Empirical Potential Energy Function Research Articles

Molecular dynamics simulation of energetic ion bombardment onto a-Si 3N 4 surfaces

Energetic ion (Ar +) bombardment onto a silicon nitride substrate was modeled using molecular dynamics simulation. An empirical potential energy function developed by Vashishta was used to describe the interactions in substrate atoms. An amorphous surface configuration was prepared by simulating the surface evolution due to successive ion impacts and structure relaxation at high temperature. We considered Ar + ion bombardment on this amorphous surface, for various incident angles ( φ i=0°, 30°, 45°, 60°, 75° and 85°) and incident energies ( E i=100 and 200 eV). The reflection characteristics of impact ions can be obtained, in addition the plasma sputtering process can also be investigated with these atomic scale simulations. The sputtering yield had its maximum in the range of incident angle, 60°< φ i<75°, and nonstoichiometric surface atom removal (Si sput : N sput=1 : 2.5) was observed.

EFFECT OF CHIRALITY ON THE STABILITY OF CARBON NANOTUBES: MOLECULAR-DYNAMICS SIMULATIONS

The effect of chirality on the structural stability of single-wall carbon nanotubes have been investigated by performing molecular-dynamics computer simulations. Calculations have been realized by using an empirical many-body potential energy function for carbon. It has been found that carbon nanotube in chiral structure is more stable under heat treatment relative to zigzag and armchair models. The diameter of the tubes is slightly enlarged under heat treatment.

MOLECULAR-DYNAMICS SIMULATIONS OF CARBON NANOCAGE STRUCTURES: NANOBALLS AND NANOTOROIDS

The structural stability of carbon nanocages, fullerens and toroids, have been investigated by performing molecular-dynamics computer simulations. The systems considered are C 120 and C 240 in ball and toroidal structures. Calculations have been realized by using an empirical many-body potential energy function for carbon. It has been found that C 120 ball is very unstable, and the other structures are relatively more strong against heat treatment.

MELTING AND FRAGMENTATION OF NICKEL NANOPARTICLES: MOLECULAR–DYNAMICS SIMULATIONS

Melting and fragmentation behaviors of Ni 429 cluster have been studied with molecular-dynamics simulations using a size-dependent empirical model potential energy function. To monitor thermal behaviors of the cluster, we calculated some physical quantities such as average potential energy per atom, specific heat, radial atomic distribution, bond length distribution, average interatomic distance, nearest neighbor distance and average coordination number as a function of temperature. The roles of the surface and core atoms in the melting and fragmentation process of the cluster are also investigated by considering the surface and the bulk coordination numbers of the cluster.

FROM CARBON NANOTUBES TO CARBON NANORODS

The structural properties of single and multi-wall carbon nanotubes and the formation of carbon nanorods from multi-wall carbon nanotubes have been investigated by performing molecular-dynamics computer simulations. Calculations have been realized by using an empirical many-body potential energy function for carbon. It has been found that carbon nanorod formation takes place with smallest possible multi-wall nanotubes under heat treatment. On the other hand, it has been also found that single-wall carbon nanotubes are stronger than the multi-wall nanotubes against heat treatment.

Modelling gold clusters with an empirical many-body potential

Molecular Dynamics Simulated Annealing has been used to probe the structure of small Au clusters consisting of between 2 and 40 atoms. The interatomic interactions within these clusters are described using an empirical Murrell-Mottram many-body potential energy function. Four distinct structural motifs are present in the structures of the predicted global minima, based on octahedra, decahedra, icosahedra and hexagonal prisms.

ENERGETICS OF ARSENIC TERMINATED GaAs(001) SURFACES

We have investigated systematically the energetics of arsenic terminated GaAs(001) surfaces. Available surface models proposed in the literature have been considered, and relaxation and surface energies of each model have been calculated using an empirical many-body potential energy function comprising two and three-body atomic interactions.

Stability of gold clusters: molecular-dynamics simulations

Structural stability and energetics of gold clusters, Au n (n=3 –555), have been investigated by molecular-dynamics simulations. An empirical model potential energy function has been used in the simulations. Stable structures of the microclusters for n=3–13 have been determined by molecular-dynamics simulation. It has been found that gold microclusters prefer to form three-dimensional compact structures. Molecular-dynamics simulations have also been performed for spherical gold clusters generated from FCC crystal structure with sizes n=13–555. It has been found that the gold nanoparticles are more stable in the FCC form.

