Structure and dynamics in liquid bismuth and Bin clusters: A density functional study

2014

Density functional/molecular dynamics simulations with more than 500 atoms have been performed on liquid bismuth at 573, 773, 923, and 1023 K and on neutral Bi clusters with up to 14 atoms. There are similar structural patterns (coordination numbers, bond angles, and ring patterns) in the liquid and the clusters, with significant differences from the rhombohedral crystalline form. We study the details of the structure (structure factor, pair, and cavity distribution functions) and dynamical properties (vibration frequencies, diffusion constants, power spectra), and compare with experimental results where available. While the three short covalent bonds typical to pnictogens are characteristi…

Nucleus-driven crystallization of amorphous Ge2Sb2Te5: A density functional study

2012

Early stages of nucleus-driven crystallization of the prototype phase change material Ge${}_{2}$Sb${}_{2}$Te${}_{5}$ have been studied by density functional/molecular dynamics simulations for amorphous samples (460 and 648 atoms) at 500, 600, and 700 K. All systems assumed a fixed cubic seed of 58 atoms and 6 vacancies. Crystallization occurs within 600 ps for the 460-atom system at 600 and 700 K, and signs of crystallization (nucleus growth, percolation) are present in the others. Crystallization is accompanied by an increase in the number of ``$ABAB$ squares'' ($A$: Ge, Sb, $B$: Te), and atoms of all elements move significantly. There is no evidence of cavity movement to the crystal-glass…

Amorphous Ge15Te85: density functional, high-energy x-ray and neutron diffraction study

2011

The structure and electronic properties of amorphous Ge15Te85 have been studied by combining density functional (DF) simulations with high-energy x-ray and neutron diffraction measurements. Three models with 560 atoms have been constructed using reverse Monte Carlo methods constrained to (1) agree with the experimental structure factors S(Q), and have (2) energies close to the DF minimum and (3) a semiconducting band structure. The best structure is based on the melt-quenched DF structure and has a small number of Ge–Ge bonds. It shows interlocking networks of Te and GeTe with a significant fraction (22–24%) of voids (cavities). Ge occurs with both tetrahedral and 3 + 3 defective octahedral…

Density functional simulations of structure and polymorphism in Ga/Sb films.

2013

Thin films of gallium/antimony alloys are promising candidates for phase change memories requiring rapid crystallization at high crystallization temperatures. Prominent examples are the stoichiometric form GaSb and alloys near the eutectic composition GaSb(7), but little is known about their amorphous structures or the differences between the 'as-deposited' (AD) and 'melt-quenched' (MQ) forms. We have generated these structures using 528-atom density functional/molecular dynamics simulations, and we have studied in detail and compared structural parameters (pair distribution functions, structure factors, coordination numbers, bond and ring size distributions) and electronic properties (dens…

Vierasmolekyylien sitoutumisen mallintaminen lipokaliiniproteiineissa

2008

Tässä työssä tutkittiin DigA16- ja 1KT7-proteiineja. Proteiineille suoritettiin klassisia MD-simulaatioita käyttämällä Orac4.0-ohjelmistoa. DigA16-proteiinin kokeellisesti mitattu rakenne täydennettiin tietokoneella ja kokonaisesta proteiinista simuloitiin kolmea eri rakennetta. 1KT7-proteiinin simulaation lähtörakenteena oli kokeellisesti mitattu rakenne, jota ei tarvinnut täydentää. Simulaatioita suoritettiin kutakin 10,751 nanosekunnin verran, joista 0,751 ns oli alustusta ja 10 ns simulointia 300 Kelvinissä. Tästä 10 ns vaiheesta kerättiin analysoitu data. Simulaation aikana kokonaisenergia kasvoi tasaisesti. Kasvu oli niin pientä, että sen voidaan katsoa johtuneen täysin MD-simulaatios…

Density functional/molecular dynamics simulations of phase-change materials

2013