Transition metal complexes forming agostic interactions have been extensively surveyed. However, the dynamic behaviour of these interactions is less documented though it could be crucial in chemical processes. For this purpose, ab initio molecular dynamics simulations (AIMD) of some representative T-shaped Pt(II) complexes (quantum mechanics) have been performed in an explicit dichloromethane s...

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed ex...

We apply the phase field crystal model to study the structure and energy of symmetric tilt grain boundaries of bcc iron in 3D. The parameters for the model are obtained by using a recently developed eight-order fitting scheme [A. Jaatinen et al., (2009)]. The grain boundary free energies we obtain from the model are in good agreement with previous results from molecular dynamics simulations and...

In low resolution structures of biological assemblies one can often observe conformational deviations that require a flexible rearrangement of structural domains fitted at the atomic level. We are evaluating interpolation methods for the flexible alignment of atomic models based on coarse models. Spatial interpolation is well established in image-processing and visualization to describe the ove...

The present study involves a novel computational technique, regarding simultaneous use of the pseudo particle method, Poisson integral method and a special-purpose computer originally designed for molecular dynamics simulations (MDGRAPE-3). In the present calculations, the dynamics of two colliding vortex rings have been studied using the vortex method. The present acceleration technique allows...

A theory for jammed granular materials is developed with the aid of a nonequilibrium steady-state distribution function. The approximate nonequilibrium steady-state distribution function is explicitly given in the weak dissipation regime by means of the relaxation time. The theory quantitatively agrees with the results of the molecular dynamics simulation on the critical behavior of the viscosi...

We examine a possible connection between the anisotropic distribution of satellite galaxies around giant spiral galaxies and the evolution of satellite systems. The observed polar anisotropy (Zaritsky et al. 1997) is either imprinted by initial conditions or develops from an initially symmetric distribution. We attempt to discriminate between these two possibilities by exploring the implication...

Graphene sheets are combined of Honeycombs lattice carbon-carbon bonds which have high natural frequencies, high strength, and high conductivity. Due to important applications of the graphene sheets particularly at higher frequencies, the study of their dynamic behavior is important in this frequency range. From Molecular Dynamics (MD) point of view as the dimensions of graphene sheet incline, ...

The Technology Acceptance Model (TAM) and Theory of Planned Behavior (TPB) are widely used in the information systems (IS) literature to explain and predict user technology acceptance behavior. Although these models have been utilized separately in the earlier studies, to increase the richness and predictive power of their studies, scholars have combined both theories in more recent studies. Ho...

Construction of stochastic models that describe the effective dynamics of observables of interest is an useful instrument in various fields of application, such as physics, climate science, and finance. We present a new technique for the construction of such models. From the timeseries of an observable, we construct a discretein-time Markov chain and calculate the eigenspectrum of its transitio...