clearly demonstrated that the nature of defects present in the domain influences the dislocation activities during nano-indentation. Using Schmid factor calculation, it is shown that the nucleation of dislocation in all the domains, except the domain containing self-interstitials, occurs only along the directions of maximum resolved stress. In the case of domain containing self-interstitials, difference in the behavior was shown due to the presence of self-interstitials loops, which influenced the state of stress beneath the region of nano-indenter. The cyclic nano-indentation responses of all the domains were quantified in terms of the value of the nano-hardness in each loading stage. In all cases, except in the case of vacancies containing domain, the value of nano-hardness tends to saturate with the increasing number of cycles. In the case of domain containing vacancies the continuous drop in the nano-hardness was observed due to the formation of defect free channels resulting in continuous softening of domain. In the present study the role of vacancies over dislocation loops in the formation of these channels has been emphasized. The current MD simulation is the first such study which shows the feasibility of localized channel formation in the presence of large concentration of vacancies during cyclic nano-indentations.

关键词： Molecular dynamics simulation   Wetting transition   Vibration   Dewetting   Coalescence dynamics  

摘要： Controllable wettability of liquids has always been attached great significance to a wide range of applications in both industrial and technological processes. Here, we report a simple and novel approach to achieve reversible and switchable wettability through the vibration of substrate. Results showed that with the increase of the vibration frequency (f), the wetting state of the liquid metal gradually transform into wetting/dewetting mixed state, and finally becomes complete dewetting state. More importantly, on the basis of our established model (involving vibration amplitude, liquid-substrate interaction), we further interpret and predict the wetting status and the wetting transition procedure of the given droplet. Additionally, the vibration-induced wettability transition can be applied to control the coalescence dynamics, which generates three patterns: free-coalescence, semifree-coalescence, restricted-coalescence. Our work would develop a new strategy to control the surface wettability by vibrating the substrate, without any mechanical or chemical modifications, which could provide guidance in the manipulation of drop dynamics.

关键词： biopolymers   diffusion   hybrid molecular mechanics-molecular dynamics simulation   mechanical properties   microcrystalline cellulose   moisture   molecular dynamics   molecular modeling   water mobility  

摘要： A hybrid molecular mechanics-molecular dynamics simulation method has been performed to study the effects of moisture content on the mechanical properties of microcrystalline cellulose (MCC) and the mobility of the water molecules. The specific volume and diffusion coefficient of the water increase with increasing moisture content in the range studied of 1.8-25.5 w/w%, while the Young's modulus decreases. The simulation results are in close agreement with the published experimental data. Both the bound scission and free-volume mechanisms contribute to the plasticization of MCC by water. The Voronoi volume increases with increasing moisture content. It is related to the free volume and the increase enhances the mobility of the water molecules and thus increases the coefficient of diffusion of the water. Moreover, with increasing moisture content, the hydrogen bonding per water molecule between MCC-water molecules decreases, thus increasing the water mobility and number of free water molecules. (c) 2019 The Authors. Journal of Polymer Science Part B: Polymer Physics published by Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019, 57, 454-464

关键词： Drp1   hFis1   mitochondrial dynamics   mitofusins   OPA1  

摘要： Mitochondrial dynamics is important for life. At center stage for mitochondrial dynamics, the balance between mitochondrial fission and fusion is a set of dynamin-related GTPases that drive mitochondrial fission and fusion. Fission is executed by the GTPases Drp1 and Dyn2, whereas the GTPases Mfn1, Mfn2, and OPA1 promote fusion. Recruitment of Drp1 to mitochondria is a critical step in fission. In yeast, Fis1p recruits the Drp1 homolog Dnm1p to mitochondria through Mdv1p and Caf4p, but whether human Fis1 (hFis1) promotes fission through a similar mechanism as in yeast is not established. Here, we show that hFis1-mediated mitochondrial fragmentation occurs in the absence of Drp1 and Dyn2, suggesting that they are dispensable for hFis1 function. hFis1 instead binds to Mfn1, Mfn2, and OPA1 and inhibits their GTPase activity, thus blocking the fusion machinery. Consistent with this, disruption of the fusion machinery in Drp1(-/-) cells phenocopies the fragmentation phenotype induced by hFis1 overexpression. In sum, our data suggest a novel role for hFis1 as an inhibitor of the fusion machinery, revealing an important functional evolutionary divergence between yeast and mammalian Fis1 proteins.