Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12−6 and 9−6 Lennard-Jones Potentials

Heinz, Hendrik; Vaia, Richard A.; Farmer, Barry L.; Naik, Rajesh R.

doi:10.1021/jp801931d

Cited by 839 publications

(927 citation statements)

References 54 publications

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“…The parameters using a 9-6 LJ potential (eqn (1)) were then transcribed to energy expressions with a 12-6 LJ potential (eqn (2)) using known trends 8,54,55 and fine-tuned to reproduce lattice constant and structural parameters. Some additional differentiation in LJ parameters σ ii , ε ii , equilibrium bond lengths r 0,ij , and angles θ 0,ijk was made due to specific scaling conventions of nonbond interactions between 1,4 bonded atoms and combination rules.…”

Section: Derivation and Interpretation Of Individual Parametersmentioning

confidence: 99%

A force field for tricalcium aluminate to characterize surface properties, initial hydration, and organically modified interfaces in atomic resolution

et al. 2014

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Tricalcium aluminate (C 3 A) is a major phase of Portland cement clinker and some dental root filling cements. An accurate all-atom force field is introduced to examine structural, surface, and hydration properties as well as organic interfaces to overcome challenges using current laboratory instrumentation. Molecular dynamics simulation demonstrates excellent agreement of computed structural, thermal, mechanical, and surface properties with available experimental data. The parameters are integrated into multiple potential energy expressions, including the PCFF, CVFF, CHARMM, AMBER, OPLS, and INTERFACE force fields. This choice enables the simulation of a wide range of inorganic-organic interfaces at the 1 to 100 nm scale at a million times lower computational cost than DFT methods. Molecular models of dry and partially hydrated surfaces are introduced to examine cleavage, agglomeration, and the role of adsorbed organic molecules. Cleavage of crystalline tricalcium aluminate requires approximately 1300 mJ m −2 and superficial hydration introduces an amorphous calcium hydroxide surface layer that reduces the agglomeration energy from approximately 850 mJ m −2 to 500 mJ m −2 , as well as to lower values upon surface displacement. The adsorption of several alcohols and amines was examined to understand their role as grinding aids and as hydration modifiers in cement. The molecules mitigate local electric fields through complexation of calcium ions, hydrogen bonds, and introduction of hydrophobicity upon binding. Molecularly thin layers of about 0.5 nm thickness reduce agglomeration energies to between 100 and 30 mJ m −2 . Molecule-specific trends were found to be similar for tricalcium aluminate and tricalcium silicate. The models allow quantitative predictions and are a starting point to provide fundamental understanding of the role of C 3 A and organic additives in cement. Extensions to impure phases and advanced hydration stages are feasible.

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Section: Derivation and Interpretation Of Individual Parametersmentioning

confidence: 99%

A force field for tricalcium aluminate to characterize surface properties, initial hydration, and organically modified interfaces in atomic resolution

et al. 2014

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“…Periodic boundary conditions were applied along all three directions. The simulations were performed using the MDS package Nanoscale Molecular Dynamics (NAMD) [30], and the CHARMM-METAL force field parameters were used [31]. The VdW interactions were modified at the distances beyond 10 Å so that they smoothly became zero at 12 Å.…”

Section: Molecular Dynamics Simulation (Mds)mentioning

confidence: 99%

Silver nanoparticle-induced hemoglobin decrease involves alteration of histone 3 methylation status

Qian

Zhang

et al. 2015

Biomaterials

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a b s t r a c tSilver nanoparticles (nanosilver, AgNPs) have been shown to induce toxicity in vitro and in vivo; however, the molecular bases underlying the detrimental effects have not been thoroughly understood. Although there are numerous studies on its genotoxicity, only a few studies have investigated the epigenetic changes, even less on the changes of histone modifications by AgNPs. In the current study, we probed the AgNP-induced alterations to histone methylation that could be responsible for globin reduction in erythroid cells. AgNP treatment caused a significant reduction of global methylation level for histone 3 (H3) in erythroid MEL cells at sublethal concentrations, devoid of oxidative stress. The ChIP-PCR analyses demonstrated that methylation of H3 at lysine (Lys) 4 (H3K4) and Lys 79 (H3K79) on the b-globin locus was greatly reduced. The reduction in methylation could be attributed to decreased histone methyltransferase DOT-1L and MLL levels as well as the direct binding between AgNPs to H3/H4 that provide steric hindrance to prevent methylation as predicted by the all-atom molecular dynamics simulations. This direct interaction was further proved by AgNP-mediated pull-down assay and immunoprecipitation assay. These changes, together with decreased RNA polymerase II activity and chromatin binding at this locus, resulted in decreased hemoglobin production. By contrast, Ag ion-treated cells showed no alterations in histone methylation level. Taken together, these results showed a novel finding in which AgNPs could alter the methylation status of histone. Our study therefore opens a new avenue to study the biological effects of AgNPs at sublethal concentrations from the perspective of epigenetic mechanisms.

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“…In this work, the L-J potential is used for two considerations. First, L-J potentials can also properly model metallic systems even with some defects, such as dislocations, surfaces and interfaces [22]. On the other hand, the failure of atomic systems is an energy competition process (kinetic energy and barriers between different states) which can be investigated using either L-J or EAM potentials.…”

Section: Computational Frameworkmentioning

confidence: 99%

Transition of mechanisms underlying the rate effects and its significance

Xiao

Wang

Yang

et al. 2015

Computational Materials Science

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Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12−6 and 9−6 Lennard-Jones Potentials

Cited by 839 publications

References 54 publications

A force field for tricalcium aluminate to characterize surface properties, initial hydration, and organically modified interfaces in atomic resolution

A force field for tricalcium aluminate to characterize surface properties, initial hydration, and organically modified interfaces in atomic resolution

Silver nanoparticle-induced hemoglobin decrease involves alteration of histone 3 methylation status

Transition of mechanisms underlying the rate effects and its significance

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