My dissertation presents fundamental and practical scientific contributions. I demonstrated the versatility of the sol-gel processing technology for the study of the basic science behind water and protein structure under confinement, and for the development of novel biotechnology and biomedical engineering applications based on cell encapsulation in nanoporous silica gels.For the basic science studies of my dissertation, silica nanoporous gels were used to investigate the kinetic and thermodynamic transitions of water under confinement. I demonstrated a direct correlation between the structure of confined water and the secondary structure of proteins in a wide range of temperatures (- 196C to 95C). I showed qualitatively that the incorporation of a highly hydrogen bonding osmolyte contributed to improve the thermal stability of encapsulated proteins by a mechanism based on prevention of adsorption at the surface of the nanoporous silica material. For the practical contributions of my dissertation, I developed two novel applications relevant to the biotechnology and biomedical engineering fields. These applications were based on the encapsulation of prokaryotic and eukaryotic cells in silica nanoporous gels. First, I developed a highly selective and efficient biodegradation platform for the removal of an herbicide, atrazine, from contaminated water. In the second application, I invented a cell capture and isolation methodology that was successfully tested as a cancer cell isolation tool from mixed populations of eukaryotic cells (normal and cancer cells). Miscellaneous applications were also investigated such as encapsulation as a means of cryopreservation of mammalian and algae cells, and were incorporated in the Appendices of this thesis.