The last decade has seen the thrilling development in material science in the nanometer scale. Nano- sized semi-conductors with well-tailored electrical, optical or mechanical properties have been synthesized. Recently, people start to realize the exciting potential of biomolecules in nanotechnology. Characterized by their high binding affinity and specificity, biomolecules are ideal for providing control in organizing technologically important (non-biological) objects into functional material. For instance, DNA strands were used to link gold nano-particles into well-defined structures with peculiar optical properties. Although nature has not selected biomolecules to bind non-biological species (e.g. semi-conductor), strong and specific binding can be achieved. For instance, antibodies that recognize fullerens have been produced and polypeptides with specific binding affinity to a number of semiconductors (GaAs, InP, Si) were selected using a combinatorial library. To obtain better control in the binding properties, much is to learn about the fundamental principles that govern the interaction between biomolecules and inorganic materials. Theoretical calculations, which have been used extensively in the studies of biomolecules and inorganic materials separately, are expected to play a leading role in the understanding of such issues. Computational work can also predict or help us to understand the dynamical, optical and other properties of those hybrid, which potentially lead to the design of new materials. A closely related research frontier is biomimetics, the technology of fabricating materials using biological systems or biomolecules. The synthesis of many inorganic nanomaterials requires stringent conditions like high temperature, pressure or pH. By contrast, low level biological systems such as bacteria are able to produce such materials under mild conditions with well-controlled morphologies. Much effort has been put forward to reveal the mechanism behind these phenomena, with the hope to design new synthetic procedures in the laboratory with similar merits. Due to the importance of silicon fabrication in semiconductor industry, much attention has been focused on diatoms and sponges, which can generate solid silica structure with precise regularity and remarkable diversity. Several polypeptides and proteins have been isolated as active components. One interesting protein filament from the sponge Tethya aurantia was dubbed "silicatein". Based on its high homology to protease cathepsin L, a catalytic mechanism similar to that involved in protease has been proposed for silicatein, which was supported by mutagenesis studies. However, a detailed understanding of the catalytic process for the polymerization of silica is still lacking. Of particular interest is the relationship between the sequence and structure of silicatein or related polypeptides and the morphology of the resulting silica polymer. Kinetic Monte Carlo simulations based on the catalytic model generated from QM/MM calculations should be able to provide useful insights into those issues. This type of work can be applied to other bacteria-material systems, and can potentially lead to the design of new fabrication procedures in the laboratory.