Browsing by Subject "molecular dynamics"
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Cation adatom diffusion on the NiO(001) surface by molecular dynamics simulation
(2001)We present results concerning the diffusion of Ni2+ adatom on the (001) surface of NiO obtained by molecular dynamics simulations based on a rigid ion potential model. A wide temperature region was covered ranging from ... 
Cation vacancy diffusion on the NiO(001) surface by molecular dynamics simulations
(1999)We present results concerning the cation vacancy diffusion mechanisms occurring on the NiO(001) surface along with their corresponding migration energies. Using a rigid ion potential and molecular dynamics simulations we ... 
Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis
(2006)Data from polyphenylalanine [poly(Phe)] synthesis determination in the presence and in the absence of erythromycin have been used in conjunction with Molecular Dynamics Simulation analysis, in order to localize the functional ... 
Determination of the number of water molecules in the proton pathway of bacteriorhodopsin using neutron diffraction data
(2003)It has been shown that water molecules participate in the proton pathway of bacteriorhodopsin. Large efforts have been made to determine with various biophysical methods the number of water molecules involved. Neutron ... 
Effects of wall roughness on flow in nanochannels
(2009)Nonequilibrium molecular dynamics simulation is applied to investigate the effect of periodic wall roughness on the flow of liquid argon through krypton nanochannels. The effect of the length of a rectangular protrusion ... 
Elastic properties of nanostructured materials with layered grain boundary structure
(2007)Atomistic calculations of the elastic constants for a bulk nanostructured material that consists of a layered structure where alternating layers meet along high angle grain boundaries and where atoms interact via a ... 
Emerging molecular networks common in ionizing radiation, immune and inflammatory responses by employing bioinformatics approaches
(2015)Efficient radiation therapy is characterized by enhanced tumor cell killing involving the activation of the immune system (tumor immunogenicity) but at the same time minimizing chronic inflammation and radiation adverse ... 
Fluid ordering effects and density variations in nanochannel flows: a quasicontinuum theory
(2014)A quasicontinuum selfdiffusion theory that can capture the fluid ordering effects and density variations predicted by nonequilibrium molecular dynamics in nanochannel flows is presented. The physics of the problem suggests ... 
Molecular dynamics simulation study of Ni2+ adatom diffusion on the NiO (001) surface
(2001)Using molecular dynamics simulations we studied the cation adatom diffusion on the NiO(001) surface. We found that there are two equilibrium adatom positions: one over an oxygen ion, that is raised by as much as 30% at ... 
Multiscale modeling in nanomaterials science
(2007)Nanoscience is an area with increasing interest both in the physicochemical phenomena involved and the potential applications such as silicon carbide films, carbon nanotubes, quantum dots, MEMS etc. These materials exhibit ... 
Ni3+ adsorbate dynamics on a NiO(001) surface
(2006)We present results concerning the dynamical behavior of a Ni3+ adsorbate on a NiO(001) surface obtained by molecular dynamics simulations. In a first place, we examined at low temperature the position of the Ni3+ ion as ... 
Oxygen adatom diffusion on the NiO(001) surface by molecular dynamics simulation
(2002)We present results concerning the diffusion processes of O2 adatom on the NiO(0 0 1) surface obtained by molecular dynamics simulations based on a rigid ion potential model. We covered a temperature region from 0.37T(m) ... 
Parallel short range molecular dynamics simulations on computer clusters: Performance evaluation and modeling
(2005)This paper describes the performance of a portable molecular dynamics code running on an eightnode PC cluster. The molecular dynamics code is based on the atom decomposition method for distributing the computation load ... 
Structure and dynamics of NiO(001) and Ni/NiO(001) surfaces by molecular dynamics simulation
(2000)Using molecular dynamics and a rigid ion potential, we studied the vibrational and structural properties of the NiO(001) surface with and without cationic adatoms. We found that the bulk phonon density of states (DOS) is ... 
Vibrational and topological properties of selected NiO surfaces
(2006)We present a study of the vibrational properties of the (100) and (110) surfaces of nickel oxide. We performed molecular dynamics simulations over a wide temperature range and we calculated the phonon local density of ... 
Vibrational properties of a Sigma 5(310) 001 NiO grain boundary: a local analysis by molecular dynamics simulation
(2002)Using molecular dynamics and a rigid ion potential we studied the vibrational properties of a Sigma5(310)[001] tilt grain boundary in NiO. We calculated the local density of states and the mean square displacement (MSD) ...