Structure, Fragmentation, and Phonons in Silicon Microclusters

1992 ◽  
Vol 293 ◽  
Author(s):  
Wei Li ◽  
Rajiv K. Kalia ◽  
Priya Vashishta
Keyword(s):  
Molecular Dynamics ◽  
Structural Information ◽  
Magic Number ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Silicon Clusters ◽  
Atom Clusters ◽  
Densities Of States ◽  
Dynamics Simulations ◽  
Pair Distribution Functions

AbstractMolecular-dynamics simulations are performed to investigate structures, vibrational spectra, and fragmentation channels of silicon microclusters ranging in size from 32 to 52 atoms. Structural information is derived from pair-distribution functions, bond-angle distributions, and the structure and statistics of rings. Molecular-dynamics simulation results for energetics suggest that 33, 39, 45 and 51 atom clusters are highly stable. These magic-number clusters have predominantly five and six membered rings. With an increase in “temperature”, most clusters tend to fragment by loosing one atom at a time. Vibrational densities of states of 32-52 atom silicon clusters show only minor deviations from the bulk behavior.

Structure and Properties of the GeAsS Glasses from Ab initio Calculations

2014 ◽  
Vol 1035 ◽  
pp. 502-507
Author(s):  
Li An Chen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ab Initio ◽  
Bond Angle ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Angle Distribution ◽  
Structure And Properties ◽  
Bond Angle Distribution ◽  
Pair Distribution Functions

The structure and properties of the GexAsxS100-2x have been studied by ab initio molecular dynamics simulation. By calculating the pair distribution functions, bond angle distribution functions, we analyze the structure and properties of the alloys. Calculations show that Ge and As are all well combined with S atoms. When x is smaller than 25.0 the binding increases with x , when x is larger than 25.0 the binding decreases with increasing x . The intervention of As atom does not affect the GeS2 formation in Ge40As40S80

Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment

2019 ◽  
Vol 52 (6) ◽  
pp. 1253-1263 ◽  
Author(s):  
Angelo Gavezzotti ◽  
Leonardo Lo Presti
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Crystal Packing ◽  
Structural Information ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Intermolecular Potential ◽  
Organic Liquids ◽  
Organic Crystals ◽  
X Ray

The CLP-dyncry molecular dynamics (MD) program suite and force field environment is introduced and validated with its ad hoc features for the treatment of organic crystalline matter. The package, stemming from a preliminary implementation on organic liquids (Gavezzotti & Lo Presti, 2019), includes modules for the preliminary generation of molecular force field files from ab initio derived force constants, and for the preparation of crystalline simulation boxes from general crystallographic information, including Cambridge Structural Database CIFs. The intermolecular potential is the atom–atom Coulomb–London–Pauli force field, well tested as calibrated on sublimation enthalpies of organic crystals. These products are then submitted to a main MD module that drives the time integration and produces dynamic information in the form of coordinate and energy trajectories, which are in turn processed by several kinds of crystal-oriented analytic modules. The whole setup is tested on a variety of bulk crystals of rigid, non-rigid and hydrogen-bonded compounds for the reproduction of radial distribution functions and of crystal-specific collective orientational variables against X-ray data. In a series of parallel tests, some advantages of a dedicated program as opposed to software more oriented to biomolecular simulation (Gromacs) are highlighted. The different and improved view of crystal packing that results from joining static structural information from X-ray analysis with dynamic upgrades is also pointed out. The package is available for free distribution with I/O examples and Fortran source codes.

scholarly journals Structural and Dynamic Properties of Hydrophobic Eutectic Solvents Based on Menthol and Fatty Acids: a Molecular Dynamics Simulation Study

2021 ◽  
Author(s):  
Samaneh Barani Pour ◽  
Jaber Jahanbin Sardroodi ◽  
Alireza Rastkar Ebrahimzadeh
Keyword(s):  
Molecular Dynamics ◽  
Fatty Acids ◽  
Dynamic Properties ◽  
Mean Square Displacement ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Eutectic Mixtures ◽  
Dynamical Properties ◽  
Reorientation Dynamics ◽  
Dynamics Simulations