An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids

Improvements in the CHARMM all-atom force field for atomic-level molecular simulations of lipids are reported. Substantial adjustments have been made to the Lennard-Jones (LJ) hydrocarbon and torsional parameters and to the partial atomic charges and torsional parameters of the phosphate moiety. These changes were motivated by a combination of unexpected simulation results and recent high-level ab initio quantum mechanical calculations. The parameter optimization procedure is described, and the resulting energy function validated by an 11 ns molecular dynamics simulation of a hydrated phospholipid bilayer. Of note is the influence of the hydrocarbon LJ parameters on the conformational properties of the aliphatic tails, emphasizing the importance of obtaining the proper balance between the bonded and nonbonded portions of the force field. Compatibility with the CHARMM all-atom parameter sets for proteins and nucleic acids has been maintained such that high quality simulations of biologically interesting me...

MOLECULAR-DYNAMICS SIMULATION OF STEPPED Si(100) SURFACE

We have investigated the relaxation of single and double layer stepped Si(100) surfaces depending on working cell size and heat treatment by MD simulation based on LJ–AT empirical potential energy function. It is found that smooth relaxation can be satisfied for both types of stepped Si(100) surfaces by continuous MD runs. The dependence of relaxation on the size of working cell is found only for single layer stepped Si(100) surface. The total potential energy calculation by MD shows that double layer Si(100) surface is more stable than the single layer stepped Si(100) surface.

MOLECULAR-DYNAMICS SIMULATIONS OF NICKEL CLUSTERS

Structural stability and energetics of nickel clusters, NiN (N =3-459), have been investigated by molecular-dynamics simulations. A size-dependent empirical model potential energy function has been used in the simulations. Stable structures of the microclusters with sizes N = 3-55 and clusters generated from fcc crystal structure with sizes N = 79-459 have been determined by molecular-dynamics simulations. It has been found that the five-fold symmetry appears on the surface of the spherical clusters. The average coordination number shows a size-dependent characteristic, on the other hand the average nearest-neighbor distance does not show a size-dependence.

MOLECULAR-DYNAMICS SIMULATION OF RADIATION DAMAGE ON COPPER CLUSTERS

The effect of radiation damage on copper clusters has been investigated by performing molecular-dynamics simulation using empirical potential energy function for interaction between copper atoms. The external radiation is modeled by giving extra kinetic energy in the range of 5–50 eV to initially chosen atom in the cluster. It has been found that the atom having extra kinetic energy dissociates independently from the amount of given energy in the studied range.

Molecular-dynamics simulations of water clusters

The local minimum geometries and corresponding energy values of water clusters, [(H 2O) n , n=2–8], have been investigated by using the molecular dynamics simulation method. In the simulations two different potential energy functions of central-force model, CF and CF2, have been used. Particular attention was paid to investigate the effectiveness of these two empirical potential energy functions. CF has been used for n=2 only, whereas CF2 has been used for n=2–8. The cage structure of the water clusters appear for n⩾6.

Computational studies on carbohydrates: in vacuo studies using a revised AMBER force field, AMB99C, designed for α-(1→4) linkages

Modifications to the AMBER force field [W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K. Merz, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, P.A. Kollman, J. Am. Chem. Soc., 117 (1995) 5179–5197] have been made to improve our ability to reproduce observed molecular properties of α-linked carbohydrates when calculated using empirical potential-energy functions. Molecular structures and energies obtained using gradient-optimized density functional methods with ab initio basis sets (B3LYP/6-31G*) on ten minimum-energy conformations of maltose [F.A. Momany, J.L. Willett, J. Comp. Chem., submitted for publication] were used to refine the empirical potentials. Molecular dynamics simulations on β-maltose (i.e., the β anomer of maltose), cyclohexamylose (α-cyclodextrin), cycloheptamylose (β-cyclodextrin) and larger cyclomaltooligosaccharide structures were carried out and compared with experimental structural studies to test the new potentials. Ring-puckering potential during dynamics as well as conformational transitions to ‘flipped’ structures were examined. Results of the tests described here suggest that the revised AMBER parameters (AMB99C) are very good for computational studies of α-(1→4)-linked carbohydrates.

