In this Thesis we present our achievements towards an understanding of atomistic strain mechanisms and interface chemistry in silicon nanocrystals. The structural control of silicon nanocrystals embedded in amorphous oxide is currently an important technological problem. First, our initial attempt is described to simulate the structural behavior of silicon nanocrystals embedded in amorphous oxide matrix based on simple valence force fields as described by Keatingtype potentials. Next, the interface chemistry of silicon nanocrystals (NCs) embedded in amorphous oxide matrix is studied through molecular dynamics simulations with the chemical environment being governed by the reactive force field model. Our results indicate that the Si NC-oxide interface is more involved than the previously proposed schemes which were based on solely simple bridge or double bonds. We identify different types of three-coordinated oxygen complexes, previously not noted. The abundance and the charge distribution of each oxygen complex is determined as a function of the NC size as well as the transitions among them. Strain has a crucial effect on the optical and electronic properties of nanostructures. We calculate the atomistic strain distribution in silicon NCsup to a diameter of 3.2 nm embedded in an amorphous silicon dioxide matrix. A seemingly conflicting picture arises when the strain field is expressed in terms of bond lengths versus volumetric strain. The strain profile in either case shows uniform behavior in the core, however it becomes nonuniform within 2- 3 ˚A distance to the NC surface: tensile for bond lengths whereas compressive for volumetric strain. We reconcile their coexistence by an atomistic strain analysis. Vibrational density of states (VDOS) affects the optical properties of Si-NCs. VDOS obtained by calculating velocity autocorrelation function (VACF) using velocities of the atoms is extracted from the molecular dynamics simulations. The information on bonding topology enables classification of atoms in the system with respect to their neighbor atoms. With help of this information we separate contributions of different type of atoms to the VDOS. Calculating VACF of different type of atoms such as surface atoms and core atoms of nanocrystal, to the system facilitates understanding of the effects of strain fields and interface chemistry to the VDOS.