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.

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.

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.

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.

scholarly journals Origin and control of ionic hydration patterns in nanopores

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Miraslau L. Barabash ◽  
William A. T. Gibby ◽  
Carlo Guardiani ◽  
Alex Smolyanitsky ◽  
Dmitry G. Luchinsky ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Water Molecules ◽  
Surrounding Water ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Water Layers ◽  
Dynamics Simulations ◽  
And Control

AbstractIn order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. Here, we study the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in a graphene nanopore in terms of experimentally accessible radial distribution functions, giving results that agree well with molecular dynamics simulations. The patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the graphene membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

scholarly journals Local structure and distortions of mixed methane-carbon dioxide hydrates

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Bernadette R. Cladek ◽  
S. Michelle Everett ◽  
Marshall T. McDonnell ◽  
Matthew G. Tucker ◽  
David J. Keffer ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Exchange Process ◽  
Carbon Dioxide Sequestration ◽  
Distribution Functions ◽  
Atomic Scale ◽  
Mixed Gas ◽  
Pure Compounds ◽  
Dynamics Simulations ◽  
Pair Distribution Functions ◽  
Methane Carbon

AbstractA vast source of methane is found in gas hydrate deposits, which form naturally dispersed throughout ocean sediments and arctic permafrost. Methane may be obtained from hydrates by exchange with hydrocarbon byproduct carbon dioxide. It is imperative for the development of safe methane extraction and carbon dioxide sequestration to understand how methane and carbon dioxide co-occupy the same hydrate structure. Pair distribution functions (PDFs) provide atomic-scale structural insight into intermolecular interactions in methane and carbon dioxide hydrates. We present experimental neutron PDFs of methane, carbon dioxide and mixed methane-carbon dioxide hydrates at 10 K analyzed with complementing classical molecular dynamics simulations and Reverse Monte Carlo fitting. Mixed hydrate, which forms during the exchange process, is more locally disordered than methane or carbon dioxide hydrates. The behavior of mixed gas species cannot be interpolated from properties of pure compounds, and PDF measurements provide important understanding of how the guest composition impacts overall order in the hydrate structure.

Molecular dynamics study of the hydrophobic 6,6-ionene oligocation in aqueous solution with sodium halides

2010 ◽  
Vol 82 (10) ◽  
pp. 1943-1955 ◽  
Author(s):  
Maksym Druchok ◽  
Vojko Vlachy
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Distribution Functions ◽  
Low Molecular Weight ◽  
Specific Effects ◽  
Sodium Cations ◽  
Counter Ions ◽  
Sodium Halides ◽  
Explicit Water ◽  
Pair Distribution Functions

An explicit water molecular dynamics (MD) simulation is presented of a solution modeling aliphatic 6,6-ionene oligocations mixed with low-molecular-weight electrolytes. In all cases, the co-ions were sodium cations and the counterions were fluoride, chloride, bromide, or iodide anions. The simple point charge/extended (SPC/E) model was used to describe water. The results of the simulation at T = 278 K (the data for 298 K were obtained earlier) and T = 318 K are presented in the form of pair distributions between various atoms and/or between ions in the system. We were interested in how temperature variation modifies the ion-specific effects, revealed by the various pair distribution functions (PDFs). The results were compared with previous calculations for the less hydrophobic 3,3-ionene solutions. Simulations of 6,6-ionene solutions containing mixtures of fluoride and iodide counter-ions at T = 298 K were also presented.

scholarly journals Effects of temperatures on pressure-induced structural changes in amorphous Si: A molecular-dynamics study

10.29007/6kp3 ◽  
2020 ◽  
Author(s):  
Renji Mukuno ◽  
Manabu Ishimaru
Keyword(s):  
Molecular Dynamics ◽  
Phase Transformation ◽  
Amorphous Phase ◽  
Structural Changes ◽  
Interatomic Potential ◽  
Activation Barrier ◽  
Distribution Functions ◽  
High Density ◽  
Angle Distribution ◽  
Dynamics Simulations

The structural changes of amorphous silicon (a-Si) under compressive pressure were examined by molecular-dynamics simulations using the Tersoff interatomic potential. a-Si prepared by melt-quenching methods was pressurized up to 30 GPa under different temperatures (300K and 500K). The density of a-Si increased from 2.26 to 3.24 g/cm3 with pressure, suggesting the occurrence of the low-density to high-density amorphous phase transformation. This phase transformation occurred at the lower pressure with increasing the temperature because the activation barrier for amorphous-to-amorphous phase transformation could be exceeded by thermal energy. The coordination number increased with pressure and time, and it was saturated at different values depending on the pressure. This suggested the existence of different metastable atomic configurations in a-Si. Atomic pair-distribution functions and bond-angle distribution functions suggested that the short-range ordered structure of high-density a-Si is similar to the structure of the high-pressure phase of crystalline Si (β-tin and Imma structures).

scholarly journals Molecular Dynamics Simulations of CO2Molecules in ZIF-11 Using Refined AMBER Force Field

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
W. Wongsinlatam ◽  
T. Remsungnen
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Binding Energies ◽  
Hydrogen Atoms ◽  
Amber Force Field ◽  
Bonding Parameters ◽  
Flexible Framework ◽  
Dynamics Simulations

Nonbonding parameters of AMBER force field have been refined based onab initiobinding energies of CO2–[C7H5N2]−complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 forεandσparameters, respectively. Molecular dynamics simulations of CO2molecules in rigid framework ZIF-11, have then been performed using original AMBER parameters (SIM I) and refined parameters (SIM II), respectively. The site-site radial distribution functions and the molecular distribution plots simulations indicate that all hydrogen atoms are favored binding site of CO2molecules. One slight but notable difference is that CO2molecules are mostly located around and closer to hydrogen atom of imidazolate ring in SIM II than those found in SIM I. The Zn-Zn and Zn-N RDFs in free flexible framework simulation (SIM III) show validity of adapting AMBER bonding parameters. Due to the limitations of computing resources and times in this study, the results of flexible framework simulation using refined nonbonding AMBER parameters (SIM IV) are not much different from those obtained in SIM II.

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