THE EFFECT OF PBC ON THE SIMULATION OF NANOTUBES

The effect of the periodic boundary condition (PBC) on the structure and energetics of nanotubes has been investigated by performing molecular-dynamics computer simulation. Calculations have been realized by using an empirical many-body potential energy function for carbon. A single-wall carbon nanotube has been considered in the simulations. It has been found that the periodic boundary condition has no effect at low temperature (1 K), however, it plays an important role even at intermediate temperature (300 K).

A COMPARATIVE STUDY OF EMPIRICAL POTENTIAL ENERGY FUNCTIONS: APPLICATIONS TO CLUSTERS

We have made a comparative study for the empirical potential energy functions proposed and parametrized for coinacal metals, namely Cu, Ag, and Au. We have considered four different potential energy functions, and applied them to investigate the structural properties and energetics of clusters of the elements considered.

Dynamics of rare gas desorption from Pt(111) induced by collisions with photogenerated hot oxygen atoms

We present a classical trajectory study of the collision-induced desorption of rare gas (Rg=Ar, Xe) atoms from Pt(111) by ‘hot’ O atoms generated by photodissociating coadsorbed O 2. Empirical potential energy functions are used to describe the Rg/O/Pt(111) systems. The calculated angular and translational energy distributions of the desorbed Ar and Xe are in good agreement with experimental observations. It is found that the desorption dynamics involves two collisions. The first collision between O and Rg supplies the necessary kinetic energy for desorption, whereas the second collision between the departing Rg atom and a coadsorbed Rg atom results in a desorption angle of 25–35° from the surface normal for Ar and 35–45° for Xe. The light oxygen atom is found to chatter between the Xe atom and the surface during an O–Xe collision, enhancing the energy transfer.

Application of a Molecular Dynamics Simulation Method with a Generalized Effective Potential to the Flexible Molecular Docking Problems

We present a new molecular dynamics method using Tsallis effective potential for the flexible docking problems of streptavidin/biotin and protein kinase C/phorbol-13-acetate. With a full flexibility of the ligands and a partial flexibility of the receptor active sites included, the new MD scheme accelerates the docking process significantly, by way of infrequent q-jumping and q-relaxation procedures between a normal potential energy surface and its transformed one by the Tsallis scheme. In the transformation, only the nonbonding interaction terms of an empirical potential energy function were employed. It has been found that the current method can predict the correctly docked structures in quite an effective way. Current results strongly indicate that this new MD method can be a very promising strategy for flexible ligand/flexible receptor docking.

Energetics and structural stability of lanthanum microclusters

The energetics and the structural stability of lanthanum microclusters (La n ) have been investigated by performing relativistic density functional calculations and molecular dynamics (MD) simulations. An empirical potential energy function has been parameterised for a lanthanum element by using the dimer interaction potential energy profile of La 2, which is calculated by relativistic density functional method. Stable structures of the microclusters for n=3–13 have been determined by MD simulation and electronic structures have been calculated by relativistic density functional method. MD simulations have also been performed for spherical clusters with sizes n=19–157.

Molecular dynamics simulations of Si etching by energetic CF3+

The development of a Tersoff-type empirical interatomic potential energy function (PEF) for the Si–C–F system is reported. As a first application of this potential, etching of a:Si by CF3+ using molecular dynamics (MD) simulations is demonstrated. Aspects of CF3+ ion bombardment through a fluence of 4×1016 cm−2 are discussed, including overlayer composition and thickness, Si etch yields, and etch product distributions. The formation of a 1-nm-thick steady-state SixCyFz overlayer occurs in the simulation, and this layer is an active participant in the etching of the underlying Si. At an ion energy of 100 eV, a steady state the etch yield of Si is predicted to be 0.06±0.01 Si/ion. A comparison of the simulation findings and experimental results from the literature leads to the conclusion that the new PEF performs well in qualitatively modeling the atomic-scale processes involved in CF3+ ion beam etching of Si. Simulations of this kind yield insight into fluorocarbon etch mechanisms, and ultimately will result in phenomenological models of etching by fluorocarbon plasmas.