Initio Molecular Dynamics Method Research Articles

Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion.

We develop a fragment-based ab initio molecular dynamics (FB-AIMD) method for efficient dynamics simulation of the combustion process. In this method, the intermolecular interactions are treated by a fragment-based many-body expansion in which three- or higher body interactions are neglected, while two-body interactions are computed if the distance between the two fragments is smaller than a cutoff value. The accuracy of the method was verified by comparing FB-AIMD calculated energies and atomic forces of several different systems with those obtained by standard full system quantum calculations. The computational cost of the FB-AIMD method scales linearly with the size of the system, and the calculation is easily parallelizable. The method is applied to methane combustion as a benchmark. Detailed reaction network of methane reaction is analyzed, and important reaction species are tracked in real time. The current result of methane simulation is in excellent agreement with known experimental findings and with prior theoretical studies.

A fully quantum description of the free-energy in high pressure hydrogen

Hydrogen is the lightest and most abundant element in the universe. Ever since Wigner and Huntington's prediction that pressure induced metallization might happen in solid hydrogen, understanding the hydrogen phase diagram has become one of the greatest challenges in condensed matter and high pressure physics. The light mass of hydrogen means that the nuclear quantum effects could be important in describing this phase diagram under high pressures. Numerical evaluations of their contributions to the structural, vibrational, and energetic properties, however, are difficult and up to now most of the theoretical simulations still remain classical. This is particularly true for the energetic properties. When the free-energies of different phases are compared in determining the ground state structure of the system at a given pressure and temperature, most of the theoretical simulations remain classical. When nuclear quantum effects must be taken into account, one often resorts to the harmonic approximation. In the very rare case, the anharmonic contributions from the nuclear statistical effects are considered by using a combination of the thermodynamic integration and the at initio molecular dynamics methods, which helps to include the classical nuclear anharmonic effects. Quantum nuclear anharmonic effects, however, are completely untouched. Here, using a self-developed combination of the thermodynamic integration and the at initio path-integral molecular dynamics methods, we calculated the free-energies of the high pressure hydrogen at 100 K from 200 GPa to 300 GPa. The harmonic lattice was taken as the reference and the Cmca phase of the solid hydrogen was chosen. When the bead number of the path-integral (P) equals one, our approach reaches the so-called classical limit. Upon increasing P until the results are converged, our approach reaches the limit when both classical and quantum nuclear anharmonic effects are included. Therefore, by comparing the free-energy of the harmonic lattice and the thermodynamic integration results at P equals one, we isolate the classical nuclear anharmonic effects. By comparing the thermodynamic integration results at P equals one and with those when they are converged with respect to P, we isolate the quantum nuclear anharmonic effects in a very clean manner. Our calculations show that the classical nuclear anharmonic contributions to the free-energy are negligible at this low temperature. Those contributions from the quantum nuclear anharmonic effects, however, are as large as ～15 meV per atom. This value also increases with pressure. This study presents an algorithm to quantitatively calculate the quantum contribution of the nuclear motion to free-energy beyond the often used harmonic approximation. The large numbers we got obtained also indicate that such quantum nuclear anharmonic effects are important in describing the phase diagram of hydrogen, at/above the pressures studied.

Structural stabilities and transformations in cationized asparagine at finite temperatures: An ab initio molecular dynamics study

The cationic complexes of Asparagine (Asn), M +( Asn ), with M + = Li +, Na +, K +, Cs +, and H +, are models for studying the interaction between cations and Asn. Ab initio molecular dynamics (AIMD) method is employed to simulate their behavior at finite temperatures. Structural transformation between conformers is observed, which becomes progressively easier as the cation varies from Li +, to Na +, K +, Cs +, and H +. The fluctuation of the M +– N and M +– O distances and rotation of torsional angles are significant even at room temperature for K +, Cs + and H +. Vibrational profiles based on AIMD trajectories provide insights into the broadening and shifts in relative intensities observed in the vibrational spectra measured by infrared multi-photon dissociation (IRMPD) experiments.

The First Molecular Wheel: A Theoretical Investigation

ABSTRACTRecently, the first molecular nanowheel was synthesized and characterized from Scanning Tunneling Microscope (STM) experiments. It was demonstrated that a specifically designed hydrocarbon molecule (C44H24) could roll on a copper substrate along the [110] surface direction. In this work we report a preliminary theoretical analysis of the isolated molecule and of its rolling processes on different Cu surfaces. We have used ab initio and classical molecular dynamics methods. The simulations showed that the rolling mechanism is only possible for the [110] surface. In this case, the spatial separation among rows of copper atoms is enough to ‘trap’ the molecule and to create the necessary torque to roll it. Other surface orientations ([111] and [100]) are too smooth and cannot provide the necessary torque for the rolling process.

The Thermal, Mechanical and Electronic Properties of Nanoscale Materials: Ab Initio Study

The mechanical, thermal and electronic properties of the nanoscale materials are studied using an ab initio molecular dynamics (TBMD) method and statistical moment method (SMM). We investigate the mechanical properties of nanoscale materials like carbon nanotubes (CNT), graphens and nanowires in comparison with those of corresponding bulk materials. The electronic density of states and electronic transports of the nanoscale materials, with and without the atomistic defects are also discussed. We will show that the thermodynamic and strength properties of the nanoscale materials are quite different from those of the corresponding bulk materials.

