Thermodynamics and Kinetics of Melting and Growth of Crystalline Silicon Clusters

MRS Proceedings ◽

10.1557/proc-536-311 ◽

1998 ◽

Vol 536 ◽

Cited By ~ 2

Author(s):

P. Keblinski

Keyword(s):

Melting Temperature ◽

Cluster Size ◽

Crystalline Silicon ◽

Md Simulations ◽

Silicon Clusters ◽

Homoepitaxial Growth ◽

Thermodynamics And Kinetics ◽

Three Body ◽

Body Potential ◽

Kinetics Of

AbstractMolecular-dynamics (MD) simulations and the Stillinger-Weber three-body potential are used to study the growth and stability of silicon clusters of diameters from 2 to 5 nm embedded in the melt. Our simulations show that the melting temperature of such nano-clusters is lower than the bulk melting temperature by an amount proportional to the inverse of the cluster size. We also show that the nature of the kinetics of such small Si clusters is essentially the same as that of the homoepitaxial growth. In particular, we show that the mobility of the highly-curved crystalliquid interface is controlled by diffusion in the adjacent melt, and is characterized by the same activation energy.

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Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

Chemical Science ◽

10.1039/d0sc04657d ◽

2021 ◽

Author(s):

Arghadwip Paul ◽

Suman Samantray ◽

Marco Anteghini ◽

Mohammed Khaled ◽

Birgit Strodel

Keyword(s):

Amyloid Β ◽

Md Simulations ◽

Amyloid Β Peptide ◽

Intrinsically Disordered ◽

Thermodynamics And Kinetics ◽

Markov State ◽

Markov State Models ◽

State Models ◽

Kinetics Of

The convergence of MD simulations is tested using varying measures for the intrinsically disordered amyloid-β peptide (Aβ). Markov state models show that 20–30 μs of MD is needed to reliably reproduce the thermodynamics and kinetics of Aβ.

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Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

10.1101/2020.07.27.223487 ◽

2020 ◽

Cited By ~ 3

Author(s):

Arghadwip Paul ◽

Suman Samantray ◽

Marco Anteghini ◽

Birgit Strodel

Keyword(s):

Alzheimer’S Disease ◽

Force Fields ◽

Amyloid Β ◽

Md Simulations ◽

Amyloid Β Peptide ◽

Thermodynamics And Kinetics ◽

Markov State ◽

Markov State Models ◽

State Models ◽

Kinetics Of

AbstractThe amlyoid-β peptide (Aβ) is closely linked to the development of Alzheimer’s disease. Molecular dynamics (MD) simulations have become an indispensable tool for studying the behavior of this peptide at the (sub)molecular level, thereby providing insight into the molecular basis of Alzheimer’s disease. General key aspects of MD simulations are the force field used for modeling the peptide or protein and its environment, which is important for accurate modeling of the system of interest, and the length of the simulations, which determines whether or not equilibrium is reached. In this study we address these points by analyzing 30-µs MD simulations acquired for Aβ40 using seven different force fields. We assess the convergence of these simulations based on the convergence of various structural properties and of NMR and fluorescence spectroscopic observables. Moreover, we calculate Markov state models for each of the seven MD simulations, which provide an unprecedented view of the thermodynamics and kinetics of the amyloid-β peptide. This further allows us to provide answers for pertinent questions, like: Which force fields are suitable for modeling Aβ? (a99SB-UCB and a99SB-ILDN/TIP4P-D); What does Aβ peptide really look like? (mostly extended and disordered) and; How long does it take MD simulations of Aβ to attain equilibrium? (20–30 µs). We believe the analyses presented in this study will provide a useful reference guide for important questions relating to the structure and dynamics of Aβin particular, and by extension other similar disordered peptides.

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Atomistic Simulations of Epitaxial Regrowth of As-doped Silicon

MRS Proceedings ◽

10.1557/proc-1070-e03-09 ◽

2008 ◽

Vol 1070 ◽

Cited By ~ 1

Author(s):

Joo Chul Yoon ◽

Scott Dunham

Keyword(s):

Crystalline Silicon ◽

Solid Phase ◽

Nearest Neighbors ◽

Surface Region ◽

Md Simulations ◽

Atomistic Simulations ◽

Dual Function ◽

Crystalline Region ◽

Kinetics Of ◽

Si Ion Implantation

ABSTRACTWe conducted molecular dynamics (MD) simulations of solid phase epitaxial growth of As-doped Si using a Tersoff potential characterized via comparison to DFT calculations, including energies of AsnV clusters. The Si:As systems were initialized by amorphizing the surface region of crystalline silicon via Si ion implantation and/or selective melting. The remaining crystalline region provides dual function of controlling temperature in system without perturbing regrowth and providing seed for recrystallization. After recrystallization, isolated As atoms occupy substitutional sites, with the average number of nearest neighbors for As changing from about 3.3 in amorphous Si to 4 after crystallization. We observe V incorporation associated with high As concentrations. A small fraction of isolated As atoms have associated vacancies, while vacancies are incorporated in the majority of cases in which there are sites with two As neighbors. These observations are consistent with our previous model developed to explain kinetics of As shallow junction formation which assumed V incorporation at sites with 2 or more As nearest neighbors to account for experimental data.

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Application of a New Three-Body Potential to Vitreous Silica and Sodium Silicate Glasses

MRS Proceedings ◽

10.1557/proc-141-207 ◽

1988 ◽

Vol 141 ◽

Author(s):

B. P. Feuston ◽

R. N. Newell ◽

S. H. Garofalini

Keyword(s):

Sodium Silicate ◽

Silicate Glass ◽

Md Simulations ◽

Pair Interaction ◽

Vitreous Silica ◽

Static Structure Factor ◽

Static Structure ◽

Three Body ◽

Body Potential ◽

Good Agreement

AbstractAn empirical three-body potential, suitable for molecular dynamics (MD) simulations, has been developed to model the natural covalency of the Si-O bond in vitreous silica and silicate glass systems. Through the addition of a small directional-dependent three-body term to a previously used modified ionic pair interaction, a narrow distribution of tetrahedral angles and a low concentration of defects were obtained, in good agreement with experiment. The structure of bulk silica resulting from the MD technique also contained a larger average ring size, no edge-sharing tetrahedra, and a calculated static structure factor in good agreement with neutron diffraction results. The simulated sodium silicate glass was also largely improved over previous simulations using pair interactions alone. All silicon atoms were found to be exactly four coordinated while the number of non-bridging oxygen nearly equaled the number of sodium ions present with a reasonable distribution of Qi species.

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Irradiation behavior of pyrolytic silicon carbide

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100074288 ◽

1983 ◽

Vol 41 ◽

pp. 72-73

Author(s):

R. J. Lauf

Keyword(s):

Silicon Carbide ◽

Fission Products ◽

Thermodynamics And Kinetics ◽

Neutron Fluences ◽

Fuel Particles ◽

Sic Coatings ◽

Irradiation Behavior ◽

Kinetics Of ◽

Htgr Fuel

Fuel particles for the High-Temperature Gas-Cooled Reactor (HTGR) contain a layer of pyrolytic silicon carbide to act as a miniature pressure vessel and primary fission product barrier. Optimization of the SiC with respect to fuel performance involves four areas of study: (a) characterization of as-deposited SiC coatings; (b) thermodynamics and kinetics of chemical reactions between SiC and fission products; (c) irradiation behavior of SiC in the absence of fission products; and (d) combined effects of irradiation and fission products. This paper reports the behavior of SiC deposited on inert microspheres and irradiated to fast neutron fluences typical of HTGR fuel at end-of-life.

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