Abstract The structural and dynamical properties of the binary mixture of Menthol (MEN) and Fatty acids (FAs) were investigated using molecular dynamics simulations. We focused on the relationship between the structural and dynamical properties of the eutectic mixtures of MEN and FAs with different molar percentages of FAs. Structural properties of the eutectic mixtures were characterized by calculating the combined distribution functions(CDFs), the radial distribution functions (RDFs), and the angular distribution functions (ADFs), and the Hydrogen bonding network between species and Spatial distribution functions (SDF). Further interaction between menthol and Caprylic acid molecules was confirmed by the results of these analyzes. Also, the transport properties of the mixtures were investigated by using the mean square displacement (MSD) of the centers of mass of the species, self-diffusion coefficients and vector reorientation dynamics (VRD) of bonds. The simulation results indicated that intermolecular interactions have a significant effect on the dynamic properties of species.

scholarly journals Molecular Dynamics Simulation of Polyacrylamide Adsorption on Cellulose Nanocrystals

Nanomaterials ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1256 ◽  
Author(s):  
Darya Gurina ◽  
Oleg Surov ◽  
Marina Voronova ◽  
Anatoly Zakharov
Keyword(s):  
Molecular Dynamics ◽  
Cellulose Nanocrystals ◽  
Water Environment ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Radial Distribution Functions ◽  
Dynamical Characteristics ◽  
Polymer Interactions ◽  
Dynamics Simulations

Classical molecular dynamics simulations of polyacrylamide (PAM) adsorption on cellulose nanocrystals (CNC) in a vacuum and a water environment are carried out to interpret the mechanism of the polymer interactions with CNC. The structural behavior of PAM is studied in terms of the radius of gyration, atom–atom radial distribution functions, and number of hydrogen bonds. The structural and dynamical characteristics of the polymer adsorption are investigated. It is established that in water the polymer macromolecules are mainly adsorbed in the form of a coil onto the CNC facets. It is found out that water and PAM sorption on CNC is a competitive process, and water weakens the interaction between the polymer and CNC.

Molecular dynamics simulations of EPON-862/DETDA epoxy networks: structure, topology, elastic constants, and local dynamics

Soft Matter ◽  
2019 ◽  
Vol 15 (4) ◽  
pp. 721-733 ◽  
Author(s):  
Spyros V. Kallivokas ◽  
Aristotelis P. Sgouros ◽  
Doros N. Theodorou
Keyword(s):  
Molecular Dynamics ◽  
Elastic Constants ◽  
Distribution Functions ◽  
Glass Temperature ◽  
Segmental Dynamics ◽  
Structure Topology ◽  
Xrd Patterns ◽  
Dynamics Simulations ◽  
Networks Structure ◽  
Pair Distribution Functions

Partial pair distribution functions, XRD patterns, segmental dynamics, elastic constants and glass temperature in EPON862/DETDA epoxy predicted through molecular dynamics.

Molecular Dynamics Studies on the Structure of Binary Metallic Glasses based on Lennard-Jones (12-6) Potentials

1983 ◽  
Vol 38 (8) ◽  
pp. 859-865 ◽  
Author(s):  
O. Beyer ◽  
C. Hoheisel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Metallic Glass ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Thermodynamic Conditions ◽  
Characteristic Features ◽  
Reduced Density ◽  
Pair Distribution Functions

Abstract For the metallic glass Ni81B19 the partial pair-distribution functions are determind up to 14Å by a molecular dynamics simulation using effective Lennard-Jones potentials. The obtained pair-distribution functions are in good agreement with the measured ones. As the simulation was carried out at the thermodynamic conditions for a liquid, we conclude that the characteristic features of the structure of the metallic glass are essentially not different from those of the fluid system Ni81B19 at high temperature and pressure. Both the high reduced density of the system and the large differences in the atomic radii of the two species dominantly determine the form of the partial structure factors of the glass. These Findings have been confirmed by our molecular dynamics simulation of a further metallic glass, the Cu57Zr43 system.