Strength and crack properties of nanoscale materials by ab initio molecular dynamics and temperature lattice Green’s function methods

The crack nucleation and propagation processes in nanoscale materials are studied using the ab initio constraint molecular dynamics method and the lattice Green’s function method. We investigate the strength and fracture behaviors of carbon related nanoscale materials, especially the graphen sheets in comparison with those of carbon nanotubes. The linear elastic parameters, non-linear elastic instabilities, thermal lattice expansion and fracture behaviors are studied in detail. We will show that the thermodynamic and strength properties of the nanoscale materials exhibit characteristic features and they are different from those of the corresponding bulk materials.

Study of dislocations in nanoscale semiconductors by ab initio molecular dynamics and lattice Green's function methods

The electronic and mechanical properties of the nanoscale materials are studied by using an ab initio molecular dynamics (TBMD) method and temperature dependent lattice Green's Function method. The core structures of dislocations in semiconductor crystallites composed of ∼1000 atoms are calculated using the ab initio TB molecular dynamics method and compared with those in the corresponding bulk semiconductors. The core structures of both 30° and 90° partial dislocations in Si crystallites are found to be similar to those of the bulk Si crystals, but excess energies of the dislocations are of considerably smaller in the small semiconductor crystallites. We also investigate the mechanical (dislocation) properties of carbon related nanoscale materials, graphen in comparison with CNT, by using the temperature dependent Lattice Green's function method and we will show that the thermodynamic and mechanical properties of the nanoscale materials are quite different from those of the corresponding bulk materials. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Optimum widths of dimer vacancy lines on Si(100)-(2×1)

We have used the ab initio multicenter molecular-dynamics method to calculate the surface energies of dimer vacancy lines (DVL's) formed on the Si(100)-(2\ifmmode\times\else\texttimes\fi{}1) surface as a result of sputtering or etching. Our results show that the optimum widths of the DVL's perpendicular to the dimer rows are two and three missing dimers. Our results also show that at higher vacancy concentrations, DVL's parallel to the dimer rows (sometimes also known as ``vacancy islands'') with widths greater than three missing dimers are favored over the perpendicular DVL's. Both of these results are in agreement with experimental observations.

Ab initiomolecular-dynamics study of pressure-induced glass-to-crystal transitions in the sodium system

We study pressure-induced glass-to-crystal transitions in the sodium system. We apply an order-$N$ ab initio molecular-dynamics (MD) method to study the transition. We use an isothermal-isobaric condition with an orbital-free density functional. The system contains 128 atoms in a supercell. We simulate the system at temperatures higher and lower than the glass-transition temperature ${T}_{g}=120\mathrm{K}.$ At 50 K the pressure enhances the onset of crystallization from the glass. The system crystallizes at pressures greater than 2.75 GPa during which the crystalline atoms appear after the complete annihilation of the icosahedral clusters. At 290 K the system crystallizes at ${10}^{\ensuremath{-}3}\mathrm{GPa},$ during which the atoms appear before the annihilation of the clusters. The application of 1 GPa at this temperature retards the crystallization which is consistent with experiments on metallic glasses. Crystallization occurs after the clusters annihilate completely which is the same feature as the transitions at 50 K. The existence of the clusters disturbs the crystallization at high pressures irrespective of temperature. The icosahedral clusters are unstable and transform to other clusters at high pressures, although the clusters are elastically stable and the hardest within $\ifmmode\pm\else\textpm\fi{}0.07\mathrm{GPa}$ at 0 K [Masaru I. Aoki and Kazuo Tsumuraya, J. Chem. Phys. 104, 6719 (1996)]. The MD methods with the empirical pair potential is found to be insufficient to simulate the transition in this system.

Theoretical predictions of expanded-volume phases of GaAs

By reducing the (4;2)-connected regular three-dimensional nets of ${\mathrm{AlPO}}_{4}$ zeolites to simply four-connected nets of III-V semiconductors such as GaAs, we introduce a variety of expanded structures for compound semiconductors. An ab initio local-orbital quantum molecular-dynamics method is used to determine the optimized geometries, energetics, and electronic properties of the proposed structures. We specifically treat GaAs, and find that even with the 90\ifmmode^\circ\else\textdegree\fi{} bond angles required for these expanded structures, most of these phases remain semiconducting with band gaps ranging from slightly above that of the zinc-blende structure, to about 0.6 eV smaller than it. Two compounds with the same volume as the room pressure phase are predicted to be metallic. The total energies of the expanded phases are in the range of 0.2 eV/atom higher than the zinc-blende structure, less than or comparable to the energies of known or predicted high-pressure phases, and are energetically less favorable than analogous expanded phases of elemental semiconductors such as Si.

Structural Band Gap Engineering

AbstractIn this paper we discuss a novel approach to the band gap engineering of semiconductors Si, Ge, GaAs and AIN. We suggest that nanoporous polymorphs of these materials may exist which would offer a significant variation of the electronic band gap. Structurally, nanoporous semiconductors are related to the zeolitic nets, and a systematic procedure of generating these structures from the (4;2) nets is described. We use the ab initio total energy quantum molecular dynamics method Fireball96 to investigate the energetics and the electronic properties of these nanoporous or “expanded” semiconductor phases.

Ab Initio Molecular Dynamics Study of Al, Ga and Si Adsorption on the Si(001) Surface

ABSTRACTThe adsorption of Al, Ga and Si on the Si(001) surface is studied by the ab initio molecular dynamics (Car-Parrinello) method based on the norm-conserving pseudopotential. In the stable structures obtained for half mono-layer coverage( ө = 1/2), these ad-atoms form dimers, but the dimer configurations are different. Al and Ga atoms form parallel dimers whose dimerization direction is parallel to that of substrate Si-dimers, while adsorbed Si atoms form (dense) orthogonal dimers. The electronic origin of the difference in the stable configurations among Al, Ga and Si ad-atoms is analyzed by calculating the local density of states (LDOS) of each atom.