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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 117 (2002), S. 4000-4009 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In this work, we present a simple approach for devising order parameters (OPs) for atomic systems based on pattern recognition techniques. It exploits the fact that all crystalline substances are characterized by a unique "signature" cell (SC) which is constructed using a central atom and its nearest NSC neighbors in a given crystal. The algorithm measures the local degree of similarity between a SC and the system to be analyzed. The best fit of a SC to NSC atoms surrounding a given atom in the system is determined by maximizing a fictitious energy of binding among those atoms and the SC atoms. The fictitious potential energy is designed to give maximum attractive energy for maximum overlap. The maximum binding energy of interaction attained in this process is used as a measure of similarity between the crystal structure and the system (i.e., as an OP). The proposed method provides a unified and intuitive approach for constructing relevant OPs for a given system. We used these OPs to characterize the order of different phases in the Lennard-Jones system and in a model silicon system. It is shown that these novel OPs give a more complete description and a better understanding of the structural order in amorphous silicon than conventional OPs. © 2002 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 2
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
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  • 3
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A tight-binding model for B–B interactions has been developed to study the stability of small boron clusters in crystalline silicon. The model was produced by fitting to the band structure determined by local-density approximation calculations on periodic supercells. This model is able to reproduce, relatively accurately, the cohesive energy of free boron clusters as determined by self-consistent field and configuration-interaction calculations. © 1998 American Institute of Physics.
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  • 4
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 9744-9755 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The characteristics of the solid/liquid transition for a modified Simple Point Charge model of water have been determined using free energy calculations supported by nonequilibrium Molecular Dynamics (NEMD) simulations. We have considered the behavior of liquid water and of a variety of ice phases. Unlike real water, the stable crystalline phase at 1 bar is not hexagonal ice I, but a denser new ice phase. The melting point of this ice was found to be near 295 K. The lower-density ices, Ih and Ic, are less stable than water down to the glass transition temperature. The conclusions are supported by NEMD simulations of the behavior of the planar crystal–liquid interface for these different cases. The first report of the growth of ice from water using molecular simulation is shown here. The influence of the components of the intermolecular potential on the stability of the ice polymorphs is investigated. It is found that, for ice I to be the stable phase, the Lennard–Jones attractive part should be reduced, and the potential switching function should be used at longer distances. Properties of the supercooled liquid water are also presented. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 9837-9840 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Simulations of water using the exnteded simple point charge (SPC/E) model at temperatures between 190 and 330 K were performed using molecular dynamics techniques. A maximum in the density at 1 bar pressure was found to occur at 235 K. The energies and diffusivities are also reported. The SPC/E-modeled water exhibits a glass transition ∼177 K. No crystallization events were observed during the course of the long simulations. © 1994 American Institute of Physics.
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  • 6
    ISSN: 1520-5134
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1749-6632
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Natural Sciences in General
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 8138-8148 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The growth and dissolution of implanted fcc nanocrystallites in a subcooled liquid have been studied using nonequilibrium Molecular Dynamics simulation techniques. The initial sizes of the 70 implanted crystals were each close to the critical cluster size of 120 atoms predicted by classical nucleation theory. The simulated system consisted of approximately 13 500 atoms interacting with a Lennard-Jones potential. The time evolution of the crystal sizes was followed in order to obtain statistics from which the kinetics and the probabilities of growth and dissolution were extracted using a Markovian technique. The growing crystallites showed facets that correspond to hexagonally packed layers. Very small crystals adopted an octahedral shape, but this shape was lost as the crystals grew. Although the implanted crystals had an fcc structure originally, the crystals grew in a mixture of hcp and fcc geometries with a larger proportion of the latter. Our analysis showed the critical cluster size for the implants to be 170 atoms, somewhat larger than the value predicted by a Gibbsian nucleation theory. The rate of growth showed minima, suggesting the existence of "magic numbers'' in crystal growth from the melt. Homogeneous nucleation was also simulated. The free energies of the subcritical crystallites is smaller than predicted by classical nucleation theory using the properties of the bulk liquid and solid phases. The rate of nucleation is compared with theoretical predictions. © 1995 American Institute of Physics.
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  • 9
    ISSN: 0001-1541
    Keywords: Chemistry ; Chemical Engineering
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The interaction between a winter flounder antifreeze polypeptide and an ice/water interface was studied using Molecular Dynamics computer simulation techniques to study the mechanism of action of this class of antifreeze molecules. Simple Point Charge models were used for the water molecules, and a molecular mechanics program (CHARMM) was used to construct the model for the polypeptide. A (2021) face was exposed on the ice surface, as this is believed to be the experimentally favored ice face for peptide binding. The polypeptide binds strongly to the ice surface even though it was placed with its four polar threonine (Thr) groups pointing away from the ice surface. This tested the previously advanced hypothesis that adsorption occurs primarily between these groups and the ice due to a matching of the spacing between oxygen atoms in the ice lattice and the polar Thr residues. As well as contacts with other polar groups on the peptide, the binding to the ice produces a good steric fit of the peptide with the corrugated ice interface. The presence of the peptide did not induce any melting of the ice at 200 K.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Clusters containing up to five boron atoms were considered as extended defects within a crystalline Si matrix. Tight-binding calculations suggest that a cluster containing two boron atoms occupying substitutional sites is stable, unlike any other small boron cluster that we studied. The formation energy increases when a third and fourth substitutional boron atom is added to the cluster. Estimates of the equilibrium concentration, using tight-binding-derived formation energies and formation entropies from the Stillinger–Weber model, indicate that B2 clusters become important when the boron doping level is ∼1018 cm−3, well below the solubility limit. In contrast, the formation energy of defect clusters involving an interstitial (BnI clusters, n=1–5, in their preferred charge states) decreases with increasing cluster size, down to 0.6 eV for B5I in a −5 charge state. None had formation energies that would lead to stable bound clusters. Several BnI clusters were found to be considerably more stable than isolated Si self-interstitials (by 1–2 eV), the BSBI cluster, assumed in some continuum modeling codes to be important, was not a particular interesting defect structure (a formation energy in the −2 charge state, EF−2, of 2.8 eV). There seemed to be little energetic penalty for creating clusters larger than about B5I, in good agreement with Sinno and Brown's Stillinger–Weber studies of self-interstitial clusters in Si [Mater. Res. Soc. Symp. Proc. 378, 95 (1997)]. Some support was found for the suggestion of Pelaz et al. [Appl. Phys. Lett. 70, 2285 (1997)] that BI2 is a nucleation site for boron clustering. Boron clusters involving a boron interstitial were generally found to be less likely to form than analogous clusters involving a Si self-interstitial. B2 clusters involving vacancies are not energetically favored, confirming the known tendency for boron to diffuse via an interstitial mechanism rather than vacancies. These results suggest that boron clusters could serve as traps, which slow the diffusion of self-interstitials under conditions of interstitial supersaturation in highly doped silicon, consistent with experimental evidence. © 1998 American Institute of Physics.
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