AB INITIO MOLECULAR DYNAMICS STUDY OF DISSOLVED SiO2 IN SUPERCRITICAL WATER

2007 ◽  
Vol 06 (01) ◽  
pp. 49-62 ◽  
Author(s):  
N. L. DOLTSINIS ◽  
M. BURCHARD ◽  
W. V. MARESCH ◽  
A. D. BOESE ◽  
T. FOCKENBERG
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Supercritical Water ◽  
Statistical Error ◽  
Distribution Functions ◽  
Time Span ◽  
Ab Initio Molecular Dynamics ◽  
Spontaneous Polymerization ◽  
Dynamics Simulations ◽  
Pair Distribution Functions

Ab initio molecular dynamics simulations of SiO 2 in supercritical water at temperatures of 900 K and 1200 K and a pressure of 1.5 GPa at concentrations of 5 wt% and 16 wt% have been carried out. The different polymeric forms SiO 4 H 4, Si 2 O 7 H 6, and Si 3 O 10 H 8 are found to be energetically similar within the statistical error, suggesting that all three polymeric forms play an important role in solutions at the above conditions. However, neither spontaneous polymerization nor depolymerization has been observed during the 10-ps time span of the simulations. The dynamic and structural properties of the supercritical solutions have been analyzed in terms of diffusion coefficients, vibrational spectra, and radial pair distribution functions.

On the Use of the Reverse Monte Carlo Technique to Generate Amorphous Carbon Structures

1998 ◽  
Vol 09 (07) ◽  
pp. 917-926 ◽  
Author(s):  
Vittorio Rosato ◽  
Juan C. Lascovich ◽  
Antonino Santoni ◽  
Luciano Colombo
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Amorphous Carbon ◽  
Radial Distribution ◽  
Tight Binding ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Reverse Monte Carlo ◽  
Atomic Structures ◽  
Dynamics Simulations

The reverse Monte Carlo (RMC) technique has been used to generate atomic structures of amorphous carbon based on the radial distribution functions and the fraction of differently coordinated sites measured on experimental samples. The resulting structures have been subsequently relaxed via a Tight Binding Molecular Dynamics simulation (TBMD). The radial distribution function, the energy and the fraction of 2-, 3- and 4-fold coordinated sites, evaluated on the relaxed structures, have been compared to those calculated for atomic systems generated on the basis of the "conventional" numerical melt-quench technique. We thus suggest the possibility of using RMC modeling as a useful and convenient tool for generating amorphous structures to be used as initial configurations in Molecular Dynamics simulations.

Comparison of the Structure of Liquid Amides as Determined by Diffraction Experiments and Molecular Dynamics Simulations

1995 ◽  
Vol 50 (1) ◽  
pp. 38-50 ◽  
Author(s):  
Pia C. Schoester ◽  
Manfred D. Zeidler ◽  
Tamäs Radnai ◽  
Philippe A. Bopp
Keyword(s):  
Molecular Dynamics ◽  
Room Temperature ◽  
Heavy Atom ◽  
Distribution Functions ◽  
X Ray ◽  
Atom Pairs ◽  
Dynamics Simulations ◽  
Pair Distribution Functions ◽  
Flexible Models ◽  
Site Pair

The intermodular structures of liquid formamide, N-methylformamide and N,N-dimethylformamide at room temperature are studied by means of NVE molecular dynamics computer simulations. Newly developed flexible models are used. X-ray and neutron weighted structure and total radial pair distribution functions are computed from the simulated site-site pair distribution functions. They are compared with experimental results. The agreement is usually satisfactory as far as heavy atom pairs are concerned while the lengths of the hydrogen bonds are found to be systematically too long in the simulations.

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